Many thanks to those of you who have submitted details of new or missing enzymes, or updates to existing enzymes.
An asterisk before 'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.
Accepted name: D-xylose reductase
Reaction: xylitol + NAD(P)+ = D-xylose + NAD(P)H + H+
Other name(s): XylR; XyrA; msXR; dsXR; monospecific xylose reductase; dual specific xylose reductase; NAD(P)H-dependent xylose reductase; xylose reductase
Systematic name: xylitol:NAD(P)+ oxidoreductase
Comments: Xylose reductase catalyses the initial reaction in the xylose utilization pathway, the NAD(P)H dependent reduction of xylose to xylitol.
References:
1. Neuhauser, W., Haltrich, D., Kulbe, K.D. and Nidetzky, B. NAD(P)H-dependent aldose reductase from the xylose-assimilating yeast Candida tenuis. Isolation, characterization and biochemical properties of the enzyme. Biochem. J. 326 (1997) 683-692. [PMID: 9307017]
2. Nidetzky, B., Bruggler, K., Kratzer, R. and Mayr, P. Multiple forms of xylose reductase in Candida intermedia: comparison of their functional properties using quantitative structure-activity relationships, steady-state kinetic analysis, and pH studies. J. Agric. Food Chem. 51 (2003) 7930-7935. [PMID: 14690376]
3. Iablochkova, E.N., Bolotnikova, O.I., Mikhailova, N.P., Nemova, N.N. and Ginak, A.I. The activity of xylose reductase and xylitol dehydrogenase in yeasts. Mikrobiologiia 72 (2003) 466-469. [PMID: 14526534] (in Russian)
4. Chen, L.C., Huang, S.C., Chuankhayan, P., Chen, C.D., Huang, Y.C., Jeyakanthan, J., Pang, H.F., Men, L.C., Chen, Y.C., Wang, Y.K., Liu, M.Y., Wu, T.K. and Chen, C.J. Purification, crystallization and preliminary X-ray crystallographic analysis of xylose reductase from Candida tropicalis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 65 (2009) 419-421. [PMID: 19342796]
5. Verduyn, C., Van Kleef, R., Frank, J., Schreuder, H., Van Dijken, J.P. and Scheffers, W.A. Properties of the NAD(P)H-dependent xylose reductase from the xylose-fermenting yeast Pichia stipitis. Biochem. J. 226 (1985) 669-677. [PMID: 3921014]
6. Fernandes, S., Tuohy, M.G. and Murray, P.G. Xylose reductase from the thermophilic fungus Talaromyces emersonii: cloning and heterologous expression of the native gene (Texr) and a double mutant (TexrK271R + N273D) with altered coenzyme specificity. J Biosci 34 (2009) 881-890. [PMID: 20093741]
7. Lee, J.K., Koo, B.S. and Kim, S.Y. Cloning and characterization of the xyl1 gene, encoding an NADH-preferring xylose reductase from Candida parapsilosis, and its functional expression in Candida tropicalis. Appl. Environ. Microbiol. 69 (2003) 6179-6188. [PMID: 14532079]
8. Woodyer, R., Simurdiak, M., van der Donk, W.A. and Zhao, H. Heterologous expression, purification, and characterization of a highly active xylose reductase from Neurospora crassa. Appl. Environ. Microbiol. 71 (2005) 1642-1647. [PMID: 15746370]
Accepted name: NDMA-dependent alcohol dehydrogenase
Reaction: ethanol + N,N-dimethyl-4-nitrosoaniline = acetaldehyde + 4-(hydroxylamino)-N,N-dimethylaniline
Glossary: N,N-dimethyl-4-nitrosoaniline = NDMA, 4-(hydroxylamino)-N,N-dimethylaniline = 4-(N,N-dimethylamino)phenylhydroxylamine
Other name(s): nicotinoprotein alcohol dehydrogenase; np-ADH
Systematic name: ethanol:N,N-dimethyl-4-nitrosoaniline oxidoreductase
Comments: Contains Zn2+. Nicotinoprotein alcohol dehydrogenases are unique medium-chain dehydrogenases/reductases (MDR) alcohol dehydrogenases that have a tightly bound NAD+/NADH cofactor that does not dissociate during the catalytic process. Instead, the cofactor is regenerated by a second substrate or electron carrier. While the in vivo electron acceptor is not known, N,N-dimethyl-4-nitrosoaniline (NDMA) can serve this function in vitro. The enzyme from the Gram-positive bacterium Amycolatopsis methanolica can accept many primary alcohols as substrates, including benzylalcohol [1].
References:
1. Van Ophem, P.W., Van Beeumen, J. and Duine, J.A. Nicotinoprotein [NAD(P)-containing] alcohol/aldehyde oxidoreductases. Purification and characterization of a novel type from Amycolatopsis methanolica. Eur. J. Biochem. 212 (1993) 819-826. [PMID: 8385013]
2. Piersma, S.R., Visser, A.J., de Vries, S. and Duine, J.A. Optical spectroscopy of nicotinoprotein alcohol dehydrogenase from Amycolatopsis methanolica: a comparison with horse liver alcohol dehydrogenase and UDP-galactose epimerase. Biochemistry 37 (1998) 3068-3077. [PMID: 9485460]
3. Schenkels, P. and Duine, J.A. Nicotinoprotein (NADH-containing) alcohol dehydrogenase from Rhodococcus erythropolis DSM 1069: an efficient catalyst for coenzyme-independent oxidation of a broad spectrum of alcohols and the interconversion of alcohols and aldehydes. Microbiology 146 (2000) 775-785. [PMID: 10784035]
4. Piersma, S.R., Norin, A., de Vries, S., Jornvall, H. and Duine, J.A. Inhibition of nicotinoprotein (NAD+-containing) alcohol dehydrogenase by trans-4-(N,N-dimethylamino)-cinnamaldehyde binding to the active site. J. Protein Chem. 22 (2003) 457-461. [PMID: 14690248]
5. Norin, A., Piersma, S.R., Duine, J.A. and Jornvall, H. Nicotinoprotein (NAD+ -containing) alcohol dehydrogenase: structural relationships and functional interpretations. Cell. Mol. Life Sci. 60 (2003) 999-1006. [PMID: 12827287]
Accepted name: NDMA-dependent methanol dehydrogenase
Reaction: methanol + N,N-dimethyl-4-nitrosoaniline = formaldehyde + 4-(hydroxylamino)-N,N-dimethylaniline
Glossary: N,N-dimethyl-4-nitrosoaniline = NDMA, 4-(hydroxylamino)-N,N-dimethylaniline = 4-(N,N-dimethylamino)phenylhydroxylamine
Other name(s): nicotinoprotein methanol dehydrogenase
Systematic name: methanol:N,N-dimethyl-4-nitrosoaniline oxidoreductase
Comments: Contains Zn2+ and Mg2+. Nicotinoprotein methanol dehydrogenases have a tightly bound NADP+/NADPH cofactor that does not dissociate during the catalytic process. Instead, the cofactor is regenerated by a second substrate or electron carrier. While the in vivo electron acceptor is not known, N,N-dimethyl-4-nitrosoaniline (NDMA) can serve this function in vitro. The enzyme has been detected in several Gram-positive methylotrophic bacteria, including Amycolatopsis methanolica, Rhodococcus rhodochrous and Rhodococcus erythropolis [1-3]. These enzymes are decameric, and possess a 5-fold symmetry [4]. Some of the enzymes can also dismutate formaldehyde to methanol and formate [5].
References:
1. Vonck, J., Arfman, N., De Vries, G.E., Van Beeumen, J., Van Bruggen, E.F. and Dijkhuizen, L. Electron microscopic analysis and biochemical characterization of a novel methanol dehydrogenase from the thermotolerant Bacillus sp. C1. J. Biol. Chem. 266 (1991) 3949-3954. [PMID: 1995642]
2. Van Ophem, P.W., Van Beeumen, J. and Duine, J.A. Nicotinoprotein [NAD(P)-containing] alcohol/aldehyde oxidoreductases. Purification and characterization of a novel type from Amycolatopsis methanolica. Eur. J. Biochem. 212 (1993) 819-826. [PMID: 8385013]
3. Bystrykh, L.V., Vonck, J., van Bruggen, E.F., van Beeumen, J., Samyn, B., Govorukhina, N.I., Arfman, N., Duine, J.A. and Dijkhuizen, L. Electron microscopic analysis and structural characterization of novel NADP(H)-containing methanol: N,N'-dimethyl-4-nitrosoaniline oxidoreductases from the gram-positive methylotrophic bacteria Amycolatopsis methanolica and Mycobacterium gastri MB19. J. Bacteriol. 175 (1993) 1814-1822. [PMID: 8449887]
4. Hektor, H.J., Kloosterman, H. and Dijkhuizen, L. Identification of a magnesium-dependent NAD(P)(H)-binding domain in the nicotinoprotein methanol dehydrogenase from Bacillus methanolicus. J. Biol. Chem. 277 (2002) 46966-46973. [PMID: 12351635]
5. Park, H., Lee, H., Ro, Y.T. and Kim, Y.M. Identification and functional characterization of a gene for the methanol : N,N'-dimethyl-4-nitrosoaniline oxidoreductase from Mycobacterium sp. strain JC1 (DSM 3803). Microbiology 156 (2010) 463-471. [PMID: 19875438]
Accepted name: anthranilate 3-monooxygenase (FAD)
Reaction: anthranilate + FADH2 + O2 = 3-hydroxyanthranilate + FAD + H2O
Glossary: anthranilate = 2-aminobenzoate
Other name(s): anthranilate 3-hydroxylase; anthranilate hydroxylase
Systematic name: anthranilate,FAD:oxygen oxidoreductase (3-hydroxylating)
Comments: This enzyme, isolated from the bacterium Geobacillus thermodenitrificans, participates in the pathway of tryptophan degradation. The enzyme is part of a system that also includes a bifunctional riboflavin kinase/FMN adenylyltransferase and an FAD reductase, which ensures ample supply of FAD to the monooxygenase.
