Enzyme Nomenclature

EC 6.1

Forming Carbon-Oxygen Bonds

Sections

EC 6.1.1 Ligases Forming Aminoacyl-tRNA and Related Compounds
EC 6.1.2 Acid—Alcohol Ligases (ester synthases)


EC 6.1.1 Ligases Forming Aminoacyl-tRNA and Related Compounds

Contents

EC 6.1.1.1 tyrosine—tRNA ligase
EC 6.1.1.2 tryptophan—tRNA ligase
EC 6.1.1.3 threonine—tRNA ligase
EC 6.1.1.4 leucine—tRNA ligase
EC 6.1.1.5 isoleucine—tRNA ligase
EC 6.1.1.6 lysine—tRNA ligase
EC 6.1.1.7 alanine—tRNA ligase
EC 6.1.1.8 deleted
EC 6.1.1.9 valine—tRNA ligase
EC 6.1.1.10 methionine—tRNA ligase
EC 6.1.1.11 serine—tRNA ligase
EC 6.1.1.12 aspartate—tRNA ligase
EC 6.1.1.13 D-alanine—poly(phosphoribitol) ligase
EC 6.1.1.14 glycine—tRNA ligase
EC 6.1.1.15 proline—tRNA ligase
EC 6.1.1.16 cysteine—tRNA ligase
EC 6.1.1.17 glutamate—tRNA ligase
EC 6.1.1.18 glutamine—tRNA ligase
EC 6.1.1.19 arginine—tRNA ligase
EC 6.1.1.20 phenylalanine—tRNA ligase
EC 6.1.1.21 histidine—tRNA ligase
EC 6.1.1.22 asparagine—tRNA ligase
EC 6.1.1.23 aspartate—tRNAAsn ligase
EC 6.1.1.24 glutamate—tRNAGln ligase
EC 6.1.1.25 deleted
EC 6.1.1.26 pyrrolysine—tRNAPyl ligase
EC 6.1.1.27 O-phosphoserine—tRNA ligase
EC 6.1.1.28 deleted


Entries

EC 6.1.1.1

Accepted name: tyrosine—tRNA ligase

Reaction: ATP + L-tyrosine + tRNATyr = AMP + diphosphate + L-tyrosyl-tRNATyr

Other name(s): tyrosyl-tRNA synthetase; L-tyrosine-tRNATyr ligase (AMP-forming); tyrosyl-transfer ribonucleate synthetase; tyrosyl-transfer RNA synthetase; tyrosyl-transfer ribonucleic acid synthetase; tyrosyl-tRNA ligase; tyrosine-transfer RNA ligase; tyrosine-transfer ribonucleate synthetase; tyrosine translase; tyrosine tRNA synthetase

Systematic name: L-tyrosine:tRNATyr ligase (AMP-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9023-45-4

References:

1. Allen, E.H., Glassman, E. and Schweet, R.S. Incorporation of amino acids into ribonucleic acid. I. The role of activating enzymes. J. Biol. Chem. 235 (1960) 1061-1067.

2. Cowles, J.R. and Key, J.L. Demonstration of two tyrosyl-tRNA synthetases of pea roots. Biochim. Biophys. Acta 281 (1972) 33-44. [PMID: 4563531]

3. Holley, R.W., Brunngraber, E.F., Saad, F. and Williams, H.H. Partial purification of the threonine- and tyrosine-activating enzymes from rat liver, and the effect of potassium ions on the activity of the tyrosine enzyme. J. Biol. Chem. 236 (1961) 197-199.

4. Schweet, R.S. and Allen, E.H. Purification and properties of tyrosine-activating enzyme of hog pancreas. J. Biol. Chem. 233 (1958) 1104-1108.

5. Brick, P., Bhat, T.N. and Blow, D.M. Structure of tyrosyl-tRNA synthetase refined at 2.3 Å resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate. J. Mol. Biol. 208 (1989) 83-98. [PMID: 2504923]

[EC 6.1.1.1 created 1961, modified 2002]

EC 6.1.1.2

Accepted name: tryptophan—tRNA ligase

Reaction: ATP + L-tryptophan + tRNATrp = AMP + diphosphate + L-tryptophyl-tRNATrp

Other name(s): tryptophanyl-tRNA synthetase; L-tryptophan-tRNATrp ligase (AMP-forming); tryptophanyl-transfer ribonucleate synthetase; tryptophanyl-transfer ribonucleic acid synthetase; tryptophanyl-transfer RNA synthetase; tryptophanyl ribonucleic synthetase; tryptophanyl-transfer ribonucleic synthetase; tryptophanyl-tRNA synthase; tryptophan translase; TrpRS

Systematic name: L-tryptophan:tRNATrp ligase (AMP-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9023-44-3

References:

1. Davie, E.W., Koningsberger, V.V. and Lipmann, F. The isolation of a tryptophan-activating enzyme from pancreas. Arch. Biochem. Biophys. 65 (1956) 21-28.

