Continued from EC 6.3.3 to EC 6.3.5
EC 6.4 Forming Carbon—Carbon Bonds
EC 6.5 Forming Phosphoric Ester Bonds
EC 6.6 Forming Nitrogen—Metal Bonds
Accepted name: pyruvate carboxylase
Reaction: ATP + pyruvate + HCO3- = ADP + phosphate + oxaloacetate
Other name(s): pyruvic carboxylase
Systematic name: pyruvate:carbon-dioxide ligase (ADP-forming)
Comments: A biotinyl-protein containing manganese (animal tissues) or zinc (yeast). The animal enzyme requires acetyl-CoA.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9014-19-1
References:
1. McClure, W.R., Lardy, H.A. and Kneifel, H.P. Rat liver pyruvate carboxylase. I. Preparation, properties, and cation specificity. J. Biol. Chem. 246 (1971) 3569-3578. [PMID: 5578910]
2. Scrutton, M.C., Young, M.R. and Utter, M.F. Pyruvate carboxylase from baker's yeast. The presence of bound zinc. J. Biol. Chem. 245 (1970) 6220-6227. [PMID: 5484476]
3. Seubert, W. and Remberger, U. Renigung und Wirkungsweise der Pyruvatcarboxylase aus Pseudomonas citronellolis. Biochem. Z. 334 (1961) 401-414.
4. Utter, M.F. and Keech, D.B. Pyruvate carboxylase. I. Nature of the reaction. J. Biol. Chem. 238 (1963) 2603-2608.
Accepted name: acetyl-CoA carboxylase
Reaction: ATP + acetyl-CoA + HCO3- = ADP + phosphate + malonyl-CoA
Other name(s): acetyl coenzyme A carboxylase
Systematic name: acetyl-CoA:carbon-dioxide ligase (ADP-forming)
Comments: A biotinyl-protein. Also catalyses transcarboxylation; the plant enzyme also carboxylates propanonyl-CoA and butanoyl-CoA.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9023-93-2
References:
1. Hatch, M.D. and Stumpf, P.K. Fat metabolism in higher plants. XVI. Acetyl coenzyme A carboxylase and acyl coenzyme A-malonyl coenzyme A transcarboxylase from wheat germ. J. Biol. Chem. 236 (1961) 2879-2885.
2. Matsuhashi, M., Matsuhashi, S. and Lynen, F. Zur Biosynthese der Fettsäuren. V. Die Acetyl-CoA Carboxylase aus Rattenleber und ihre Aktivierung durch Citronsäure. Biochem. Z. 340 (1964) 263-289.
3. Matsuhashi, M., Matsuhashi, S., Numa, S. and Lynen, F. [On the biosynthesis of fatty acids. IV. Acetyl-CoA carboxylase from yeast.] Biochem. Z. 340 (1964) 243-262.
4. Vagelos, P. Regulation of fatty acid biosynthesis. Curr. Top. Cell. Regul. 4 (1971) 119-166.
5. Wakil, S.J. A malonic acid derivative as an intermediate in fatty acid synthesis. J. Am. Chem. Soc. 80 (1958) 6465 only.
Accepted name: propionyl-CoA carboxylase
Reaction: ATP + propanoyl-CoA + HCO3- = ADP + phosphate + (S)-methylmalonyl-CoA
Systematic name: propanoyl-CoA:carbon-dioxide ligase (ADP-forming)
Other name(s): propionyl coenzyme A carboxylase
Comments: A biotinyl-protein. Also carboxylates butanoyl-CoA and catalyses transcarboxylation.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9023-94-3
References:
1. Kaziro, Y., Ochoa, S., Warner, R.C. and Chen, J.-Y. Metabolism of propionic acid in animal tissues. VIII. Crystalline propionyl carboxylase. J. Biol. Chem. 236 (1961) 1917-1923.
2. Lane, M.D., Halenz, D.R., Kosow, D.P. and Hegre, C.S. Further studies on mitochondrial propionyl carboxylase. J. Biol. Chem. 235 (1960) 3082-3086.