References:
1. Liu, X., Dong, Y., Li, X., Ren, Y., Li, Y., Wang, W., Wang, L. and Feng, L. Characterization of the anthranilate degradation pathway in Geobacillus thermodenitrificans NG80-2. Microbiology 156 (2010) 589-595. [PMID: 19942660]
[EC 2.1.1.48 Transferred entry: rRNA (adenine-N6-)-methyltransferase. Now covered by EC 2.1.1.181 [23S rRNA (adenine1618-N6)-methyltransferase], EC 2.1.1.182 [16S rRNA adenine1518-N6/adenine1519-N6)-dimethyltransferase], EC 2.1.1.183 [18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase] and EC 2.1.1.184 [23S rRNA (adenine2085-N6)-dimethyltransferase] (EC 2.1.1.48 created 1976, deleted 2010)]
[EC 2.1.1.52 Transferred entry: rRNA (guanine-N2)-methyltransferase. Now covered by EC 2.1.1.171 [16S rRNA (guanine966-N2)-methyltransferase], EC 2.1.1.172 [16S rRNA (guanine1207-N2)-methyltransferase], EC 2.1.1.173 [23S rRNA (guanine2445-N2)-methyltransferase] and EC 2.1.1.174 [23S rRNA (guanine1835-N2)-methyltransferase] (EC 2.1.1.52 created 1976, deleted 2010)]
Accepted name: 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanosine2922 in 27S pre-rRNA = S-adenosyl-L-homocysteine + 2'-O-methylguanosine2922 in 27S pre-rRNA
Other name(s): Spb1p (gene name); YCL054W (gene name)
Systematic name: S-adenosyl-L-methionine:27S pre-rRNA (guanosine2922-2'-O-)-methyltransferase
Comments: Spb1p is a site-specific 2'-O-ribose RNA methyltransferase that catalyses the formation of 2'-O-methylguanosine2922, a universally conserved position of the catalytic center of the ribosome that is essential for translation. 2'-O-Methylguanosine2922 is formed at a later stage of the processing, during the maturation of of the 27S pre-rRNA. In absence of snR52, Spb1p can also catalyse the formation of uridine2921 [1].
References:
1. Lapeyre, B. and Purushothaman, S.K. Spb1p-directed formation of Gm2922 in the ribosome catalytic center occurs at a late processing stage. Mol. Cell 16 (2004) 663-669. [PMID: 15546625]
2. Bonnerot, C., Pintard, L. and Lutfalla, G. Functional redundancy of Spb1p and a snR52-dependent mechanism for the 2'-O-ribose methylation of a conserved rRNA position in yeast. Mol. Cell 12 (2003) 1309-1315. [PMID: 14636587]
Accepted name: 21S rRNA (uridine2791-2'-O)-methyltransferase
Reaction: S-adenosyl-L-methionine + uridine2791 in 21S rRNA = S-adenosyl-L-homocysteine + 2'-O-methyluridine2791 in 21S rRNA
Other name(s): MRM2 (gene name); mitochondrial 21S rRNA methyltransferase; mitochondrial rRNA MTase 2
Systematic name: S-adenosyl-L-methionine:21S rRNA (uridine2791-2'-O-)-methyltransferase
Comments: The enzyme catalyses the methylation of uridine2791 of mitochondrial 21S rRNA.
References:
1. Pintard, L., Bujnicki, J.M., Lapeyre, B. and Bonnerot, C. MRM2 encodes a novel yeast mitochondrial 21S rRNA methyltransferase. EMBO J. 21 (2002) 1139-1147. [PMID: 11867542]
Accepted name: tricetin 3',4',5'-O-trimethyltransferase
Reaction: (1) 3 S-adenosyl-L-methionine + tricetin = 3 S-adenosyl-L-homocysteine + 3',4',5'-O-trimethyltricetin (overall reaction)
(1a) S-adenosyl-L-methionine + tricetin = S-adenosyl-L-homocysteine + 3'-O-methyltricetin
(1b) S-adenosyl-L-methionine + 3'-O-methyltricetin = S-adenosyl-L-homocysteine + 3',5'-O-dimethyltricetin
(1c) S-adenosyl-L-methionine + 3',5'-O-dimethyltricetin = S-adenosyl-L-homocysteine + 3',4',5'-O-trimethyltricetin
Other name(s): FOMT; TaOMT1; TaCOMT1; TaOMT2
Systematic name: S-adenosyl-L-methionine:tricetin 3',4',5'-O-trimethyltransferase
Comments: The enzyme from Triticum aestivum catalyses the sequential O-methylation of tricetin via 3'-O-methyltricetin, 3',5'-O-methyltricetin to 3',4',5'-O-trimethyltricetin [2].
References:
1. Kornblatt, J.A., Zhou, J.M. and Ibrahim, R.K. Structure-activity relationships of wheat flavone O-methyltransferase: a homodimer of convenience. FEBS J. 275 (2008) 2255-2266. [PMID: 18397325]
2. Zhou, J.M., Gold, N.D., Martin, V.J., Wollenweber, E. and Ibrahim, R.K. Sequential O-methylation of tricetin by a single gene product in wheat. Biochim. Biophys. Acta 1760 (2006) 1115-1124. [PMID: 16730127]
3. Zhou, J.M., Seo, Y.W. and Ibrahim, R.K. Biochemical characterization of a putative wheat caffeic acid O-methyltransferase. Plant Physiol. Biochem. 47 (2009) 322-326. [PMID: 19211254]
Accepted name: 16S rRNA (guanine527-N7)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanine527 in 16S rRNA = S-adenosyl-L-homocysteine + N7-methylguanine527 in 16S rRNA
Other name(s): ribosomal RNA small subunit methyltransferase G; 16S rRNA methyltransferase RsmG; GidB; rsmG (gene name)
Systematic name: S-adenosyl-L-methionine:16S rRNA (guanine527-N7)-methyltransferase
Comments: The enzyme specifically methylates guanine527 at N7 in 16S rRNA.
References:
1. Okamoto, S., Tamaru, A., Nakajima, C., Nishimura, K., Tanaka, Y., Tokuyama, S., Suzuki, Y. and Ochi, K. Loss of a conserved 7-methylguanosine modification in 16S rRNA confers low-level streptomycin resistance in bacteria. Mol. Microbiol. 63 (2007) 1096-1106. [PMID: 17238915]
2. Romanowski, M.J., Bonanno, J.B. and Burley, S.K. Crystal structure of the Escherichia coli glucose-inhibited division protein B (GidB) reveals a methyltransferase fold. Proteins 47 (2002) 563-567. [PMID: 12001236]
Accepted name: 16S rRNA (guanine966-N2)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanine966 in 16S rRNA = S-adenosyl-L-homocysteine + N2-methylguanine966 in 16S rRNA
Other name(s): yhhF (gene name); rsmD (gene name); m2G966 methyltransferase
Systematic name: S-adenosyl-L-methionine:16S rRNA (guanine966-N2)-methyltransferase
Comments: The enzyme efficiently methylates guanine966 of the assembled 30S subunits in vitro. Protein-free 16S rRNA is not a substrate for RsmD [1]. The enzyme specifically methylates guanine966 at N2 in 16S rRNA.
References:
1. Lesnyak, D.V., Osipiuk, J., Skarina, T., Sergiev, P.V., Bogdanov, A.A., Edwards, A., Savchenko, A., Joachimiak, A. and Dontsova, O.A. Methyltransferase that modifies guanine 966 of the 16 S rRNA: functional identification and tertiary structure. J. Biol. Chem. 282 (2007) 5880-5887. [PMID: 17189261]
Accepted name: 16S rRNA (guanine1207-N2)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanine1207 in 16S rRNA = S-adenosyl-L-homocysteine + N2-methylguanine1207 in 16S rRNA
Other name(s): m2G1207 methyltransferase
Systematic name: S-adenosyl-L-methionine:16S rRNA (guanine1207-N2)-methyltransferase
Comments: The enzyme reacts well with 30S subunits reconstituted from 16S RNA transcripts and 30S proteins but is almost inactive with the corresponding free RNA [1]. The enzyme specifically methylates guanine1207 at N2 in 16S rRNA.
References:
1. Tscherne, J.S., Nurse, K., Popienick, P. and Ofengand, J. Purification, cloning, and characterization of the 16 S RNA m2G1207 methyltransferase from Escherichia coli. J. Biol. Chem. 274 (1999) 924-929. [PMID: 9873033]
2. Sunita, S., Purta, E., Durawa, M., Tkaczuk, K.L., Swaathi, J., Bujnicki, J.M. and Sivaraman, J. Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC. Nucleic Acids Res. 35 (2007) 4264-4274. [PMID: 17576679]
Accepted name: 23S rRNA (guanine2445-N2)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanine2445 in 23S rRNA = S-adenosyl-L-homocysteine + N2-methylguanine2445 in 23S rRNA
Other name(s): ycbY (gene name); rlmL (gene name)
Systematic name: S-adenosyl-L-methionine:23S rRNA (guanine2445-N2)-methyltransferase
Comments: The enzyme methylates 23S rRNA in vitro, assembled 50S subunits are not a substrate [1]. The enzyme specifically methylates guanine2445 at N2 in 23S rRNA.
References:
1. Lesnyak, D.V., Sergiev, P.V., Bogdanov, A.A. and Dontsova, O.A. Identification of Escherichia coli m2G methyltransferases: I. the ycbY gene encodes a methyltransferase specific for G2445 of the 23 S rRNA. J. Mol. Biol. 364 (2006) 20-25. [PMID: 17010378]
Accepted name: 23S rRNA (guanine1835-N2)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanine1835 in 23S rRNA = S-adenosyl-L-homocysteine + N2-methylguanine1835 in 23S rRNA
Other name(s): ygjO (gene name); rlmG (gene name); ribosomal RNA large subunit methyltransferase G
Systematic name: S-adenosyl-L-methionine:23S rRNA (guanine1835-N2)-methyltransferase
Comments: The enzyme methylates 23S rRNA in vitro, assembled 50S subunits are not a substrate [1]. The enzyme specifically methylates guanine1835 at N2 in 23S rRNA.