2. Preddie, E.C. Tryptophanyl transfer ribonucleic acid synthetase from bovine pancreas. II. The chemically different subunits. J. Biol. Chem. 244 (1969) 3958-3968. [PMID: 5805407]

3. Wong, K.K., Meister, A. and Moldave, K. Enzymic formation of ribonucleic acid-amino acid from synthetic aminoacyladenylate and ribonucleic acid. Biochim. Biophys. Acta 36 (1959) 531-533.

[EC 6.1.1.2 created 1961, modified 2002]

EC 6.1.1.3

Accepted name: threonine—tRNA ligase

Reaction: ATP + L-threonine + tRNAThr = AMP + diphosphate + L-threonyl-tRNAThr

Other name(s): threonyl-tRNA synthetase; threonyl-transfer ribonucleate synthetase; threonyl-transfer RNA synthetase; threonyl-transfer ribonucleic acid synthetase; threonyl ribonucleic synthetase; threonine-transfer ribonucleate synthetase; threonine translase; threonyl-tRNA synthetase; TRS

Systematic name: L-threonine:tRNAThr ligase (AMP-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9023-46-5

References:

1. Allen, E.H., Glassman, E. and Schweet, R.S. Incorporation of amino acids into ribonucleic acid. I. The role of activating enzymes. J. Biol. Chem. 235 (1960) 1061-1067.

2. Holley, R.W., Brunngraber, E.F., Saad, F. and Williams, H.H. Partial purification of the threonine- and tyrosine-activating enzymes from rat liver, and the effect of potassium ions on the activity of the tyrosine enzyme. J. Biol. Chem. 236 (1961) 197-199.

[EC 6.1.1.3 created 1961]

EC 6.1.1.4

Accepted name: leucine—tRNA ligase

Reaction: ATP + L-leucine + tRNALeu = AMP + diphosphate + L-leucyl-tRNALeu

Other name(s): leucyl-tRNA synthetase; leucyl-transfer ribonucleate synthetase; leucyl-transfer RNA synthetase; leucyl-transfer ribonucleic acid synthetase; leucine-tRNA synthetase; leucine translase

Systematic name: L-leucine:tRNALeu ligase (AMP-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9031-15-6

References:

1. Allen, E.H., Glassman, E. and Schweet, R.S. Incorporation of amino acids into ribonucleic acid. I. The role of activating enzymes. J. Biol. Chem. 235 (1960) 1061-1067.

2. Berg, P., Bergmann, F.H., Ofengand, E.J. and Dieckmann, M. The enzymic synthesis of amino acyl derivatives of ribonucleic acid. I. The mechanism of leucyl-, valyl-, isoleucyl- and methionyl ribonucleic acid formation. J. Biol. Chem. 236 (1961) 1726-1734.

3. Bergmann, F.H., Berg, P. and Dieckmann, M. The enzymic synthesis of amino acyl derivatives of ribonucleic acid. II. The preparation of leucyl-, valyl-, isoleucyl- and methionyl ribonucleic acid synthetases from Escherichia coli. J. Biol. Chem. 236 (1961) 1735-1740.

[EC 6.1.1.4 created 1961]

EC 6.1.1.5

Accepted name: isoleucine—tRNA ligase

Reaction: ATP + L-isoleucine + tRNAIle = AMP + diphosphate + L-isoleucyl-tRNAIle

Other name(s): isoleucyl-tRNA synthetase; isoleucyl-transfer ribonucleate synthetase; isoleucyl-transfer RNA synthetase; isoleucine-transfer RNA ligase; isoleucine-tRNA synthetase; isoleucine translase

Systematic name: L-isoleucine:tRNAIle ligase (AMP-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9030-96-0

References:

1. Allen, E.H., Glassman, E. and Schweet, R.S. Incorporation of amino acids into ribonucleic acid. I. The role of activating enzymes. J. Biol. Chem. 235 (1960) 1061-1067.

2. Berg, P., Bergmann, F.H., Ofengand, E.J. and Dieckmann, M. The enzymic synthesis of amino acyl derivatives of ribonucleic acid. I. The mechanism of leucyl-, valyl-, isoleucyl- and methionyl ribonucleic acid formation. J. Biol. Chem. 236 (1961) 1726-1734.

3. Bergmann, F.H., Berg, P. and Dieckmann, M. The enzymic synthesis of amino acyl derivatives of ribonucleic acid. II. The preparation of leucyl-, valyl-, isoleucyl- and methionyl ribonucleic acid synthetases from Escherichia coli. J. Biol. Chem. 236 (1961) 1735-1740.

[EC 6.1.1.5 created 1961]

EC 6.1.1.6

Accepted name: lysine—tRNA ligase

Reaction: ATP + L-lysine + tRNALys = AMP + diphosphate + L-lysyl-tRNALys

Other name(s): lysyl-tRNA synthetase; lysyl-transfer ribonucleate synthetase; lysyl-transfer RNA synthetase; L-lysine-transfer RNA ligase; lysine-tRNA synthetase; lysine translase

Systematic name: L-lysine:tRNALys ligase (AMP-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9031-26-9

References:

1. Allen, E.H., Glassman, E. and Schweet, R.S. Incorporation of amino acids into ribonucleic acid. I. The role of activating enzymes. J. Biol. Chem. 235 (1960) 1061-1067.