3. Meyer, H., Nevaldine, B. and Meyer, F. Acyl-coenzyme A carboxylase of the free-living nematode Turbatrix aceti. 1. Its isolation and molecular characteristics. Biochemistry 17 (1978) 1822-1827. [PMID: 656363]
4. Moss, J. and Lane, M.D. The biotin-dependent enzymes. Adv. Enzymol. Relat. Areas Mol. Biol. 35 (1971) 321-442. [PMID: 4150153]
5. Vagelos, P. Regulation of fatty acid biosynthesis. Curr. Top. Cell. Regul. 4 (1971) 119-166.
Accepted name: methylcrotonoyl-CoA carboxylase
Reaction: ATP + 3-methylcrotonoyl-CoA + HCO3- = ADP + phosphate + 3-methylglutaconyl-CoA
Other name(s): methylcrotonyl coenzyme A carboxylase; β-methylcrotonyl coenzyme A carboxylase; β-methylcrotonyl CoA carboxylase; methylcrotonyl-CoA carboxylase
Systematic name: 3-methylcrotonoyl-CoA:carbon-dioxide ligase (ADP-forming)
Comments: A biotinyl-protein.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9023-95-4
References:
1. Knappe, J., Schlegel, H.-G. and Lynen, F. Zur biochemischen Funktion des Biotins. I. Die Beteilligung der β-Methyl-crotonyl-Carboxylase an der Bildung von β-Hydroxy-β-methyl-glutaryl-CoA from β-Hydroxy-isovaleryl-CoA. Biochem. Z. 335 (1961) 101-122.
2. Lynen, F., Knappe, J., Lorch, E., Jütting, G., Ringelmann, E. and Lachance, J.-P. Zur biochemischen Funktion des Biotins. II. Reinigung und Wirkungsweise der β-Methyl-crotonyl-Carboxlase. Biochem. Z. 335 (1961) 123-166.
3. Rilling, H.C. and Coon, M.J. The enzymatic isomerization of α-methylvinylacetyl coenzyme A and the specificity of a bacterial α-methylcrotonyl coenzyme A carboxylase. J. Biol. Chem. 235 (1960) 3087-3092.
4. Vagelos, P. Regulation of fatty acid biosynthesis. Curr. Top. Cell. Regul. 4 (1971) 119-166.
Accepted name: geranoyl-CoA carboxylase
Reaction: ATP + geranoyl-CoA + HCO3- = ADP + phosphate + 3-(4-methylpent-3-en-1-yl)pent-2-enedioyl-CoA
Other name(s): geranoyl coenzyme A carboxylase; geranyl-CoA carboxylase
Systematic name: geranoyl-CoA:carbon-dioxide ligase (ADP-forming)
Comments: A biotinyl-protein. Also carboxylates dimethylpropenoyl-CoA and farnesoyl-CoA.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, UM-BBD, CAS registry number: 37324-35-9
References:
1. Seubert, W., Fass, E. and Remberger, U. Untersuchungen über den bakteriellen Abbau von Isoprenoiden. III. Reinigung und Eigenschaften der Geranylcarboxylase. Biochem. Z. 338 (1963) 265-275.
Accepted name: acetone carboxylase
Reaction: acetone + CO2 + ATP + 2 H2O = acetoacetate + AMP + 2 phosphate
Systematic name: acetone:carbon-dioxide ligase (AMP-forming)
Comments: Requires Mg2+ and ATP. The enzyme from Xanthobacter sp. strain Py2 also carboxylates butan-2-one to 3-oxopentanoate.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 189258-15-9
References:
1. Sluis, M.K. and Ensign, S.A. Purification and characterization of acetone carboxylase from Xanthobacter strain Py2. Proc. Natl. Acad. Sci. USA 94 (1997) 8456-8461. [PMID: 9237998]
Accepted name: 2-oxoglutarate carboxylase
Reaction: ATP + 2-oxoglutarate + HCO3- = ADP + phosphate + oxalosuccinate
For diagram click here.