References:
1. Sergiev, P.V., Lesnyak, D.V., Bogdanov, A.A. and Dontsova, O.A. Identification of Escherichia coli m2G methyltransferases: II. The ygjO gene encodes a methyltransferase specific for G1835 of the 23 S rRNA. J. Mol. Biol. 364 (2006) 26-31. [PMID: 17010380]
Accepted name: tricin synthase
Reaction: (1) 2 S-adenosyl-L-methionine + tricetin = 2 S-adenosyl-L-homocysteine + 3',5'-O-dimethyltricetin
(1a) S-adenosyl-L-methionine + tricetin = S-adenosyl-L-homocysteine + 3'-O-methyltricetin
(1b) S-adenosyl-L-methionine + 3'-O-methyltricetin = S-adenosyl-L-homocysteine + 3',5'-O-dimethyltricetin
Glossary: tricin = 3',5'-O-dimethyltricetin
Other name(s): ROMT-17; ROMT-15; HvOMT1; ZmOMT1
Systematic name: S-adenosyl-L-methionine:tricetin 3',5'-O-dimethyltransferase
Comments: The enzymes from Oryza sativa (ROMT-15 and ROMT-17) catalyses the stepwise methylation of tricetin to its 3'-mono- and 3',5'-dimethyl ethers. In contrast with the wheat enzyme (EC 2.1.1.169, tricetin 3',4',5'-O-trimethyltransferase), tricetin dimethyl ether is not converted to its 3',4',5'-trimethylated ether derivative [1]. The enzymes from Hordeum vulgare (HvOMT1) and from Zea mays (ZmOMT1) form the 3',5'-dimethyl derivative as the major product [2].
References:
1. Lee, Y.J., Kim, B.G., Chong, Y., Lim, Y. and Ahn, J.H. Cation dependent O-methyltransferases from rice. Planta 227 (2008) 641-647. [PMID: 17943312]
2. Zhou, J.-M., Fukushi, Y., Wollenweber, E., Ibrahim, R.K. Characterization of two O-methyltransferase-like genes in barley and maize. Pharm. Biol. 46 (2008) 26-34.
Accepted name: 16S rRNA (cytosine967-C5)-methyltransferase
Reaction: S-adenosyl-L-methionine + cytosine967 in 16S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine967 in 16S rRNA
Other name(s): rsmB (gene name); fmu (gene name); 16S rRNA m5C967 methyltransferase
Systematic name: S-adenosyl-L-methionine:16S rRNA (cytosine967-C5)-methyltransferase
Comments: The enzyme specifically methylates cytosine967 at C5 in 16S rRNA.
References:
1. Tscherne, J.S., Nurse, K., Popienick, P., Michel, H., Sochacki, M. and Ofengand, J. Purification, cloning, and characterization of the 16S RNA m5C967 methyltransferase from Escherichia coli. Biochemistry 38 (1999) 1884-1892. [PMID: 10026269]
2. Gu, X.R., Gustafsson, C., Ku, J., Yu, M. and Santi, D.V. Identification of the 16S rRNA m5C967 methyltransferase from Escherichia coli. Biochemistry 38 (1999) 4053-4057. [PMID: 10194318]
3. Foster, P.G., Nunes, C.R., Greene, P., Moustakas, D. and Stroud, R.M. The first structure of an RNA m5C methyltransferase, Fmu, provides insight into catalytic mechanism and specific binding of RNA substrate. Structure 11 (2003) 1609-1620. [PMID: 14656444]
Accepted name: 23S rRNA (pseudouridine1915-N3)-methyltransferase
Reaction: S-adenosyl-L-methionine + pseudouridine1915 in 23S rRNA = S-adenosyl-L-homocysteine + N3-methylpseudouridine1915 in 23S rRNA
Other name(s): YbeA; RlmH; pseudouridine methyltransferase; m3Ψ methyltransferase; Ψ1915-specific methyltransferase; rRNA large subunit methyltransferase H
Systematic name: S-adenosyl-L-methionine:23S rRNA (pseudouridine1915-N3)-methyltransferase
Comments: YbeA does not methylate uridine at position 1915 [1].
References:
1. Ero, R., Peil, L., Liiv, A. and Remme, J. Identification of pseudouridine methyltransferase in Escherichia coli. RNA 14 (2008) 2223-2233. [PMID: 18755836]
2. Purta, E., Kaminska, K.H., Kasprzak, J.M., Bujnicki, J.M. and Douthwaite, S. YbeA is the m3Ψ methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA. RNA 14 (2008) 2234-2244. [PMID: 18755835]
Accepted name: 16S rRNA (cytosine1407-C5)-methyltransferase
Reaction: S-adenosyl-L-methionine + cytosine1407 in 16S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA
Other name(s): RNA m5C methyltransferase YebU; RsmF; YebU
Systematic name: S-adenosyl-L-methionine:16S rRNA (cytosine1407-C5)-methyltransferase
Comments: The enzyme specifically methylates cytosine1407 at C5 in 16S rRNA.
References:
1. Andersen, N.M. and Douthwaite, S. YebU is a m5C methyltransferase specific for 16 S rRNA nucleotide 1407. J. Mol. Biol. 359 (2006) 777-786. [PMID: 16678201]
2. Hallberg, B.M., Ericsson, U.B., Johnson, K.A., Andersen, N.M., Douthwaite, S., Nordlund, P., Beuscher, A.E., 4th and Erlandsen, H. The structure of the RNA m5C methyltransferase YebU from Escherichia coli reveals a C-terminal RNA-recruiting PUA domain. J. Mol. Biol. 360 (2006) 774-787. [PMID: 16793063]
Accepted name: 16S rRNA (guanine1405-C7)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanine1405 in 16S rRNA = S-adenosyl-L-homocysteine + 7-methylguanine1405 in 16S rRNA
Other name(s): methyltransferase Sgm; m7G1405 Mtase; Sgm Mtase; Sgm; sisomicin-gentamicin methyltransferase; sisomicin-gentamicin methylase; GrmA
Systematic name: S-adenosyl-L-methionine:16S rRNA (guanine1405-C7)-methyltransferase
Comments: The enzyme specifically methylates guanine1405 at C7 in 16S rRNA. The enzyme from the antibiotic-producing bacterium Micromonospora zionensis methylates guanine1405 in 16S rRNA to 7-methylguanine, thereby rendering the ribosome resistant to 4,6-disubstituted deoxystreptamine aminoglycosides, which include gentamicins and kanamycins [2].
References:
1. Husain, N., Tkaczuk, K.L., Tulsidas, S.R., Kaminska, K.H., Cubrilo, S., Maravic-Vlahovicek, G., Bujnicki, J.M. and Sivaraman, J. Structural basis for the methylation of G1405 in 16S rRNA by aminoglycoside resistance methyltransferase Sgm from an antibiotic producer: a diversity of active sites in m7G methyltransferases. Nucleic Acids Res. 38 (2010) 4120-4132. [PMID: 20194115]
2. Savic, M., Lovric, J., Tomic, T.I., Vasiljevic, B. and Conn, G.L. Determination of the target nucleosides for members of two families of 16S rRNA methyltransferases that confer resistance to partially overlapping groups of aminoglycoside antibiotics. Nucleic Acids Res. 37 (2009) 5420-5431. [PMID: 19589804]
3. Tomic, T.I., Moric, I., Conn, G.L. and Vasiljevic, B. Aminoglycoside resistance genes sgm and kgmB protect bacterial but not yeast small ribosomal subunits in vitro despite high conservation of the rRNA A-site. Res. Microbiol. 159 (2008) 658-662. [PMID: 18930134]
4. Savic, M., Ilic-Tomic, T., Macmaster, R., Vasiljevic, B. and Conn, G.L. Critical residues for cofactor binding and catalytic activity in the aminoglycoside resistance methyltransferase Sgm. J. Bacteriol. 190 (2008) 5855-5861. [PMID: 18586937]
5. Maravic Vlahovicek, G., Cubrilo, S., Tkaczuk, K.L. and Bujnicki, J.M. Modeling and experimental analyses reveal a two-domain structure and amino acids important for the activity of aminoglycoside resistance methyltransferase Sgm. Biochim. Biophys. Acta 1784 (2008) 582-590. [PMID: 18343347]
6. Kojic, M., Topisirovic, L. and Vasiljevic, B. Cloning and characterization of an aminoglycoside resistance determinant from Micromonospora zionensis. J. Bacteriol. 174 (1992) 7868-7872. [PMID: 1447159]
Accepted name: 16S rRNA (adenine1408-N1)-methyltransferase
Reaction: S-adenosyl-L-methionine + adenine1408 in 16S rRNA = S-adenosyl-L-homocysteine + N1-methyladenine1408 in 16S rRNA
Other name(s): kanamycin-apramycin resistance methylase; 16S rRNA:m1A1408 methyltransferase; KamB; NpmA; 16S rRNA m1A1408 methyltransferase
Systematic name: S-adenosyl-L-methionine:16S rRNA (adenine1408-N1)-methyltransferase
Comments: The enzyme provides a panaminoglycoside-resistant nature through interference with the binding of aminoglycosides toward the A site of 16S rRNA through N1-methylation at position adenine1408 [4].
References:
1. Beauclerk, A.A. and Cundliffe, E. Sites of action of two ribosomal RNA methylases responsible for resistance to aminoglycosides. J. Mol. Biol. 193 (1987) 661-671. [PMID: 2441068]
2. Koscinski, L., Feder, M. and Bujnicki, J.M. Identification of a missing sequence and functionally important residues of 16S rRNA:m1A1408 methyltransferase KamB that causes bacterial resistance to aminoglycoside antibiotics. Cell Cycle 6 (2007) 1268-1271. [PMID: 17495534]
3. Holmes, D.J., Drocourt, D., Tiraby, G. and Cundliffe, E. Cloning of an aminoglycoside-resistance-encoding gene, kamC, from Saccharopolyspora hirsuta: comparison with kamB from Streptomyces tenebrarius. Gene 102 (1991) 19-26. [PMID: 1840536]
4. Wachino, J., Shibayama, K., Kurokawa, H., Kimura, K., Yamane, K., Suzuki, S., Shibata, N., Ike, Y. and Arakawa, Y. Novel plasmid-mediated 16S rRNA m1A1408 methyltransferase, NpmA, found in a clinically isolated Escherichia coli strain resistant to structurally diverse aminoglycosides. Antimicrob. Agents Chemother. 51 (2007) 4401-4409. [PMID: 17875999]
Accepted name: 23S rRNA (adenine1618-N6)-methyltransferase
Reaction: S-adenosyl-L-methionine + adenine1618 in 23S rRNA = S-adenosyl-L-homocysteine + N6-methyladenine1618 in 23S rRNA
Other name(s): rRNA large subunit methyltransferase F; YbiN protein; rlmF (gene name); m6A1618 methyltransferase
Systematic name: S-adenosyl-L-methionine:23S rRNA (adenine1618-N6)-methyltransferase
Comments: The recombinant YbiN protein is able to methylate partially deproteinized 50 S ribosomal subunit, but neither the completely assembled 50 S subunits nor completely deproteinized 23 S rRNA [1].