2. Chiumecka, V., von Tigerstrom, M., D'Obrenan, P. and Smith, C.J. Purification and properties of lysyl transfer ribonucleic acid synthetase from bakers' yeast. J. Biol. Chem. 244 (1969) 5481-5488. [PMID: 4310598]

3. Lagerkvist, U., Rymo, L., Lindqvist, O. and Andersson, E. Some properties of crystals of lysine transfer ribonucleic acid ligase from yeast. J. Biol. Chem. 247 (1972) 3897-3899. [PMID: 4555953]

4. Stern, R. and Mehler, A.H. Lysyl-sRNA synthetase from Escherichia coli. Biochem. Z. 342 (1965) 400-409. [PMID: 4284804]

[EC 6.1.1.6 created 1961]

EC 6.1.1.7

Accepted name: alanine—tRNA ligase

Reaction: ATP + L-alanine + tRNAAla = AMP + diphosphate + L-alanyl-tRNAAla

Other name(s): alanyl-tRNA synthetase; alanyl-transfer ribonucleate synthetase; alanyl-transfer RNA synthetase; alanyl-transfer ribonucleic acid synthetase; alanine-transfer RNA ligase; alanine transfer RNA synthetase; alanine tRNA synthetase; alanine translase; alanyl-transfer ribonucleate synthase; AlaRS; Ala-tRNA synthetase

Systematic name: L-alanine:tRNAAla ligase (AMP-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9031-71-4

References:

1. Holley, R.W. and Goldstein, J. An alanine-dependent, ribonuclease-inhibited conversion of adenosine 5'-phosphate to adenosine triphosphate. J. Biol. Chem. 234 (1959) 1765-1768.

2. Webster, G.C. Isolation of an alanine-activating enzyme from pig liver. Biochim. Biophys. Acta 49 (1961) 141-152.

[EC 6.1.1.7 created 1961]

[EC 6.1.1.8 Deleted entry: D-alanine-sRNA synthetase (created 1961, deleted 1965)]

EC 6.1.1.9

Accepted name: valine—tRNA ligase

Reaction: ATP + L-valine + tRNAVal = AMP + diphosphate + L-valyl-tRNAVal

Other name(s): valyl-tRNA synthetase; valyl-transfer ribonucleate synthetase; valyl-transfer RNA synthetase; valyl-transfer ribonucleic acid synthetase; valine transfer ribonucleate ligase; valine translase

Systematic name: L-valine:tRNAVal ligase (AMP-forming)

Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9023-47-6

References:

1. Berg, P., Bergmann, F.H., Ofengand, E.J. and Dieckmann, M. The enzymic synthesis of amino acyl derivatives of ribonucleic acid. I. The mechanism of leucyl-, valyl-, isoleucyl- and methionyl ribonucleic acid formation. J. Biol. Chem. 236 (1961) 1726-1734.

2. Bergmann, F.H., Berg, P. and Dieckmann, M. The enzymic synthesis of amino acyl derivatives of ribonucleic acid. II. The preparation of leucyl-, valyl-, isoleucyl- and methionyl ribonucleic acid synthetases from Escherichia coli. J. Biol. Chem. 236 (1961) 1735-1740.

[EC 6.1.1.9 created 1961]

EC 6.1.1.10

Accepted name: methionine—tRNA ligase

Reaction: ATP + L-methionine + tRNAMet = AMP + diphosphate + L-methionyl-tRNAMet

Other name(s): methionyl-tRNA synthetase; methionyl-transfer ribonucleic acid synthetase; methionyl-transfer ribonucleate synthetase; methionyl-transfer RNA synthetase; methionine translase; MetRS

Systematic name: L-methionine:tRNAMet ligase (AMP-forming)

Comments: In those organisms producing N-formylmethionyl-tRNAfMet for translation initiation, this enzyme also recognizes the initiator tRNAfMet and catalyses the formation of L-methionyl-tRNAfMet, the substrate for EC 2.1.2.9, methionyl-tRNA formyltransferase.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9033-22-1

References:

1. Bergmann, F.H., Berg, P. and Dieckmann, M. The enzymic synthesis of amino acyl derivatives of ribonucleic acid. II. The preparation of leucyl-, valyl-, isoleucyl- and methionyl ribonucleic acid synthetases from Escherichia coli. J. Biol. Chem. 236 (1961) 1735-1740.

