EC 6.1

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

Contents

Entries

Accepted name: tyrosine—tRNA ligase

Reaction: ATP + L-tyrosine + tRNA^Tyr = AMP + diphosphate + L-tyrosyl-tRNA^Tyr

Other name(s): tyrosyl-tRNA synthetase; L-tyrosine-tRNA^Tyr 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:tRNA^Tyr 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 6.1.1.2

Accepted name: tryptophan—tRNA ligase

Reaction: ATP + L-tryptophan + tRNA^Trp = AMP + diphosphate + L-tryptophyl-tRNA^Trp

Other name(s): tryptophanyl-tRNA synthetase; L-tryptophan-tRNA^Trp 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:tRNA^Trp 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 6.1.1.3

Accepted name: threonine—tRNA ligase

Reaction: ATP + L-threonine + tRNA^Thr = AMP + diphosphate + L-threonyl-tRNA^Thr

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:tRNA^Thr 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 6.1.1.4

Accepted name: leucine—tRNA ligase

Reaction: ATP + L-leucine + tRNA^Leu = AMP + diphosphate + L-leucyl-tRNA^Leu

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:tRNA^Leu 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 6.1.1.5

Accepted name: isoleucine—tRNA ligase

Reaction: ATP + L-isoleucine + tRNA^Ile = AMP + diphosphate + L-isoleucyl-tRNA^Ile

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:tRNA^Ile 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 6.1.1.6

Accepted name: lysine—tRNA ligase

Reaction: ATP + L-lysine + tRNA^Lys = AMP + diphosphate + L-lysyl-tRNA^Lys

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:tRNA^Lys 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 6.1.1.7

Accepted name: alanine—tRNA ligase

Reaction: ATP + L-alanine + tRNA^Ala = AMP + diphosphate + L-alanyl-tRNA^Ala

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:tRNA^Ala 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 6.1.1.8 Deleted entry: D-alanine-sRNA synthetase (created 1961, deleted 1965)]

EC 6.1.1.9

Accepted name: valine—tRNA ligase

Reaction: ATP + L-valine + tRNA^Val = AMP + diphosphate + L-valyl-tRNA^Val

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:tRNA^Val 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 6.1.1.10

Accepted name: methionine—tRNA ligase

Reaction: ATP + L-methionine + tRNA^Met = AMP + diphosphate + L-methionyl-tRNA^Met

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:tRNA^Met ligase (AMP-forming)

Comments: In those organisms producing N-formylmethionyl-tRNA^fMet for translation initiation, this enzyme also recognizes the initiator tRNA^fMet and catalyses the formation of L-methionyl-tRNA^fMet, 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 6.1.1.11

Accepted name: serine—tRNA ligase

Reaction: ATP + L-serine + tRNA^Ser = AMP + diphosphate + L-seryl-tRNA^Ser

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:tRNA^Ser ligase (AMP-forming)

Comments: This enzyme also recognizes tRNA^Sec, the special tRNA for selenocysteine, and catalyses the formation of L-seryl-tRNA^Sec, the substrate for EC 2.9.1.1, L-seryl-tRNA^Sec 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 6.1.1.12

Accepted name: aspartate—tRNA ligase

Reaction: ATP + L-aspartate + tRNA^Asp = AMP + diphosphate + L-aspartyl-tRNA^Asp

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:tRNA^Asp 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 6.1.1.13

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 6.1.1.14

Accepted name: glycine—tRNA ligase

Reaction: ATP + glycine + tRNA^Gly = AMP + diphosphate + glycyl-tRNA^Gly

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

Systematic name: glycine:tRNA^Gly 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 6.1.1.15

Accepted name: proline—tRNA ligase

Reaction: ATP + L-proline + tRNA^Pro = AMP + diphosphate + L-prolyl-tRNA^Pro

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:tRNA^Pro 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 6.1.1.16

Accepted name: cysteine—tRNA ligase

Reaction: ATP + L-cysteine + tRNA^Cys = AMP + diphosphate + L-cysteinyl-tRNA^Cys

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

Systematic name: L-cysteine:tRNA^Cys 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 6.1.1.17

Accepted name: glutamate—tRNA ligase

Reaction: ATP + L-glutamate + tRNA^Glu = AMP + diphosphate + L-glutamyl-tRNA^Glu

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:tRNA^Glu 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 6.1.1.18

Accepted name: glutamine—tRNA ligase

Reaction: ATP + L-glutamine + tRNA^Gln = AMP + diphosphate + L-glutaminyl-tRNA^Gln

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:tRNA^Gln 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 6.1.1.19

Accepted name: arginine—tRNA ligase

Reaction: ATP + L-arginine + tRNA^Arg = AMP + diphosphate + L-arginyl-tRNA^Arg

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:tRNA^Arg 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 6.1.1.20

Accepted name: phenylalanine—tRNA ligase

Reaction: ATP + L-phenylalanine + tRNA^Phe = AMP + diphosphate + L-phenylalanyl-tRNA^Phe

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:tRNA^Phe 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 6.1.1.21

Accepted name: histidine—tRNA ligase

Reaction: ATP + L-histidine + tRNA^His = AMP + diphosphate + L-histidyl-tRNA^His

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

Systematic name: L-histidine:tRNA^His 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 6.1.1.22

Accepted name: asparagine—tRNA ligase

Reaction: ATP + L-asparagine + tRNA^Asn = AMP + diphosphate + L-asparaginyl-tRNA^Asn