Glossary: oxalosuccinate = 1-oxopropane-1,2,3-tricarboxylate
Other name(s): oxalosuccinate synthetase; carboxylating factor for ICDH (incorrect); CFI; OGC
Comments: A biotin-containing enzyme that requires Mg2+ for activity. It was originally thought [1] that this enzyme was a promoting factor for the carboxylation of 2-oxoglutarate by EC 1.1.1.41, isocitrate dehydrogenase (NAD+), but this has since been disproved [2]. The product of the reaction is unstable and is quickly converted into isocitrate by the action of EC 1.1.1.41 [2].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 60382-75-4
References:
1. Aoshima, M., Ishii, M. and Igarashi, Y. A novel biotin protein required for reductive carboxylation of 2-oxoglutarate by isocitrate dehydrogenase in Hydrogenobacter thermophilus TK-6. Mol. Microbiol. 51 (2004) 791-798. [PMID: 14731279]
2. Aoshima, M. and Igarashi, Y. A novel oxalosuccinate-forming enzyme involved in the reductive carboxylation of 2-oxoglutarate in Hydrogenobacter thermophilus TK-6. Mol. Microbiol. 62 (2006) 748-759. [PMID: 17076668]
Accepted name: acetophenone carboxylase
Reaction: 2 ATP + acetophenone + HCO3- + H2O + H+ = 2 ADP + 2 phosphate + 3-oxo-3-phenylpropanoate
Systematic name: acetophenone:carbon-dioxide ligase (ADP-forming)
Comments: The enzyme is involved in anaerobic degradation of ethylbenzene. No activity with acetone, butanone, 4-hydroxy-acetophenone or 4-amino-acetophenone.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, UM-BBD, CAS registry number:
References:
1. Jobst, B., Schuhle, K., Linne, U. and Heider, J. ATP-dependent carboxylation of acetophenone by a novel type of carboxylase. J. Bacteriol. 192 (2010) 1387-1394. [PMID: 20047908]
Accepted name: DNA ligase (ATP)
Reaction: ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m = AMP + diphosphate + (deoxyribonucleotide)n+m
Other name(s): polydeoxyribonucleotide synthase (ATP); polynucleotide ligase; sealase; DNA repair enzyme; DNA joinase; DNA ligase; deoxyribonucleic ligase; deoxyribonucleate ligase; DNA-joining enzyme; deoxyribonucleic-joining enzyme; deoxyribonucleic acid-joining enzyme; deoxyribonucleic repair enzyme; deoxyribonucleic joinase; deoxyribonucleic acid ligase; deoxyribonucleic acid joinase; deoxyribonucleic acid repair enzyme
Systematic name: poly(deoxyribonucleotide):poly(deoxyribonucleotide) ligase (AMP-forming)
Comments: Catalyses the formation of a phosphodiester at the site of a single-strand break in duplex DNA. RNA can also act as substrate, to some extent.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9015-85-4
References:
1. Becker, A., Lyn, G., Gefter, M. and Hurwitz, J. The enzymatic repair of DNA. II. Characterization of phage-induced sealase. Proc. Natl. Acad. Sci. USA 58 (1967) 1996-2003. [PMID: 4295584]
2. Bertazzoni, U., Mathelet, M. and Campagnari, F. Purification and properties of a polynucleotide ligase from calf thymus glands. Biochim. Biophys. Acta 287 (1972) 404-414. [PMID: 4641251]
3. Weiss, B. and Richardson, C.C. Enzymatic breakage and joining of deoxyribonucleic acid. I. Repair of single-strand breaks in DNA by an enzyme system from Escherichia coli infected with T4 bacteriophage. Proc. Natl. Acad. Sci. USA 57 (1967) 1021-1028. [PMID: 5340583]
Accepted name: DNA ligase (NAD+)
Reaction: NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m = AMP + nicotinamide β-D-nucleotide + (deoxyribonucleotide)n+m
Other name(s): polydeoxyribonucleotide synthase (NAD); polynucleotide ligase (NAD); DNA repair enzyme; DNA joinase; DNA ligase (NAD); polynucleotide synthetase (nicotinamide adenine dinucleotide); deoxyribonucleic-joining enzyme; deoxyribonucleic ligase; deoxyribonucleic repair enzyme; deoxyribonucleic joinase; DNA ligase; DNA joinase; deoxyribonucleate ligase; polynucleotide ligase; deoxyribonucleic acid ligase; polynucleotide synthetase; deoxyribonucleic acid joinase; DNA-joining enzyme; deoxyribonucleic joinase; deoxyribonucleic repair enzyme; polynucleotide ligase (nicotinamide adenine dinucleotide); polydeoxyribonucleotide synthase (NAD+)
Systematic name: poly(deoxyribonucleotide):poly(deoxyribonucleotide) ligase (AMP-forming, NMN-forming)
Comments: Catalyses the formation of a phosphodiester at the site of a single-strand break in duplex DNA. RNA can also act as substrate, to some extent.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37259-52-2
References:
1. Zimmerman, S.B., Little, J.W., Oshinsky, C.K. and Gellert, M. Enzymatic joining of DNA strands: a novel reaction of diphosphopyridine nucleotide. Proc. Natl. Acad. Sci. USA 57 (1967) 1841-1848. [PMID: 4291949]