References:
1. Sergiev, P.V., Serebryakova, M.V., Bogdanov, A.A. and Dontsova, O.A. The ybiN gene of Escherichia coli encodes adenine-N6 methyltransferase specific for modification of A1618 of 23 S ribosomal RNA, a methylated residue located close to the ribosomal exit tunnel. J. Mol. Biol. 375 (2008) 291-300. [PMID: 18021804]
Accepted name: 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase
Reaction: 4 S-adenosyl-L-methionine + adenine1518/adenine1519 in 16S rRNA = 4 S-adenosyl-L-homocysteine + N6-dimethyladenine1518/N6-dimethyladenine1519 in 16S rRNA
Other name(s): S-adenosylmethionine-6-N',N'-adenosyl (rRNA) dimethyltransferase; KsgA; ksgA methyltransferase
Systematic name: S-adenosyl-L-methionine:16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase
Comments: KsgA introduces the most highly conserved ribosomal RNA modification, the dimethylation of adenine1518 and adenine1519 in 16S rRNA. Strains lacking the methylase are resistant to kasugamycin [1].
References:
1. Helser, T.L., Davies, J.E. and Dahlberg, J.E. Change in methylation of 16S ribosomal RNA associated with mutation to kasugamycin resistance in Escherichia coli. Nat. New Biol. 233 (1971) 12-14. [PMID: 4329247]
2. Helser, T.L., Davies, J.E. and Dahlberg, J.E. Mechanism of kasugamycin resistance in Escherichia coli. Nat. New Biol. 235 (1972) 6-9. [PMID: 4336392]
3. van Buul, C.P. and van Knippenberg, P.H. Nucleotide sequence of the ksgA gene of Escherichia coli: comparison of methyltransferases effecting dimethylation of adenosine in ribosomal RNA. Gene 38 (1985) 65-72. [PMID: 3905517]
4. Formenoy, L.J., Cunningham, P.R., Nurse, K., Pleij, C.W. and Ofengand, J. Methylation of the conserved A1518-A1519 in Escherichia coli 16S ribosomal RNA by the ksgA methyltransferase is influenced by methylations around the similarly conserved U1512.G1523 base pair in the 3' terminal hairpin. Biochimie 76 (1994) 1123-1128. [PMID: 7538324]
5. O'Farrell, H.C., Scarsdale, J.N. and Rife, J.P. Crystal structure of KsgA, a universally conserved rRNA adenine dimethyltransferase in Escherichia coli. J. Mol. Biol. 339 (2004) 337-353. [PMID: 15136037]
6. Poldermans, B., Roza, L. and Van Knippenberg, P.H. Studies on the function of two adjacent N6,N6-dimethyladenosines near the 3' end of 16 S ribosomal RNA of Escherichia coli. III. Purification and properties of the methylating enzyme and methylase-30 S interactions. J. Biol. Chem. 254 (1979) 9094-9100. [PMID: 383712]
7. Demirci, H., Belardinelli, R., Seri, E., Gregory, S.T., Gualerzi, C., Dahlberg, A.E. and Jogl, G. Structural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 5'-methylthioadenosine. J. Mol. Biol. 388 (2009) 271-282. [PMID: 19285505]
8. Tu, C., Tropea, J.E., Austin, B.P., Court, D.L., Waugh, D.S. and Ji, X. Structural basis for binding of RNA and cofactor by a KsgA methyltransferase. Structure 17 (2009) 374-385. [PMID: 19278652]
Accepted name: 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase
Reaction: 4 S-adenosyl-L-methionine + adenine1779/adenine1780 in 18S rRNA = 4 S-adenosyl-L-homocysteine + N6-dimethyladenine1779/N6-dimethyladenine1780 in 18S rRNA
Other name(s): 18S rRNA dimethylase Dim1p; Dim1p; ScDim1; m2(6)A dimethylase; KIDIM1
Systematic name: S-adenosyl-L-methionine:18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase
Comments: DIM1 is involved in pre-rRNA processing [1].
References:
1. Lafontaine, D., Vandenhaute, J. and Tollervey, D. The 18S rRNA dimethylase Dim1p is required for pre-ribosomal RNA processing in yeast. Genes Dev. 9 (1995) 2470-2481. [PMID: 7590228]
2. Lafontaine, D.L., Preiss, T. and Tollervey, D. Yeast 18S rRNA dimethylase Dim1p: a quality control mechanism in ribosome synthesis. Mol. Cell Biol. 18 (1998) 2360-2370. [PMID: 9528805]
3. Pulicherla, N., Pogorzala, L.A., Xu, Z., O. Farrell, H.C., Musayev, F.N., Scarsdale, J.N., Sia, E.A., Culver, G.M. and Rife, J.P. Structural and functional divergence within the Dim1/KsgA family of rRNA methyltransferases. J. Mol. Biol. 391 (2009) 884-893. [PMID: 19520088]
4. Lafontaine, D., Delcour, J., Glasser, A.L., Desgres, J. and Vandenhaute, J. The DIM1 gene responsible for the conserved m6(2)Am6(2)A dimethylation in the 3'-terminal loop of 18 S rRNA is essential in yeast. J. Mol. Biol. 241 (1994) 492-497. [PMID: 8064863]
5. Brown, J. and Trafimow, D. Generalization of the negativity effect to self-attributions. Psychol Rep 93 (2003) 638-640. [PMID: 14650698]
Accepted name: 23S rRNA (adenine2085-N6)-dimethyltransferase
Reaction: 2 S-adenosyl-L-methionine + adenine2085 in 23S rRNA = 2 S-adenosyl-L-homocysteine + N6-dimethyladenine2085 in 23S rRNA
Other name(s): ErmC' methyltransferase; ermC methylase; ermC 23S rRNA methyltransferase; rRNA:m6A methyltransferase ErmC'; ErmC'; rRNA methyltransferase ErmC'
Systematic name: S-adenosyl-L-methionine:23S rRNA (adenine2085-N6)-dimethyltransferase
Comments: ErmC is a methyltransferase that confers resistance to the macrolide-lincosamide-streptogramin B group of antibiotics by catalysing the methylation of 23S rRNA at adenine2085.
References:
1. Zhong, P., Pratt, S.D., Edalji, R.P., Walter, K.A., Holzman, T.F., Shivakumar, A.G. and Katz, L. Substrate requirements for ErmC' methyltransferase activity. J. Bacteriol. 177 (1995) 4327-4332. [PMID: 7543473]
2. Denoya, C. and Dubnau, D. Mono- and dimethylating activities and kinetic studies of the ermC 23 S rRNA methyltransferase. J. Biol. Chem. 264 (1989) 2615-2624. [PMID: 2492520]
3. Denoya, C.D. and Dubnau, D. Site and substrate specificity of the ermC 23S rRNA methyltransferase. J. Bacteriol. 169 (1987) 3857-3860. [PMID: 2440853]
4. Bussiere, D.E., Muchmore, S.W., Dealwis, C.G., Schluckebier, G., Nienaber, V.L., Edalji, R.P., Walter, K.A., Ladror, U.S., Holzman, T.F. and Abad-Zapatero, C. Crystal structure of ErmC', an rRNA methyltransferase which mediates antibiotic resistance in bacteria. Biochemistry 37 (1998) 7103-7112. [PMID: 9585521]
5. Schluckebier, G., Zhong, P., Stewart, K.D., Kavanaugh, T.J. and Abad-Zapatero, C. The 2.2 Å structure of the rRNA methyltransferase ErmC' and its complexes with cofactor and cofactor analogs: implications for the reaction mechanism. J. Mol. Biol. 289 (1999) 277-291. [PMID: 10366505]
6. Maravic, G., Bujnicki, J.M., Feder, M., Pongor, S. and Flogel, M. Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC' redefines the substrate-binding site and suggests a model for protein-RNA interactions. Nucleic Acids Res. 31 (2003) 4941-4949. [PMID: 12907737]
Accepted name: 23S rRNA (guanosine2251-2'-O)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanosine2251 in 23S rRNA = S-adenosyl-L-homocysteine + 2'-O-methylguanosine2251 in 23S rRNA
Other name(s): rlmB (gene name); yifH (gene name)
Systematic name: S-adenosyl-L-methionine:23S rRNA (guanosine2251-2'-O)-methyltransferase
Comments: The enzyme catalyses the methylation of guanosine2251, a modification conserved in the peptidyltransferase domain of 23S rRNA.
References:
1. Lovgren, J.M. and Wikstrom, P.M. The rlmB gene is essential for formation of Gm2251 in 23S rRNA but not for ribosome maturation in Escherichia coli. J. Bacteriol. 183 (2001) 6957-6960. [PMID: 11698387]
2. Michel, G., Sauve, V., Larocque, R., Li, Y., Matte, A. and Cygler, M. The structure of the RlmB 23S rRNA methyltransferase reveals a new methyltransferase fold with a unique knot. Structure 10 (2002) 1303-1315. [PMID: 12377117]
Accepted name: 23S rRNA (cytidine2498-2'-O)-methyltransferase
Reaction: S-adenosyl-L-methionine + cytidine2498 in 23S rRNA = S-adenosyl-L-homocysteine + 2'-O-methylcytidine2498 in 23S rRNA
Other name(s): YgdE; rRNA large subunit methyltransferase M; RlmM
Systematic name: S-adenosyl-L-methionine:23S rRNA (cytidine2498-2'-O)-methyltransferase
References:
1. Purta, E., O'Connor, M., Bujnicki, J.M. and Douthwaite, S. YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA. Mol. Microbiol. 72 (2009) 1147-1158. [PMID: 19400805]
Accepted name: peptidyltransferase
Reaction: peptidyl-tRNA1 + aminoacyl-tRNA2 = tRNA1 + peptidyl(aminoacyl-tRNA2)
Other name(s): transpeptidase; ribosomal peptidyltransferase
Systematic name: peptidyl-tRNA:aminoacyl-tRNA N-peptidyltransferase
Comments: The enzyme is a ribozyme. Two non-equivlant ribonucleoprotein subunits operate in non-concerted fashion in peptide elongation. The small subunit forms the mRNA-binding machinery and decoding center, the large subunit performs the main ribosomal catalytic function in the peptidyl-transferase center.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 9059-29-4
References:
1. Rychlik, I. Release of lysine peptides by puromycin from polylysyl-transfer ribonucleic acid in the presence of ribosomes. Biochim. Biophys. Acta 114 (1966) 425-427. [PMID: 5329275]
2. Rychlik, I., Cerná, J., Chládek, S., Zemlicka, J. and Haladová, Z. Substrate specificity of ribosomal peptidyl transferase: 2'(3')-O-aminoacyl nucleosides as acceptors of the peptide chain on the amino acid site. J. Mol. Biol. 43 (1969) 13-24. [PMID: 4897787]
3. Traut, R.R. and Monro, R.E. The puromycin reaction and its relation to protein synthesis. J. Mol. Biol. 10 (1964) 63-72.