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:tRNA^Asn 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 6.1.1.23

Accepted name: aspartate—tRNA^Asn ligase

Reaction: ATP + L-aspartate + tRNA^Asx = AMP + diphosphate + L-aspartyl-tRNA^Asx

Other name(s): nondiscriminating aspartyl-tRNA synthetase

Systematic name: L-aspartate:tRNA^Asx ligase (AMP-forming)

Comments: When this enzyme acts on tRNA^Asp, 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-tRNA^Asn. 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 tRNA^Asp (GUC anticodon) and tRNA^Asn (GUU anticodon). The aspartyl-tRNA^Asn is not used in protein synthesis until it is converted by EC 6.3.5.6, asparaginyl-tRNA synthase (glutamine-hydrolysing), into asparaginyl-tRNA^Asn.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, 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 6.1.1.24

Accepted name: glutamate—tRNA^Gln ligase

Reaction: ATP + L-glutamate + tRNA^Glx = AMP + diphosphate + L-glutamyl-tRNA^Glx

Other name(s): nondiscriminating glutamyl-tRNA synthetase

Systematic name: L-glutamate:tRNA^Glx ligase (AMP-forming)

Comments: When this enzyme acts on tRNA^Glu, 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-tRNA^Gln. 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 tRNA₁^Gln (UUG anticodon) and tRNA^Glu (UUC anticodon) but not tRNA₂^Gln (CUG anticodon). The ability of this enzyme to recognize both tRNA^Glu and one of the tRNA^Gln isoacceptors derives from their sharing a major identity element, a hypermodified derivative of U³⁴ (5-methylaminomethyl-2-thiouridine). The glutamyl-tRNA^Gln is not used in protein synthesis until it is converted by EC 6.3.5.7, glutaminyl-tRNA synthase (glutamine-hydrolysing), into glutaminyl-tRNA^Gln.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, 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 6.1.1.25 Deleted entry: lysine—tRNA^Pyl ligase. The tRNA^Pyl 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—tRNA^Pyl ligase

Reaction: ATP + L-pyrrolysine + tRNA^Pyl = AMP + diphosphate + L-pyrrolysyl-tRNA^Pyl

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:tRNA^Pyl ligase (AMP-forming)

Comments: In organisms such as Methanosarcina barkeri that incorporate the modified amino acid pyrrolysine (Pyl) into certain methylamine methyltransferases, an unusual tRNA^Pyl, 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 6.1.1.27

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

Reaction: ATP + O-phospho-L-serine + tRNA^Cys = AMP + diphosphate + O-phospho-L-seryl-tRNA^Cys

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

Systematic name: O-phospho-L-serine:tRNA^Cys ligase (AMP-forming)

Comments: In organisms like Archaeoglobus fulgidus lacking EC 6.1.1.16 (cysteine—tRNA ligase) for the direct Cys-tRNA^Cys formation, Cys-tRNA^Cys is produced by an indirect pathway, in which EC 6.1.1.27 ligates O-phosphoserine to tRNA^Cys, and EC 2.5.1.73 (O-phospho-L-seryl-tRNA: Cys-tRNA synthase) converts the produced O-phospho-L-seryl-tRNA^Cys to Cys-tRNA^Cys. 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-tRNA^Cys in Methanosarcina mazei. J. Biol. Chem. 283 (2008) 22007-22017. [PMID: 18559341]

[EC 6.1.1.28 Deleted entry: proline/cysteineÑtRNA 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)]

Contents

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

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 6.1.2.2

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 6.1.3 Cyclo-ligases

EC 6.1.3.1

Accepted name: olefin β-lactone synthetase

Reaction: ATP + a (2R,3S)-2-alkyl-3-hydroxyalkanoate = AMP + diphosphate + a cis-3-alkyl-4-alkyloxetan-2-one

Other name(s): oleC (gene name)

Systematic name: (2R,3S)-2-alkyl-3-hydroxyalkanoate ligase (β-lactone,AMP-forming)

Comments: The enzyme, found in certain bacterial species, participates in a pathway for the production of olefins. It forms a β-lactone. The alkyl group at C² of the substrate ends up as the 3-alkyl group of the product.

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

References:

1. Sukovich, D.J., Seffernick, J.L., Richman, J.E., Hunt, K.A., Gralnick, J.A. and Wackett, L.P. Structure, function, and insights into the biosynthesis of a head-to-head hydrocarbon in Shewanella oneidensis strain MR-1. Appl. Environ. Microbiol. 76 (2010) 3842-3849. [PMID: 20418444]

2. Frias, J.A., Goblirsch, B.R., Wackett, L.P. and Wilmot, C.M. Cloning, purification, crystallization and preliminary X-ray diffraction of the OleC protein from Stenotrophomonas maltophilia involved in head-to-head hydrocarbon biosynthesis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 66 (2010) 1108-1110. [PMID: 20823539]

3. Kancharla, P., Bonnett, S.A. and Reynolds, K.A. Stenotrophomonas maltophilia OleC-catalyzed ATP-dependent formation of long-chain Z-olefins from 2-alkyl-3-hydroxyalkanoic acids. Chembiochem 17 (2016) 1426-1429. [PMID: 27238740]

4. Christenson, J.K., Richman, J.E., Jensen, M.R., Neufeld, J.Y., Wilmot, C.M. and Wackett, L.P. β-Lactone synthetase found in the olefin biosynthesis pathway. Biochemistry 56 (2017) 348-351. [PMID: 28029240]