2. Lee, C.P., Dyson, M.R., Mandal, N., Varshney, U., Bahramian, B. and RajBhandary, U.L. Striking effects of coupling mutations in the acceptor stem on recognition of tRNAs by Escherichia coli Met-tRNA synthetase and Met-tRNA transformylase. 89 (1992) 9262-9266. [PMID: 1409632]

[EC 6.1.1.10 created 1961, modified 2002]

EC 6.1.1.11

Accepted name: serine—tRNA ligase

Reaction: ATP + L-serine + tRNASer = AMP + diphosphate + L-seryl-tRNASer

Other name(s): seryl-tRNA synthetase; SerRS; seryl-transfer ribonucleate synthetase; seryl-transfer RNA synthetase; seryl-transfer ribonucleic acid synthetase; serine translase

Systematic name: L-serine:tRNASer ligase (AMP-forming)

Comments: This enzyme also recognizes tRNASec, the special tRNA for selenocysteine, and catalyses the formation of L-seryl-tRNASec, the substrate for EC 2.9.1.1, L-seryl-tRNASec selenium transferase.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9023-48-7

References:

1. Katze, J.R. and Konigsberg, W. Purification and properties of seryl transfer ribonucleic acid synthetase from Escherichia coli. J. Biol. Chem. 245 (1970) 923-930. [PMID: 4906848]

2. Makman, M.H. and Cantoni, G.L. Isolation of seryl and phenylalanyl ribonucleic acid synthetases from baker's yeast. Biochemistry 4 (1965) 1434-1442.

3. Webster, L.T. and Davie, E.W. Purification and properties of serine-activating enzyme from beef pancreas. J. Biol. Chem. 236 (1961) 479-484.

4. Ohama, T., Yang, D.C. and Hatfield, D.L. Selenocysteine tRNA and serine tRNA are aminoacylated by the same synthetase, but may manifest different identities with respect to the long extra arm. Arch. Biochem. Biophys. 315 (1994) 293-301. [PMID: 7986071]

[EC 6.1.1.11 created 1961, modified 2002]

EC 6.1.1.12

Accepted name: aspartate—tRNA ligase

Reaction: ATP + L-aspartate + tRNAAsp = AMP + diphosphate + L-aspartyl-tRNAAsp

Other name(s): aspartyl-tRNA synthetase; aspartyl ribonucleic synthetase; aspartyl-transfer RNA synthetase; aspartic acid translase; aspartyl-transfer ribonucleic acid synthetase; aspartyl ribonucleate synthetase

Systematic name: L-aspartate:tRNAAsp ligase (AMP-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9027-32-1

References:

1. Gangloff, J. and Dirheimer, G. Studies on aspartyl-tRNA synthetase from baker's yeast. I. Purification and properties of the enzyme. Biochim. Biophys. Acta 294 (1973) 263-272.

2. Norton, S.J., Ravel, J.M., Lee, C. and Shive, W. Purification and properties of the aspartyl ribonucleic acid synthetase of Lactobacillus arabinosus. J. Biol. Chem. 238 (1963) 269-274.

[EC 6.1.1.12 created 1965]

EC 6.1.1.13

Accepted name: D-alanine—poly(phosphoribitol) ligase

Reaction: ATP + D-alanine + poly(ribitol phosphate) = AMP + diphosphate + O-D-alanyl-poly(ribitol phosphate)

Other name(s): D-alanyl-poly(phosphoribitol) synthetase; D-alanine: membrane acceptor ligase; D-alanine-D-alanyl carrier protein ligase; D-alanine-membrane acceptor ligase; D-alanine-activating enzyme

Systematic name: D-alanine:poly(phosphoribitol) ligase (AMP-forming)

Comments: A thioester bond is formed transiently between D-alanine and the sulfhydryl group of the 4'-phosphopantetheine prosthetic group of D-alanyl carrier protein during the activation of the alanine. Involved in the synthesis of teichoic acids.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9023-65-8

References:

1. Baddiley, J. and Neuhaus, F.C. The enzymic activation of D-alanine. Biochem. J. 75 (1960) 579.

2. Reusch, V.M. and Neuhaus, F.C. D-Alanine:membrane acceptor ligase from Lactobacillus casei. J. Biol. Chem. 246 (1971) 6136-6143. [PMID: 4399593]

3. Perego, M., Glaser, P., Minutello, A., Strauch, M.A., Leopold, K. and Fischer, W. Incorporation of D-alanine into lipoteichoic acid and wall teichoic acid in Bacillus subtilis. J. Biol. Chem. 270 (1995) 15598-15606. [PMID: 7797557]

4. Heaton, M.P. and Neuhaus, F.C. Role of D-alanyl carrier protein in the biosynthesis of D-alanyl-lipoteichoic acid. J. Bacteriol. 176 (1994) 681-690. [PMID: 8300523]

5. Debabov, D.V., Heaton, M.P., Zhang, Q., Stewart, K.D., Lambalot, R.H. and Neuhaus, F.C. The D-alanyl carrier protein in Lactobacillus casei: cloning, sequencing and expression of dltC. J. Bacteriol. 178 (1996) 3869-3876. [PMID: 8682792]

[EC 6.1.1.13 created 1965, modified 2001]

EC 6.1.1.14

Accepted name: glycine—tRNA ligase

Reaction: ATP + glycine + tRNAGly = AMP + diphosphate + glycyl-tRNAGly

Other name(s): glycyl-tRNA synthetase; glycyl-transfer ribonucleate synthetase; glycyl-transfer RNA synthetase; glycyl-transfer ribonucleic acid synthetase; glycyl translase

Systematic name: glycine:tRNAGly ligase (AMP-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9037-62-1

References:

1. Fraser, M.J. Glycyl-RNA synthetase of rat liver: partial purification and effects of some metal ions on its activity. Can. J. Biochem. Physiol. 41 (1963) 1123-1233.