Accepted name: RNA ligase (ATP)
Reaction: ATP + (ribonucleotide)n + (ribonucleotide)m = AMP + diphosphate + (ribonucleotide)n+m
Other name(s): polyribonucleotide synthase (ATP); RNA ligase; polyribonucleotide ligase; ribonucleic ligase
Systematic name: poly(ribonucleotide):poly(ribonucleotide) ligase (AMP-forming)
Comments: Converts linear RNA to a circular form by transfer of the 5'-phosphate to the 3'-hydroxy terminus.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37353-39-2
References:
1. Silber, R., Malathi, V.G. and Hurwitz, J. Purification and properties of bacteriophage T4-induced RNA ligase. Proc. Natl. Acad. Sci. USA 69 (1972) 3009-3013. [PMID: 4342972]
Accepted name: RNA-3'-phosphate cyclase
Reaction: ATP + RNA 3'-terminal-phosphate = AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate
Other name(s): RNA cyclase
Systematic name: RNA-3'-phosphate:RNA ligase (cyclizing, AMP-forming)
Comments: Adenosine 5'-(γ-thio)triphosphate can act instead of ATP.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 85638-41-1
References:
1. Filipowicz, W., Konarska, M., Gross, H.J. and Shatkin, A.J. RNA 3'-terminal phosphate cyclase activity and RNA ligation in HeLa cell extract. Nucleic Acids Res. 11 (1983) 1405-1418. [PMID: 6828385]
2. Reinberg, D., Arenas, J. and Hurwitz, J. The enzymatic conversion of 3'-phosphate terminated RNA chains to 2',3'-cyclic phosphate derivatives. J. Biol. Chem. 260 (1985) 6088-6097. [PMID: 2581947]
EC 6.6.1 Forming coordination complexes
Accepted name: magnesium chelatase
Reaction: ATP + protoporphyrin IX + Mg2+ + H2O = ADP + phosphate + Mg-protoporphyrin IX + 2 H+
For diagram of reaction click here (heme and chlorophyll biosynthesis).
Other name(s): protoporphyrin IX magnesium-chelatase; protoporphyrin IX Mg-chelatase; magnesium-protoporphyrin IX chelatase; magnesium-protoporphyrin chelatase; magnesium-chelatase; Mg-chelatase; Mg-protoporphyrin IX magnesio-lyase
Systematic name: Mg-protoporphyrin IX magnesium-lyase
Comments: This is the first committed step of chlorophyll biosynthesis and is a branchpoint of two major routes in the tetrapyrrole pathway.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9074-88-8
References:
1. Walker, C.J. and Weinstein, J.D. In vitro assay of the chlorophyll biosynthetic enzyme Mg-chelatase: resolution of the activity into soluble and membrane-bound fractions. Proc. Natl. Acad. Sci. USA 88 (1991) 5789-5793. [PMID: 11607197]
2. Walker, C.J. and Willows, R.D. Mechanism and regulation of Mg-chelatase. Biochem. J. 327 (1997) 321-333. [PMID: 9359397]
3. Fodje, M.N., Hansson, A., Hansson, M., Olsen, J.G., Gough, S., Willows, R.D. and Al-Karadaghi, S. Interplay between an AAA module and an integrin I domain may regulate the function of magnesium chelatase. J. Mol. Biol. 311 (2001) 111-122. [PMID: 11469861]
Accepted name: cobaltochelatase
Reaction: ATP + hydrogenobyrinic acid a,c-diamide + Co2+ = ADP + phosphate + cob(II)yrinic acid a,c-diamide + H+
For diagram click here.
Other name(s): hydrogenobyrinic acid a,c-diamide cobaltochelatase; CobNST; CobN–CobST
Systematic name: hydrogenobyrinic-acid-a,c-diamide:cobalt cobalt-ligase (ADP-forming)
Comments: This enzyme, which forms part of the aerobic cobalamin biosynthesis pathway, is a type I chelatase, being heterotrimeric and ATP-dependent. It comprises two components, one of which corresponds to CobN and the other is composed of two polypeptides, specified by cobS and cobT in Pseudomonas denitrificans, and named CobST [1]. Hydrogenobyrinic acid is a very poor substrate. ATP can be replaced by dATP or CTP but the reaction proceeds more slowly. CobN exhibits a high affinity for hydrogenobyrinic acid a,c-diamide. The oligomeric protein CobST possesses at least one sulfhydryl group that is essential for ATP-binding. Once the Co2+ is inserted, the next step in the pathway ensures that the cobalt is ligated securely by reducing Co(II) to Co(I). This step is carried out by EC 1.16.8.1, cob(II)yrinic acid a,c-diamide reductase.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 81295-49-0
References:
1. Debussche, L., Couder, M., Thibaut, D., Cameron, B., Crouzet, J. and Blanche, F. Assay, purification, and characterization of cobaltochelatase, a unique complex enzyme catalyzing cobalt insertion in hydrogenobyrinic acid a,c-diamide during coenzyme B12 biosynthesis in Pseudomonas denitrificans. J. Bacteriol. 174 (1992) 7445-7451. [PMID: 1429466]
2. Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390-412. [PMID: 12195810]