4. Voorhees, R.M., Weixlbaumer, A., Loakes, D., Kelley, A.C. and Ramakrishnan, V. Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome. Nat. Struct. Mol. Biol. 16 (2009) 528-533. [PMID: 19363482]
Accepted name: protein N-acetylglucosaminyltransferase
Reaction: UDP-N-acetyl-D-glucosamine + [protein]-L-asparagine = UDP + [protein]-N4-(N-acetyl-D-glucosaminyl)-L-asparagine
Other name(s): uridine diphosphoacetylglucosamine-protein acetylglucosaminyltransferase; uridine diphospho-N-acetylglucosamine:polypeptide β-N-acetylglucosaminyltransferase; N-acetylglucosaminyltransferase I
Systematic name: UDP-N-acetyl-D-glucosamine:[protein]-L-asparagine β-N-acetyl-D-glucosaminyl-transferase
Comments: The acceptor is the asparagine residue in a sequence of the form Asn-Xaa-Thr or Asn-Xaa-Ser.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 72319-34-7
References:
1. Khalkhali, Z. and Marshall, R.D. Glycosylation of ribonuclease A catalysed by rabbit liver extracts. Biochem. J. 146 (1975) 299-307. [PMID: 1156375]
2. Khalkhali, Z. and Marshall, R.D. UDP-N-acetyl-D-glucosamine-asparagine sequon N-acetyl-β-D-glucosaminyl-transferase-activity in human serum. Carbohydr. Res. 49 (1976) 455-473. [PMID: 986874]
3. Khalkhali, Z., Marshall, R.D., Reuvers, F., Habets-Willems, C. and Boer, P. Glycosylation in vitro of an asparagine sequon catalysed by preparations of yeast cell membranes. Biochem. J. 160 (1976) 37-41. [PMID: 795426]
Accepted name: lipid IVA 4-amino-4-deoxy-L-arabinosyltransferase
Reaction: 4-amino-4-deoxy-α-L-arabinopyranosyl ditrans,polycis-undecaprenyl phosphate + lipid IVA = lipid IIA + ditrans,polycis-undecaprenyl phosphate
Glossary: lipid IVA = 2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-α-D-glucopyranose lipid IIA = 2-deoxy-2-{[(3R)-3-hydroxypentadecanoyl]amino}-3-O-[(3R)-3-hydroxytetradecanoyl]-4-O-phosphono-β-D-glucopyranosyl-(1→6)-2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-α-D-glucopyranose
Other name(s): undecaprenyl phosphate-α-L-Ara4N transferase; 4-amino-4-deoxy-L-arabinose lipid A transferase; polymyxin resistance protein PmrK
Systematic name: 4-amino-4-deoxy-α-L-2-aminoarabinopyranosyl ditrans,polycis-undecaprenyl phosphate:lipid IVA L-2-aminoarabinopyranosyltransferase
References:
1. Trent, M.S., Ribeiro, A.A., Lin, S., Cotter, R.J. and Raetz, C.R. An inner membrane enzyme in Salmonella and Escherichia coli that transfers 4-amino-4-deoxy-L-arabinose to lipid A: induction on polymyxin-resistant mutants and role of a novel lipid-linked donor. J. Biol. Chem. 276 (2001) 43122-43131. [PMID: 11535604]
2. Trent, M.S., Ribeiro, A.A., Doerrler, W.T., Lin, S., Cotter, R.J. and Raetz, C.R. Accumulation of a polyisoprene-linked amino sugar in polymyxin-resistant Salmonella typhimurium and Escherichia coli: structural characterization and transfer to lipid A in the periplasm. J. Biol. Chem. 276 (2001) 43132-43144. [PMID: 11535605]
[EC 2.5.1.11 Transferred entry: trans-octaprenyltranstransferase. Now covered by EC 2.5.1.84 (all-trans-nonaprenyl-diphosphate synthase [geranyl-diphosphate specific]) and EC 2.5.1.85 (all-trans-nonaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific]) (EC 2.5.1.11 created 1972, deleted 2010)]
Accepted name: heptaprenyl diphosphate synthase
Reaction: (2E,6E)-farnesyl diphosphate + 4 isopentenyl diphosphate = 4 diphosphate + all-trans-heptaprenyl diphosphate For diagram of terpenoid biosynthesis, click here
Other name(s): all-trans-heptaprenyl-diphosphate synthase; heptaprenyl pyrophosphate synthase; heptaprenyl pyrophosphate synthetase; HepPP synthase; HepPS; heptaprenylpyrophosphate synthetase
Systematic name: (2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate farnesyltranstransferase (adding 4 isopentenyl units)
Comments: all-trans-Heptaprenyl-diphosphate is involved in the biosynthesis of the side-chain of menaquinone-7 [2].
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 74506-59-5
References:
1. Takahashi, I., Ogura, K. and Seto, S. Heptaprenyl pyrophosphate synthetase from Bacillus subtilis. J. Biol. Chem. 255 (1980) 4539-4543. [PMID: 6768722]
2. Zhang, Y.W., Koyama, T., Marecak, D.M., Prestwich, G.D., Maki, Y. and Ogura, K. Two subunits of heptaprenyl diphosphate synthase of Bacillus subtilis form a catalytically active complex. Biochemistry 37 (1998) 13411-13420. [PMID: 9748348]
3. Zhang, Y.W., Li, X.Y., Sugawara, H. and Koyama, T. Site-directed mutagenesis of the conserved residues in component I of Bacillus subtilis heptaprenyl diphosphate synthase. Biochemistry 38 (1999) 14638-14643. [PMID: 10545188]
4. Suzuki, T., Zhang, Y.W., Koyama, T., Sasaki, D.Y. and Kurihara, K. Direct observation of substrate-enzyme complexation by surface forces measurement. J. Am. Chem. Soc. 128 (2006) 15209-15214. [PMID: 17117872]
Accepted name: ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
Reaction: (2E,6E)-farnesyl diphosphate + 8 isopentenyl diphosphate = 8 diphosphate + ditrans,polycis-undecaprenyl diphosphate
For diagram of polyprenol biosynthesis, click here
Other name(s): di-trans,poly-cis-undecaprenyl-diphosphate synthase; undecaprenyl-diphosphate synthase; bactoprenyl-diphosphate synthase; UPP synthetase; undecaprenyl diphosphate synthetase; undecaprenyl pyrophosphate synthetase
Systematic name: (2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate cistransferase (adding 8 isopentenyl units)
Comments: Undecaprenyl pyrophosphate synthase catalyses the consecutive condensation reactions of a farnesyl diphosphate with eight isopentenyl diphosphates, in which new cis-double bonds are formed, to generate undecaprenyl diphosphate that serves as a lipid carrier for peptidoglycan synthesis of bacterial cell wall [3].
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 52350-87-5
References:
1. Muth, J.D. and Allen, C.M. Undecaprenyl pyrophosphate synthetase from Lactobacillus plantarum: a dimeric protein. Arch. Biochem. Biophys. 230 (1984) 49-60. [PMID: 6712246]
2. Takahashi, I. and Ogura, K. Prenyltransferases of Bacillus subtilis: undecaprenyl pyrophosphate synthetase and geranylgeranyl pyrophosphate synthetase. J. Biochem. (Tokyo) 92 (1982) 1527-1537. [PMID: 6818223]
3. Guo, R.T., Ko, T.P., Chen, A.P., Kuo, C.J., Wang, A.H. and Liang, P.H. Crystal structures of undecaprenyl pyrophosphate synthase in complex with magnesium, isopentenyl pyrophosphate, and farnesyl thiopyrophosphate: roles of the metal ion and conserved residues in catalysis. J. Biol. Chem. 280 (2005) 20762-20774. [PMID: 15788389]
4. Ko, T.P., Chen, Y.K., Robinson, H., Tsai, P.C., Gao, Y.G., Chen, A.P., Wang, A.H. and Liang, P.H. Mechanism of product chain length determination and the role of a flexible loop in Escherichia coli undecaprenyl-pyrophosphate synthase catalysis. J. Biol. Chem. 276 (2001) 47474-47482. [PMID: 11581264]
5. Fujikura, K., Zhang, Y.W., Fujihashi, M., Miki, K. and Koyama, T. Mutational analysis of allylic substrate binding site of Micrococcus luteus B-P 26 undecaprenyl diphosphate synthase. Biochemistry 42 (2003) 4035-4041. [PMID: 12680756]
6. Fujihashi, M., Zhang, Y.W., Higuchi, Y., Li, X.Y., Koyama, T. and Miki, K. Crystal structure of cis-prenyl chain elongating enzyme, undecaprenyl diphosphate synthase. Proc. Natl. Acad. Sci. USA 98 (2001) 4337-4342. [PMID: 11287651]
7. Pan, J.J., Chiou, S.T. and Liang, P.H. Product distribution and pre-steady-state kinetic analysis of Escherichia coli undecaprenyl pyrophosphate synthase reaction. Biochemistry 39 (2000) 10936-10942. [PMID: 10978182]
8. Kharel, Y., Zhang, Y.W., Fujihashi, M., Miki, K. and Koyama, T. Significance of highly conserved aromatic residues in Micrococcus luteus B-P 26 undecaprenyl diphosphate synthase. J. Biochem. 134 (2003) 819-826. [PMID: 14769870]
[EC 2.5.1.33 Transferred entry: trans-pentaprenyltranstransferase. Now covered by EC 2.5.1.82 (hexaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific]) and EC 2.5.1.83 (hexaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]) (EC 2.5.1.33 created 1984, deleted 2010)]
Accepted name: geranylfarnesyl diphosphate synthase
Reaction: geranylgeranyl diphosphate + isopentenyl diphosphate = (2E,6E,10E,14E)-geranylfarnesyl diphosphate + diphosphate
Other name(s): FGPP synthase; (all-E) geranylfarnesyl diphosphate synthase; GFPS; Fgs
Systematic name: geranylgeranyl-diphosphate:isopentenyl-diphosphate transtransferase (adding 1 isopentenyl unit)
Comments: The enzyme from Methanosarcina mazei is involved in biosynthesis of the polyprenyl side-chain of methanophenazine, an electron carrier utilized for methanogenesis. It prefers geranylgeranyl diphosphate and farnesyl diphosphate as allylic substrate [1]. The enzyme from Aeropyrum pernix prefers farnesyl diphosphate as allylic substrate. The enzyme is involved in the biosynthesis of C25-C25 membrane lipids [2].