2. Niyomporn, B., Dahl, J.L. and Strominger, J.L. Biosynthesis of the peptidoglycan of bacterial cell walls. IX. Purification and properties of glycyl transfer ribonucleic acid synthetase from Staphylococcus aureus. J. Biol. Chem. 243 (1968) 773-778. [PMID: 4295604]

[EC 6.1.1.14 created 1972]

EC 6.1.1.15

Accepted name: proline—tRNA ligase

Reaction: ATP + L-proline + tRNAPro = AMP + diphosphate + L-prolyl-tRNAPro

Other name(s): prolyl-tRNA synthetase; prolyl-transferRNA synthetase; prolyl-transfer ribonucleate synthetase; proline translase; prolyl-transfer ribonucleic acid synthetase; prolyl-s-RNA synthetase; prolinyl-tRNA ligase

Systematic name: L-proline:tRNAPro ligase (AMP-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9055-68-9

References:

1. Norton, S.J. Purification and properties of the prolyl RNA synthetase of Escherichia coli. Arch. Biochem. Biophys. 106 (1964) 147-152.

2. Peterson, P.J. and Fowden, L. Purification, properties and comparative specificities of the enzyme prolyl-transfer ribonucleic acid synthetase from Phaseolus aureus and Polygonatum multiflorum. Biochem. J. 97 (1965) 112-124.

[EC 6.1.1.15 created 1972]

EC 6.1.1.16

Accepted name: cysteine—tRNA ligase

Reaction: ATP + L-cysteine + tRNACys = AMP + diphosphate + L-cysteinyl-tRNACys

Other name(s): cysteinyl-tRNA synthetase; cysteinyl-transferRNA synthetase; cysteinyl-transfer ribonucleate synthetase; cysteine translase

Systematic name: L-cysteine:tRNACys ligase (AMP-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37318-56-2

References:

1. McCorquodale, D.J. The separation and partial purification of aminoacyl-RNA synthetases from Escherichia coli. Biochim. Biophys. Acta 91 (1964) 541-548.

[EC 6.1.1.16 created 1972]

EC 6.1.1.17

Accepted name: glutamate—tRNA ligase

Reaction: ATP + L-glutamate + tRNAGlu = AMP + diphosphate + L-glutamyl-tRNAGlu

Other name(s): glutamyl-tRNA synthetase; glutamyl-transfer ribonucleate synthetase; glutamyl-transfer RNA synthetase; glutamyl-transfer ribonucleic acid synthetase; glutamate-tRNA synthetase; glutamic acid translase

Systematic name: L-glutamate:tRNAGlu ligase (AMP-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9068-76-2

References:

1. Ravel, J.M., Wang, S., Heinemeyer, C. and Shive, W. Glutamyl and glutaminyl ribonucleic acid synthetases of Escherichia coli W. Separation, properties, and stimulation of adenosine triphosphate-pyrophosphate exchange by acceptor ribonucleic acid. J. Biol. Chem. 240 (1965) 432-438.

[EC 6.1.1.17 created 1972]

EC 6.1.1.18

Accepted name: glutamine—tRNA ligase

Reaction: ATP + L-glutamine + tRNAGln = AMP + diphosphate + L-glutaminyl-tRNAGln

Other name(s): glutaminyl-tRNA synthetase; glutaminyl-transfer RNA synthetase; glutaminyl-transfer ribonucleate synthetase; glutamine-tRNA synthetase; glutamine translase; glutamate-tRNA ligase; glutaminyl ribonucleic acid; GlnRS

Systematic name: L-glutamine:tRNAGln ligase (AMP-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9075-59-6

References:

1. Ravel, J.M., Wang, S., Heinemeyer, C. and Shive, W. Glutamyl and glutaminyl ribonucleic acid synthetases of Escherichia coli W. Separation, properties, and stimulation of adenosine triphosphate-pyrophosphate exchange by acceptor ribonucleic acid. J. Biol. Chem. 240 (1965) 432-438.

[EC 6.1.1.18 created 1972]

EC 6.1.1.19

Accepted name: arginine—tRNA ligase

Reaction: ATP + L-arginine + tRNAArg = AMP + diphosphate + L-arginyl-tRNAArg

Other name(s): arginyl-tRNA synthetase; arginyl-transfer ribonucleate synthetase; arginyl-transfer RNA synthetase; arginyl transfer ribonucleic acid synthetase; arginine-tRNA synthetase; arginine translase

Systematic name: L-arginine:tRNAArg ligase (AMP-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37205-35-9

References:

1. Allende, C.C. and Allende, J.E. Purification and substrate specificity of arginyl-ribonucleic acid synthetase from rat liver. J. Biol. Chem. 239 (1964) 1102-1106.

2. Mehler, A.H. and Mitra, S.K. The activation of arginyl transfer ribonucleic acid synthetase by transfer ribonucleic acid. J. Biol. Chem. 242 (1967) 5495-5499.

3. Mitra, S.K. and Mehler, A.H. The arginyl transfer ribonucleic acid synthetase of Escherichia coli. J. Biol. Chem. 242 (1967) 5491-5494.

[EC 6.1.1.19 created 1972]

EC 6.1.1.20

Accepted name: phenylalanine—tRNA ligase

Reaction: ATP + L-phenylalanine + tRNAPhe = AMP + diphosphate + L-phenylalanyl-tRNAPhe

Other name(s): phenylalanyl-tRNA synthetase; phenylalanyl-transfer ribonucleate synthetase; phenylalanine-tRNA synthetase; phenylalanyl-transfer RNA synthetase; phenylalanyl-tRNA ligase; phenylalanyl-transfer RNA ligase; L-phenylalanyl-tRNA synthetase; phenylalanine translase

Systematic name: L-phenylalanine:tRNAPhe ligase (AMP-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9055-66-7

References:

1. Stulberg, M.P. The isolation and properties of phenylalanyl ribonucleic acid synthetase from Escherichia coli B. J. Biol. Chem. 242 (1967) 1060-1064. [PMID: 5335910]

[EC 6.1.1.20 created 1972]

EC 6.1.1.21

Accepted name: histidine—tRNA ligase

Reaction: ATP + L-histidine + tRNAHis = AMP + diphosphate + L-histidyl-tRNAHis

Other name(s): histidyl-tRNA synthetase; histidyl-transfer ribonucleate synthetase; histidine translase

Systematic name: L-histidine:tRNAHis ligase (AMP-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9068-78-4

References:

1. Tigerstrom, M.V. and Tener, G.M. Histidyl transfer ribonucleic acid synthetase from bakers' yeast. Can. J. Biochem. 45 (1967) 1067-1074. [PMID: 6035970]

[EC 6.1.1.21 created 1972]

EC 6.1.1.22

Accepted name: asparagine—tRNA ligase

Reaction: ATP + L-asparagine + tRNAAsn = AMP + diphosphate + L-asparaginyl-tRNAAsn

Other name(s): asparaginyl-tRNA synthetase; asparaginyl-transfer ribonucleate synthetase; asparaginyl transfer RNA synthetase; asparaginyl transfer ribonucleic acid synthetase; asparagyl-transfer RNA synthetase; asparagine translase

Systematic name: L-asparagine:tRNAAsn ligase (AMP-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37211-76-0

References:

1. Davies, M.R. and Marshall, R.D. Partial purification of L-asparginyl-tRNA synthetase from rabbit liver. Biochem. Biophys. Res. Commun. 47 (1972) 1386-1395.

[EC 6.1.1.22 created 1976]

EC 6.1.1.23

Accepted name: aspartate—tRNAAsn ligase

Reaction: ATP + L-aspartate + tRNAAsx = AMP + diphosphate + L-aspartyl-tRNAAsx

Other name(s): nondiscriminating aspartyl-tRNA synthetase

Systematic name: L-aspartate:tRNAAsx ligase (AMP-forming)

Comments: When this enzyme acts on tRNAAsp, it catalyses the same reaction as EC 6.1.1.12, aspartate—tRNA ligase. It has, however, diminished discrimination, so that it can also form aspartyl-tRNAAsn. This relaxation of specificity has been found to result from the absence of a loop in the tRNA that specifically recognizes the third position of the anticodon [1]. This accounts for the ability of this enzyme in, for example, Thermus thermophilus, to recognize both tRNAAsp (GUC anticodon) and tRNAAsn (GUU anticodon). The aspartyl-tRNAAsn is not used in protein synthesis until it is converted by EC 6.3.5.6, asparaginyl-tRNA synthase (glutamine-hydrolysing), into asparaginyl-tRNAAsn.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9027-32-1

References:

1. Ibba, M. and Söll, D. Aminoacyl-tRNA synthesis. Annu. Rev. Biochem. 69 (2000) 617-650. [PMID: 10966471]

2. Schmitt, E., Moulinier, L., Fujiwara, S., Imanaka, T., Thierry, J.C. and Moras, D. Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation. EMBO J. 17 (1998) 5227-5237. [PMID: 9724658]

3. Becker, H.D. and Kern, D. Thermus thermophilus: a link in evolution of the tRNA-dependent amino acid amidation pathways. Proc. Natl. Acad. Sci. USA 95 (1998) 12832-12837. [PMID: 9789000]

[EC 6.1.1.23 created 2002]

EC 6.1.1.24

Accepted name: glutamate—tRNAGln ligase

Reaction: ATP + L-glutamate + tRNAGlx = AMP + diphosphate + L-glutamyl-tRNAGlx

Other name(s): nondiscriminating glutamyl-tRNA synthetase

Systematic name: L-glutamate:tRNAGlx ligase (AMP-forming)