References:
1. Ogawa, T., Yoshimura, T. and Hemmi, H. Geranylfarnesyl diphosphate synthase from Methanosarcina mazei: Different role, different evolution. Biochem. Biophys. Res. Commun. 393 (2010) 16-20. [PMID: 20097171]
2. Tachibana, A., Yano, Y., Otani, S., Nomura, N., Sako, Y. and Taniguchi, M. Novel prenyltransferase gene encoding farnesylgeranyl diphosphate synthase from a hyperthermophilic archaeon, Aeropyrum pernix. Molecular evolution with alteration in product specificity. Eur. J. Biochem. 267 (2000) 321-328. [PMID: 10632701]
3. Tachibana, A. A novel prenyltransferase, farnesylgeranyl diphosphate synthase, from the haloalkaliphilic archaeon, Natronobacterium pharaonis. FEBS Lett. 341 (1994) 291-294. [PMID: 8137956]
4. Lee, P.C., Mijts, B.N., Petri, R., Watts, K.T. and Schmidt-Dannert, C. Alteration of product specificity of Aeropyrum pernix farnesylgeranyl diphosphate synthase (Fgs) by directed evolution. Protein Eng Des Sel 17 (2004) 771-777. [PMID: 15548566]
Accepted name: hexaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific]
Reaction: geranylgeranyl diphosphate + 2 isopentenyl diphosphate = 2 diphosphate + all-trans-hexaprenyl diphosphate
Other name(s): HexPS(ambiguous); (
Systematic name: geranylgeranyl-diphosphate:isopentenyl-diphosphate transferase (adding 2 isopentenyl units)
Comments: The enzyme prefers geranylgeranyl diphosphate to farnesyl diphosphate as an allylic substrate and does not show activity for geranyl diphosphate and dimethylallyl diphosphate. Requires Mg2+ [1].
References:
1. Hemmi, H., Ikejiri, S., Yamashita, S. and Nishino, T. Novel medium-chain prenyl diphosphate synthase from the thermoacidophilic archaeon Sulfolobus solfataricus. J. Bacteriol. 184 (2002) 615-620. [PMID: 11790729]
2. Hemmi, H., Noike, M., Nakayama, T. and Nishino, T. Change of product specificity of hexaprenyl diphosphate synthase from Sulfolobus solfataricus by introducing mimetic mutations. Biochem. Biophys. Res. Commun. 297 (2002) 1096-1101. [PMID: 12372398]
3. Sun, H.Y., Ko, T.P., Kuo, C.J., Guo, R.T., Chou, C.C., Liang, P.H. and Wang, A.H. Homodimeric hexaprenyl pyrophosphate synthase from the thermoacidophilic crenarchaeon Sulfolobus solfataricus displays asymmetric subunit structures. J. Bacteriol. 187 (2005) 8137-8148. [PMID: 16291686]
Accepted name: hexaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific]
Reaction: (2E,6E)-farnesyl diphosphate + 3 isopentenyl diphosphate = 3 diphosphate + all-trans-hexaprenyl diphosphate
Other name(s): HexPS (ambiguous); hexaprenyl pyrophosphate synthetase (ambiguous); hexaprenyl diphosphate synthase (ambiguous)
Systematic name: (2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate farnesyltranstransferase (adding 3 isopentenyl units)
Comments: The enzyme prefers farnesyl diphosphate to geranylgeranyl diphosphate as an allylic substrate and does not show activity for geranyl diphosphate and dimethylallyl diphosphate [1].
References:
1. Fujii, H., Koyama, T. and Ogura, K. Hexaprenyl pyrophosphate synthetase from Micrococcus luteus B-P 26. Separation of two essential components. J. Biol. Chem. 257 (1982) 14610-14612. [PMID: 7174655]
2. Shimizu, N., Koyama, T. and Ogura, K. Molecular cloning, expression, and characterization of the genes encoding the two essential protein components of Micrococcus luteus B-P 26 hexaprenyl diphosphate synthase. J. Bacteriol. 180 (1998) 1578-1581. [PMID: 9515931]
3. Nagaki, M., Kimura, K., Kimura, H., Maki, Y., Goto, E., Nishino, T. and Koyama, T. Artificial substrates of medium-chain elongating enzymes, hexaprenyl- and heptaprenyl diphosphate synthases. Bioorg. Med. Chem. Lett. 11 (2001) 2157-2159. [PMID: 11514159]
Accepted name: all-trans-nonaprenyl-diphosphate synthase [geranyl-diphosphate specific]
Reaction: geranyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + all-trans-nonaprenyl diphosphate
Glossary: solanesyl diphosphate = all-trans-nonaprenyl diphosphate
Other name(s): nonaprenyl diphosphate synthase (ambiguous); solanesyl diphosphate synthase (ambiguous); SolPP synthase (ambiguous); SPP-synthase (ambiguous); SPP synthase (ambiguous); solanesyl-diphosphate synthase (ambiguous); OsSPS2
Systematic name: geranyl-diphosphate:isopentenyl-diphosphate transtransferase (adding 7 isopentenyl units)
Comments: (2E,6E)-Farnesyl diphosphate and geranylgeranyl diphosphate are less effective as substrates than geranyl diphosphate. The enzyme is involved in the synthesis of the side chain of menaquinone-9 [1]. In Oryza sativa the enzyme SPS2 is involved in providing solanesyl diphosphate for plastoquinone-9 formation [3].
References:
1. Sagami, H., Ogura, K. and Seto, S. Solanesyl pyrophosphate synthetase from Micrococcus lysodeikticus. Biochemistry 16 (1977) 4616-4622. [PMID: 911777]
2. Fujii, H., Sagami, H., Koyama, T., Ogura, K., Seto, S., Baba, T. and Allen, C.M. Variable product specificity of solanesyl pyrophosphate synthetase. Biochem. Biophys. Res. Commun. 96 (1980) 1648-1653. [PMID: 7447947]
3. Ohara, K., Sasaki, K. and Yazaki, K. Two solanesyl diphosphate synthases with different subcellular localizations and their respective physiological roles in Oryza sativa. J. Exp. Bot. (2010) . [PMID: 20421194]
4. Ohnuma, S., Koyama, T. and Ogura, K. Purification of solanesyl-diphosphate synthase from Micrococcus luteus. A new class of prenyltransferase. J. Biol. Chem. 266 (1991) 23706-23713. [PMID: 1748647]
5. Gotoh, T., Koyama, T. and Ogura, K. Farnesyl diphosphate synthase and solanesyl diphosphate synthase reactions of diphosphate-modified allylic analogs: the significance of the diphosphate linkage involved in the allylic substrates for prenyltransferase. J. Biochem. 112 (1992) 20-27. [PMID: 1429508]
6. Teclebrhan, H., Olsson, J., Swiezewska, E. and Dallner, G. Biosynthesis of the side chain of ubiquinone:trans-prenyltransferase in rat liver microsomes. J. Biol. Chem. 268 (1993) 23081-23086. [PMID: 8226825]
Accepted name: all-trans-nonaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific]
Reaction: geranylgeranyl diphosphate + 5 isopentenyl diphosphate = 5 diphosphate + all-trans-nonaprenyl diphosphate
Glossary: solanesyl diphosphate = all-trans-nonaprenyll diphosphate
Other name(s): nonaprenyl diphosphate synthase (ambiguous); solanesyl diphosphate synthase (ambiguous); At-SPS2; At-SPS1; SPS1; SPS2
Systematic name: geranylgeranyl-diphosphate:isopentenyl-diphosphate transtransferase (adding 5 isopentenyl units)
Comments: Geranylgeranyl diphosphate is preferred over farnesyl diphosphate as allylic substrate [1]. The plant Arabidopsis thaliana has two different enzymes that catalyse this reaction. SPS1 contributes to the biosynthesis of the ubiquinone side-chain while SPS2 supplies the precursor of the plastoquinone side-chains [2].
References:
1. Hirooka, K., Bamba, T., Fukusaki, E. and Kobayashi, A. Cloning and kinetic characterization of Arabidopsis thaliana solanesyl diphosphate synthase. Biochem. J. 370 (2003) 679-686. [PMID: 12437513]
2. Hirooka, K., Izumi, Y., An, C.I., Nakazawa, Y., Fukusaki, E. and Kobayashi, A. Functional analysis of two solanesyl diphosphate synthases from Arabidopsis thaliana. Biosci. Biotechnol. Biochem. 69 (2005) 592-601. [PMID: 15784989]
3. Jun, L., Saiki, R., Tatsumi, K., Nakagawa, T. and Kawamukai, M. Identification and subcellular localization of two solanesyl diphosphate synthases from Arabidopsis thaliana. Plant Cell Physiol. 45 (2004) 1882-1888. [PMID: 15653808]
Accepted name: trans,polycis-decaprenyl diphosphate synthase
Reaction: (2Z,6E)-farnesyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + (2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E)-decaprenyl diphosphate
Glossary: (2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E)-decaprenyl diphosphate = trans,polycis-decaprenyl diphosphate
Other name(s): Rv2361c; (2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E)-decaprenyl diphosphate synthase
Systematic name: (2Z,6E)-farnesyl-diphosphate:isopentenyl-diphosphate farnesylcistransferase (adding 7 isopentenyl units)
Comments: The enzyme is involved in the biosynthesis of decaprenyl phosphate, which plays a central role in the biosynthesis of essential mycobacterial cell wall components, such as the mycolyl-arabinogalactan-peptidoglycan complex and lipoarabinomannan [2].