Comments: When this enzyme acts on tRNAGlu, it catalyses the same reaction as EC 6.1.1.17, glutamate—tRNA ligase. It has, however, diminished discrimination, so that it can also form glutamyl-tRNAGln. This relaxation of specificity has been found to result from the absence of a loop in the tRNA that specifically recognizes the third position of the anticodon [1]. This accounts for the ability of this enzyme in, for example, Bacillus subtilis, to recognize both tRNA1Gln (UUG anticodon) and tRNAGlu (UUC anticodon) but not tRNA2Gln (CUG anticodon). The ability of this enzyme to recognize both tRNAGlu and one of the tRNAGln isoacceptors derives from their sharing a major identity element, a hypermodified derivative of U34 (5-methylaminomethyl-2-thiouridine). The glutamyl-tRNAGln is not used in protein synthesis until it is converted by EC 6.3.5.7, glutaminyl-tRNA synthase (glutamine-hydrolysing), into glutaminyl-tRNAGln.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9068-76-2

References:

1. Ibba, M. and Söll, D. Aminoacyl-tRNA synthesis. Annu. Rev. Biochem. 69 (2000) 617-650. [PMID: 10966471]

2. Schmitt, E., Moulinier, L., Fujiwara, S., Imanaka, T., Thierry, J.C. and Moras, D. Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation. EMBO J. 17 (1998) 5227-5237. [PMID:9724658]

3. Kim, S.I. and Söll, D. Major identity element of glutamine tRNAs from Bacillus subtilis and Escherichia coli in the reaction with B. subtilis glutamyl-tRNA synthetase. Mol. Cells 8 (1998) 459-465. [PMID: 9749534]

[EC 6.1.1.24 created 2002]

[EC 6.1.1.25 Deleted entry: lysine—tRNAPyl ligase. The tRNAPyl is now known only to be charged with pyrrolysine (cf. EC 6.1.1.26). (EC 6.1.1.25 created 2002, deleted 2012)]

EC 6.1.1.26

Accepted name: pyrrolysine—tRNAPyl ligase

Reaction: ATP + L-pyrrolysine + tRNAPyl = AMP + diphosphate + L-pyrrolysyl-tRNAPyl

Glossary: pyrrolysine = N6-[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-ylcarbonyl]-L-lysine

Other name(s): PylS; pyrrolysyl-tRNA synthetase

Systematic name: L-pyrrolysine:tRNAPyl ligase (AMP-forming)

Comments: In organisms such as Methanosarcina barkeri that incorporate the modified amino acid pyrrolysine (Pyl) into certain methylamine methyltransferases, an unusual tRNAPyl, with a CUA anticodon, can be charged directly with pyrrolysine by this class II aminoacyl—tRNA ligase. The enzyme is specific for pyrrolysine as substrate as it cannot be replaced by lysine or any of the other natural amino acids [1].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Blight, S.K., Larue, R.C., Mahapatra, A., Longstaff, D.G., Chang, E., Zhao, G., Kang, P.T., Green-Church, K.B., Chan, M.K. and Krzycki, J.A. Direct charging of tRNA(CUA) with pyrrolysine in vitro and in vivo. Nature 431 (2004) 333-335. [PMID: 15329732]

2. Polycarpo, C., Ambrogelly, A., Bérubé, A., Winbush, S.M., McCloskey, J.A., Crain, P.F., Wood, J.L. and Söll, D. An aminoacyl-tRNA synthetase that specifically activates pyrrolysine. Proc. Natl. Acad. Sci. USA 101 (2004) 12450-12454. [PMID: 15314242]

3. Schimmel, P. and Beebe, K. Molecular biology: genetic code seizes pyrrolysine. Nature 431 (2004) 257-258. [PMID: 15372017]

[EC 6.1.1.26 created 2007]

EC 6.1.1.27

Accepted name: O-phospho-L-serine—tRNA ligase

Reaction: ATP + O-phospho-L-serine + tRNACys = AMP + diphosphate + O-phospho-L-seryl-tRNACys

Other name(s): non-canonical O-phosphoseryl-tRNA synthetase; SepRS; O-phosphoseryl-tRNA ligase

Systematic name: O-phospho-L-serine:tRNACys ligase (AMP-forming)

Comments: In organisms like Archaeoglobus fulgidus lacking EC 6.1.1.16 (cysteine—tRNA ligase) for the direct Cys-tRNACys formation, Cys-tRNACys is produced by an indirect pathway, in which EC 6.1.1.27 ligates O-phosphoserine to tRNACys, and EC 2.5.1.73 (O-phospho-L-seryl-tRNA: Cys-tRNA synthase) converts the produced O-phospho-L-seryl-tRNACys to Cys-tRNACys. The SepRS/SepCysS pathway is the sole route for cysteine biosynthesis in the organism [1]. Methanosarcina mazei can use both pathways, the direct route using EC 6.1.1.16 (cysteine—tRNA ligase) and the indirect pathway with EC 6.1.1.27 and EC 2.5.1.73 (O-phospho-L-seryl-tRNA: Cys-tRNA synthase) [2].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Fukunaga, R. and Yokoyama, S. Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea. Nat. Struct. Mol. Biol. 14 (2007) 272-279. [PMID: 17351629]

2. Hauenstein, S.I. and Perona, J.J. Redundant synthesis of cysteinyl-tRNACys in Methanosarcina mazei. J. Biol. Chem. 283 (2008) 22007-22017. [PMID: 18559341]

[EC 6.1.1.27 created 2009]