References:
1. Kaur, D., Brennan, P.J. and Crick, D.C. Decaprenyl diphosphate synthesis in Mycobacterium tuberculosis. J. Bacteriol. 186 (2004) 7564-7570. [PMID: 15516568]
2. Wang, W., Dong, C., McNeil, M., Kaur, D., Mahapatra, S., Crick, D.C. and Naismith, J.H. The structural basis of chain length control in Rv1086. J. Mol. Biol. 381 (2008) 129-140. [PMID: 18597781]
3. Crick, D.C., Schulbach, M.C., Zink, E.E., Macchia, M., Barontini, S., Besra, G.S. and Brennan, P.J. Polyprenyl phosphate biosynthesis in Mycobacterium tuberculosis and Mycobacterium smegmatis. J. Bacteriol. 182 (2000) 5771-5778. [PMID: 11004176]
Accepted name: ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific]
Reaction: (2E,6E)-farnesyl diphosphate + n isopentenyl diphosphate = n diphosphate + ditrans,polycis-polyprenyl diphosphate (n = 10-55)
Other name(s): RER2; Rer2p; Rer2p Z-prenyltransferase; Srt1p; Srt2p Z-prenyltransferase; ACPT; dehydrodolichyl diphosphate synthase 1
Systematic name: (2E,6E)-farnesyl-diphosphate:isopentenyl-diphosphate cistransferase (adding 10-55 isopentenyl units)
Comments: The enzyme is involved in biosynthesis of dolichol (a long-chain polyprenol with a saturated α-isoprene unit, which serves as a glycosyl carrier in protein glycosylation [1]. The yeast Saccharomyces cerevisiae has two different enzymes that catalyse this reaction. Rer2p synthesizes a well-defined family of polyprenols of 13-18 isoprene residues with dominating C80 (16 isoprene residues) extending to C120, while Srt1p synthesizes mainly polyprenol with 22 isoprene subunits. Largest Srt1p products reach C290 [2]. The enzyme from Arabidopsis thaliana catalyses the formation of polyprenyl diphosphates with predominant carbon number C120 [4].
References:
1. Sato, M., Fujisaki, S., Sato, K., Nishimura, Y. and Nakano, A. Yeast Saccharomyces cerevisiae has two cis-prenyltransferases with different properties and localizations. Implication for their distinct physiological roles in dolichol synthesis. Genes Cells 6 (2001) 495-506. [PMID: 11442630]
2. Poznanski, J. and Szkopinska, A. Precise bacterial polyprenol length control fails in Saccharomyces cerevisiae. Biopolymers 86 (2007) 155-164. [PMID: 17345630]
3. Sato, M., Sato, K., Nishikawa, S., Hirata, A., Kato, J. and Nakano, A. The yeast RER2 gene, identified by endoplasmic reticulum protein localization mutations, encodes cis-prenyltransferase, a key enzyme in dolichol synthesis. Mol. Cell Biol. 19 (1999) 471-483. [PMID: 9858571]
4. Oh, S.K., Han, K.H., Ryu, S.B. and Kang, H. Molecular cloning, expression, and functional analysis of a cis-prenyltransferase from Arabidopsis thaliana. Implications in rubber biosynthesis. J. Biol. Chem. 275 (2000) 18482-18488. [PMID: 10764783]
5. Cunillera, N., Arro, M., Fores, O., Manzano, D. and Ferrer, A. Characterization of dehydrodolichyl diphosphate synthase of Arabidopsis thaliana, a key enzyme in dolichol biosynthesis. FEBS Lett. 477 (2000) 170-174. [PMID: 10908715]
Accepted name: trans,polycis-polyprenyl diphosphate synthase [(2Z,6E)-farnesyl diphosphate specific]
Reaction: (2Z,6E)-farnesyl diphosphate + n isopentenyl diphosphate = n diphosphate + trans,polycis-polyprenyl diphosphate (n = 9-11)
Systematic name: (2Z,6E)-farnesyl-diphosphate:isopentenyl-diphosphate cistransferase (adding 9-11 isopentenyl units)
Comments: Highest activity with (2Z,6E)-farnesyl diphosphate as allylic substrate. Broad product specificity with the major product being dodecaprenyl diphosphate. Synthesizes even C70 prenyl diphosphate as the maximum chain-length product [1].
References:
1. Ambo, T., Noike, M., Kurokawa, H. and Koyama, T. Cloning and functional analysis of cis-prenyltransferase from Thermobifida fusca. J. Biosci. Bioeng. 107 (2009) 620-622. [PMID: 19447338]
Accepted name: tritrans,polycis-undecaprenyl-diphosphate synthase [geranylgeranyl-diphosphate specific]
Reaction: geranylgeranyl diphosphate + 7 isopentenyl diphosphate = 7 diphosphate + tritrans,polycis-undecaprenyl diphosphate
Systematic name: geranylgeranyl-diphosphate:isopentenyl-diphosphate cistransferase (adding 7 isopentenyl units)
Comments: This enzyme is involved in the biosynthesis of the glycosyl carrier lipid in some archaebacteria. Unlike EC 2.5.1.31, its counterpart in most bacteria, it prefers geranylgeranyl diphosphate to farnesyl diphosphate as the allylic substrate, resulting in production of a tritrans,polycis variant of undecaprenyl diphosphate [1].
References:
1. Hemmi, H., Yamashita, S., Shimoyama, T., Nakayama, T. and Nishino, T. Cloning, expression, and characterization of cis-polyprenyl diphosphate synthase from the thermoacidophilic archaeon Sulfolobus acidocaldarius. J. Bacteriol. 183 (2001) 401-404. [PMID: 11114943]
Accepted name: GDP-L-galactose phosphorylase
Reaction: GDP-L-galactose + phosphate = α-L-galactose 1-phosphate + GDP
Other name(s): VTC2; VTC5
Systematic name: GDP:α-L-galactose 1-phosphate guanylyltransferase
Comments: The enzyme catalyses a reaction of the Smirnoff-Wheeler pathway, the major route to ascorbate biosynthesis in plants.
References:
1. Linster, C.L., Gomez, T.A., Christensen, K.C., Adler, L.N., Young, B.D., Brenner, C. and Clarke, S.G. Arabidopsis VTC2 encodes a GDP-L-galactose phosphorylase, the last unknown enzyme in the Smirnoff-Wheeler pathway to ascorbic acid in plants. J. Biol. Chem. 282 (2007) 18879-18885. [PMID: 17462988]
2. Linster, C.L., Adler, L.N., Webb, K., Christensen, K.C., Brenner, C. and Clarke, S.G. A second GDP-L-galactose phosphorylase in arabidopsis en route to vitamin C. Covalent intermediate and substrate requirements for the conserved reaction. J. Biol. Chem. 283 (2008) 18483-18492. [PMID: 18463094]
3. Dowdle, J., Ishikawa, T., Gatzek, S., Rolinski, S. and Smirnoff, N. Two genes in Arabidopsis thaliana encoding GDP-L-galactose phosphorylase are required for ascorbate biosynthesis and seedling viability. Plant J. 52 (2007) 673-689. [PMID: 17877701]
4. Muller-Moule, P. An expression analysis of the ascorbate biosynthesis enzyme VTC2. Plant Mol. Biol. 68 (2008) 31-41. [PMID: 18516687]
Accepted name: L-serine-phosphatidylethanolamine phosphatidyltransferase
Reaction: L-1-phosphatidylethanolamine + L-serine = L-1-phosphatidylserine + ethanolamine
Other name(s): phosphatidylserine synthase 2; serine-exchange enzyme II; PTDSS2 (gene name)
Systematic name: L-1-phosphatidylethanolamine:L-serine phosphatidyltransferase
Comments: This mammalian enzyme catalyses an exchange reaction in which the polar head group of phosphatidylethanolamine is replaced by L-serine.
References:
1. Stone, S.J. and Vance, J.E. Cloning and expression of murine liver phosphatidylserine synthase (PSS)-2: differential regulation of phospholipid metabolism by PSS1 and PSS2. Biochem. J. 342 (1999) 57-64. [PMID: 10432300]
2. Tomohiro, S., Kawaguti, A., Kawabe, Y., Kitada, S. and Kuge, O. Purification and characterization of human phosphatidylserine synthases 1 and 2. Biochem. J. 418 (2009) 421-429. [PMID: 19014349]
Accepted name: undecaprenyl-phosphate 4-deoxy-4-formamido-L-arabinose transferase
Reaction: UDP-4-deoxy-4-formamido-α-L-arabinopyranose + ditrans,polycis-undecaprenyl phosphate = UDP + 4-deoxy-4-formamido-α-L-arabinopyranosyl ditrans,polycis-undecaprenyl phosphate
Other name(s): undecaprenyl-phosphate Ara4FN transferase; Ara4FN transferase; polymyxin resistance protein PmrF
Systematic name: UDP-4-amino-4-deoxy-α-L-arabinose:ditrans,polycis-undecaprenyl phosphate 4-amino-4-deoxy-α-L-arabinosyltransferase
Comments: The enzyme shows no activity with UDP-4-amino-4-deoxy-β-L-arabinose.
References:
1. Breazeale, S.D., Ribeiro, A.A. and Raetz, C.R. Oxidative decarboxylation of UDP-glucuronic acid in extracts of polymyxin-resistant Escherichia coli. Origin of lipid a species modified with 4-amino-4-deoxy-L-arabinose. J. Biol. Chem. 277 (2002) 2886-2896. [PMID: 11706007]
2. Breazeale, S.D., Ribeiro, A.A., McClerren, A.L. and Raetz, C.R.H. A formyltransferase required for polymyxin resistance in Escherichia coli and the modification of lipid A with 4-amino-4-deoxy-L-arabinose. Identification and function of UDP-4-deoxy-4-formamido-L-arabinose. J. Biol. Chem. 280 (2005) 14154-14167. [PMID: 15695810]
Accepted name: farnesyl diphosphatase
Reaction: (2E,6E)-farnesyl diphosphate + H2O = (2E,6E)-farnesol + diphosphate
Other name(s): FPP phosphatase
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphohydrolase
References:
1. Song, L. A soluble form of phosphatase in Saccharomyces cerevisiae capable of converting farnesyl diphosphate into E,E-farnesol. Appl. Biochem. Biotechnol. 128 (2006) 149-158. [PMID: 16484724]
2. Tsai, S.-C. and Gaylor, J.L. Testicular sterols. V. Preparation and partial purification of a microsomal prenol pyrophosphate pyrophosphohydrolase. J. Biol. Chem. 241 (1966) 4043-4050. [PMID: 4288361]
Accepted name: spore photoproduct lyase
Reaction: (5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'→5')-thymidylate (in double-helical DNA)
For diagram click here
Other name(s): SAM; SP lyase; SPL; SplB; SplG
Systematic name: spore photoproduct pyrimidine-lyase
Comments: This enzyme is a member of the 'AdoMet radical' (radical SAM) family. The enzyme binds a [4Fe-4S] cluster. The cluster is coordinated by 3 cysteines and an exchangeable SAM molecule [3]. The 5'-deoxy-adenosine radical formed after electron transfer from the [4Fe-4S] cluster to the S-adenosyl-L-methionine, initiates the repair by abstracting the C-6 hydrogen of the spore photoproduct lesion. During the second part of the repair process the SAM molecule is regenerated [3].