[EC 6.1.1.28 Deleted entry: proline/cysteine�tRNA ligase. Later published work having demonstrated that this was not a genuine enzyme, EC 6.1.1.28 was withdrawn at the public-review stage before being made official. (EC 6.1.1.28 created 2014, deleted 2014)]


EC 6.1.2 Acid—Alcohol Ligases (ester synthases)

Contents

EC 6.1.2.1 D-alanine—(R)-lactate ligase
EC 6.1.2.2 nebramycin 5' synthase


EC 6.1.2.1

Accepted name: D-alanine—(R)-lactate ligase

Reaction: D-alanine + (R)-lactate + ATP = D-alanyl-(R)-lactate + ADP + phosphate

Glossary: (R)-lactate = D-lactate
D-alanyl-(R)-lactate = D-alanyl-D-lactate = (2R)-2-(D-alanyloxy)propanoic acid = (R)-2-[(R)-2-aminopropanoyloxy]propanoic acid

Other name(s): VanA; VanB; VanD

Systematic name: D-alanine:(R)-lactate ligase (ADP-forming)

Comments: The product of this enzyme, the depsipeptide D-alanyl-(R)-lactate, 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.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Bugg, T.D., Wright, G.D., Dutka-Malen, S., Arthur, M., Courvalin, P. and Walsh, C.T. Molecular basis for vancomycin resistance in Enterococcus faecium BM4147: biosynthesis of a depsipeptide peptidoglycan precursor by vancomycin resistance proteins VanH and VanA. Biochemistry 30 (1991) 10408-10415. [PMID: 1931965]

2. Meziane-Cherif, D., Badet-Denisot, M.A., Evers, S., Courvalin, P. and Badet, B. Purification and characterization of the VanB ligase associated with type B vancomycin resistance in Enterococcus faecalis V583. FEBS Lett. 354 (1994) 140-142. [PMID: 7957913]

3. Perichon, B., Reynolds, P. and Courvalin, P. VanD-type glycopeptide-resistant Enterococcus faecium BM4339. Antimicrob. Agents Chemother. 41 (1997) 2016-2018. [PMID: 9303405]

[EC 6.1.2.1 created 2010]

EC 6.1.2.2

Accepted name: nebramycin 5' synthase

Reaction: (1) tobramycin + carbamoyl phosphate + ATP + H2O = nebramycin 5' + AMP + diphosphate + phosphate (overall reaction)
(1a) carbamoyl phosphate + ATP + H2O = diphosphate + O-carbamoyladenylate + phosphate
(1b) O-carbamoyladenylate + tobramycin = AMP + nebramycin 5'
(2) kanamycin A + carbamoyl phosphate + ATP + H2O = 6''-O-carbamoylkanamycin A + AMP + diphosphate + phosphate (overall reaction)
(2a) carbamoyl phosphate + ATP + H2O = diphosphate + O-carbamoyladenylate + phosphate
(2b) O-carbamoyladenylate + kanamycin A = AMP + 6''-O-carbamoylkanamycin A

For diagram of reaction click here.

Glossary: tobramycin = (1S,2S,3R,4S,6R)-4,6-diamino-3-(2,6-diamino-2,3,6-trideoxy-α-D-ribo-hexopyranosyloxy)-2-hydroxycyclohexyl 3-amino-3-deoxy-α-D-glucopyranoside
nebramycin 5' = (1S,2S,3R,4S,6R)-4,6-diamino-3-[(2,6-diamino-2,3,6-trideoxy-α-D-ribo-hexopyranosyl)oxy]-2-hydroxycyclohexyl 3-amino-6-O-carbamoyl-3-deoxy-α-D-glucopyranoside
kanamycin A = (1S,2R,3R,4S,6R)-4,6-diamino-3-(6-amino-6-deoxy--D-glucopyranosyloxy)-2-hydroxycyclohexyl 3-amino-3-deoxy--D-glucopyranoside
6''-O-carbamoylkanamycin A = (1S,2R,3R,4S,6R)-4,6-diamino-3-[(6-amino-6-deoxy-α-D-glucopyranosyl)oxy]-2-hydroxycyclohexyl 3-amino-6-O-carbamoyl-3-deoxy-α-D-glucopyranoside

Other name(s): tobramycin carbamoyltransferase; TobZ

Systematic name: tobramycin:carbamoyl phosphate ligase (AMP,phosphate-forming)

Comments: Requires Fe(III). The enzyme from the bacterium Streptoalloteichus tenebrarius catalyses the activation of carbamoyl phosphate to O-carbamoyladenylate and the subsequent carbamoylation of kanamycin and tobramycin.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Parthier, C., Gorlich, S., Jaenecke, F., Breithaupt, C., Brauer, U., Fandrich, U., Clausnitzer, D., Wehmeier, U.F., Bottcher, C., Scheel, D. and Stubbs, M.T. The O-carbamoyltransferase TobZ catalyzes an ancient enzymatic reaction. Angew. Chem. Int. Ed. Engl. 51 (2012) 4046-4052. [PMID: 22383337]

[EC 6.1.2.2 created 2014]


Continued with EC 6.2.1.1 to EC 6.2.1.32
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