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number: 37290-70-3
References:
1. Chandor, A., Berteau, O., Douki, T., Gasparutto, D., Sanakis, Y., Ollagnier-de-Choudens, S., Atta, M. and Fontecave, M. Dinucleotide spore photoproduct, a minimal substrate of the DNA repair spore photoproduct lyase enzyme from Bacillus subtilis. J. Biol. Chem. 281 (2006) 26922-26931. [PMID: 16829676]
2. Pieck, J.C., Hennecke, U., Pierik, A.J., Friedel, M.G. and Carell, T. Characterization of a new thermophilic spore photoproduct lyase from Geobacillus stearothermophilus (SplG) with defined lesion containing DNA substrates. J. Biol. Chem. 281 (2006) 36317-36326. [PMID: 16968710]
3. Buis, J.M., Cheek, J., Kalliri, E. and Broderick, J.B. Characterization of an active spore photoproduct lyase, a DNA repair enzyme in the radical S-adenosylmethionine superfamily. J. Biol. Chem. 281 (2006) 25994-26003. [PMID: 16829680]
4. Mantel, C., Chandor, A., Gasparutto, D., Douki, T., Atta, M., Fontecave, M., Bayle, P.-A., Mouesca, J.-M. and Bardet, M. Combined NMR and DFT studies for the absolute configuration elucidation of the spore photoproduct, a UV-induced DNA lesion. J. Am. Chem. Soc. 130 (2008) 16978-16984. [PMID: 19012397]
5. Silver, S.C., Chandra, T., Zilinskas, E., Ghose, S., Broderick, W.E. and Broderick, J.B. Complete stereospecific repair of a synthetic dinucleotide spore photoproduct by spore photoproduct lyase. J. Biol. Inorg. Chem. (2010) . [PMID: 20405152]
[EC 4.1.99.15 Deleted entry: S-specific spore photoproduct lyase. This enzyme was classified on the basis of an incorrect reaction. The activity is covered by EC 4.1.99.14, spore photoproduct lyase (EC 4.1.99.15 created 2009, deleted 2010)]
Accepted name: oligogalacturonide lyase
Reaction: 4-(4-deoxy-α-D-galact-4-enuronosyl)-D-galacturonate = 2 5-dehydro-4-deoxy-D-glucuronate
Other name(s): oligogalacturonate lyase; unsaturated oligogalacturonate transeliminase; OGTE
Systematic name: oligogalacturonide lyase
Comments: Also catalyses eliminative removal of unsaturated terminal residues from oligosaccharides of D-galacturonate.
Links to other databases:
BRENDA,
EXPASY,
KEGG,
CAS registry number: 9031-33-8
References:
1. Moran, F., Nasuno, S. and Starr, M.P. Oligogalacturonide trans-eliminase of Erwinia carotovora. Arch. Biochem. Biophys. 125 (1968) 734-741. [PMID: 5671040]
Accepted name: (3S,6E)-nerolidol synthase
Reaction: (2E,6E)-farnesyl diphosphate + H2O = (3S,6E)-nerolidol + diphosphate
Glossary: (3S,6E)-nerolidol = (3R,6E)-3,7,11-trimethyldodeca-1,6,10-trien-3-ol
Other name(s): (E)-nerolidol synthase; nerolidol synthase; (3S)-(E)-nerolidol synthase; FaNES1
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(3S,6E)-nerolidol-forming]
Comments: The enzyme catalyses a step in the formation of 4,8-dimethyl-1,3(E),7-nonatriene, a key signal molecule in induced plant defense mediated by the attraction of enemies of herbivores [2]. Nerolidol is a naturally occurring sesquiterpene found in the essential oils of many types of plants.
References:
1. Aharoni, A., Giri, A.P., Verstappen, F.W., Bertea, C.M., Sevenier, R., Sun, Z., Jongsma, M.A., Schwab, W. and Bouwmeester, H.J. Gain and loss of fruit flavor compounds produced by wild and cultivated strawberry species. Plant Cell 16 (2004) 3110-3131. [PMID: 15522848]
2. Bouwmeester, H.J., Verstappen, F.W., Posthumus, M.A. and Dicke, M. Spider mite-induced (3S)-(E)-nerolidol synthase activity in cucumber and lima bean. The first dedicated step in acyclic C11-homoterpene biosynthesis. Plant Physiol. 121 (1999) 173-180. [PMID: 10482672]
3. Degenhardt, J. and Gershenzon, J. Demonstration and characterization of (E)-nerolidol synthase from maize: a herbivore-inducible terpene synthase participating in (3E)-4,8-dimethyl-1,3,7-nonatriene biosynthesis. Planta 210 (2000) 815-822. [PMID: 10805454]
4. Arimura, G., Garms, S., Maffei, M., Bossi, S., Schulze, B., Leitner, M., Mithofer, A. and Boland, W. Herbivore-induced terpenoid emission in Medicago truncatula: concerted action of jasmonate, ethylene and calcium signaling. Planta 227 (2008) 453-464. [PMID: 17924138]
Accepted name: (3R,6E)-nerolidol synthase
Reaction: (2E,6E)-farnesyl diphosphate + H2O = (3R,6E)-nerolidol + diphosphate
Other name(s): terpene synthase 1
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(3R,6E)-nerolidol-forming]
Comments: The enzyme catalyses a step in the formation of (3E)-4,8-dimethyl-1,3,7-nonatriene, a key signal molecule in induced plant defense mediated by the attraction of enemies of herbivores [1]. Nerolidol is a naturally occurring sesquiterpene found in the essential oils of many types of plants.
References:
1. Schnee, C., Kollner, T.G., Gershenzon, J. and Degenhardt, J. The maize gene terpene synthase 1 encodes a sesquiterpene synthase catalyzing the formation of (E)-β-farnesene, (E)-nerolidol, and (E,E)-farnesol after herbivore damage. Plant Physiol. 130 (2002) 2049-2060. [PMID: 12481088]
Accepted name: diphthine—ammonia ligase
Reaction: ATP + diphthine + NH3 = ADP + phosphate + diphthamide
Other name(s): diphthamide synthase; diphthamide synthetase
Systematic name: diphthine:ammonia ligase (ADP-forming)
Comments: This amidase catalyses the last step in the conversion of an L-histidine residue in the translation elongation factor eEF-2 to diphthamide. This factor is found in all archaebacteria and eukaryotes, but not in eubacteria, and is the target of bacterial toxins such as the diphtheria toxin and the Pseudomonas exotoxin A (see EC 2.4.2.36, NAD+—diphthamide ADP-ribosyltransferase). The substrate of the enzyme, diphthine, is produced by EC 2.1.1.98, diphthine synthase. The nature of the ammonia donor is not known.
References:
1. Moehring, J.M. and Moehring, T.J. The post-translational trimethylation of diphthamide studied in vitro. J. Biol. Chem. 263 (1988) 3840-3844. [PMID: 3346227]
2. Moehring, T.J. and Moehring, J.M. Mutant cultured cells used to study the synthesis of diphthamide. UCLA Symp. Mol. Cell. Biol. New Ser. 45 (1987) 53-63.
Accepted name: D-alanine—D-serine ligase
Reaction: D-alanine + D-serine + ATP = D-alanyl-D-serine + ADP + phosphate
Other name(s): VanC; VanE; VanG
Systematic name: D-alanine:D-serine ligase (ADP-forming)
Comments: The product of this enzyme, D-alanyl-D-serine, can be incorporated into the peptidoglycan pentapeptide instead of the usual D-alanyl-D-alanine dipeptide, which is formed by EC 6.3.2.4, D-alanine—D-alanine ligase. The resulting peptidoglycan does not bind the glycopeptide antibiotics vancomycin and teicoplanin, conferring resistance on the bacteria.
References:
1. Dutka-Malen, S., Molinas, C., Arthur, M. and Courvalin, P. Sequence of the vanC gene of Enterococcus gallinarum BM4174 encoding a D-alanine:D-alanine ligase-related protein necessary for vancomycin resistance. Gene 112 (1992) 53-58. [PMID: 1551598]
2. Park, I.S., Lin, C.H. and Walsh, C.T. Bacterial resistance to vancomycin: overproduction, purification, and characterization of VanC2 from Enterococcus casseliflavus as a D-Ala-D-Ser ligase. Proc. Natl. Acad. Sci. USA 94 (1997) 10040-10044. [PMID: 9294159]
3. Fines, M., Perichon, B., Reynolds, P., Sahm, D.F. and Courvalin, P. VanE, a new type of acquired glycopeptide resistance in Enterococcus faecalis BM4405. Antimicrob. Agents Chemother. 43 (1999) 2161-2164. [PMID: 10471558]
4. Depardieu, F., Bonora, M.G., Reynolds, P.E. and Courvalin, P. The vanG glycopeptide resistance operon from Enterococcus faecalis revisited. Mol. Microbiol. 50 (2003) 931-948. [PMID: 14617152]
5. Watanabe, S., Kobayashi, N., Quinones, D., Hayakawa, S., Nagashima, S., Uehara, N. and Watanabe, N. Genetic Diversity of the Low-Level Vancomycin Resistance Gene vanC-2/vanC-3 and Identification of a Novel vanC Subtype (vanC-4) in Enterococcus casseliflavus. Microb. Drug Resist. 15 (2009) 1-9. [PMID: 19216682]
[EC 6.3.2.22 Transferred entry: diphthine—ammonia ligase. Now EC 6.3.1.14, diphthine—ammonia ligase. (EC 6.3.2.22 created 1990, deleted 2010)]