Lyases;
Carbon-sulfur lyases;
Carbon-sulfur lyases (only sub-subclass identified to date)

[LarE]-S-[1-(5-O-phosphono-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium-3-carbonyl]-L-cysteine pyridin-1-ium-3,5-dicarbothioate-mononucleotide-lyase (ATP-consuming)

(1) [LarE]-L-cysteine + pyridin-1-ium-3,5-dicarboxylate mononucleotide + ATP = [LarE]-dehydroalanine + pyridin-1-ium-3-carboxylate-5-thiocarboxylate mononucleotide + AMP + diphosphate (overall reaction) [RN:R12062];
(1a) ATP + pyridin-1-ium-3,5-dicarboxylate mononucleotide = diphosphate + 5-carboxy-1-(5-O-phospho-beta-D-ribofuranosyl)pyridin-1-ium-3-carbonyl adenylate [RN:R12059];
(1b) 5-carboxy-1-(5-O-phospho-beta-D-ribofuranosyl)pyridin-1-ium-3-carbonyl adenylate + [LarE]-L-cysteine = AMP + [LarE]-S-[5-carboxy-1-(5-O-phosphono-beta-D-ribofuranosyl)pyridin-1-ium-3-carbonyl]-L-cysteine [RN:R12060];
(1c) [LarE]-S-[5-carboxy-1-(5-O-phosphono-beta-D-ribofuranosyl)pyridin-1-ium-3-carbonyl]-L-cysteine = [LarE]-dehydroalanine + pyridin-1-ium-3-carboxylate-5-thiocarboxylate mononucleotide [RN:R12061];
(2) [LarE]-L-cysteine + pyridin-1-ium-3-carboxylate-5-thiocarboxylate mononucleotide + ATP = [LarE]-dehydroalanine + pyridin-1-ium-3,5-bisthiocarboxylate mononucleotide + AMP + diphosphate (overall reaction) [RN:R12066];
(2a) ATP + pyridin-1-ium-3-carboxylate-5-thiocarboxylate mononucleotide = diphosphate + 1-(5-O-phospho-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium-3-carbonyl adenylate [RN:R12063];
(2b) 1-(5-O-phospho-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium-3-carbonyl adenylate + [LarE]-L-cysteine = AMP + [LarE]-S-[1-(5-O-phosphono-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium-3-carbonyl]-L-cysteine [RN:R12064];
(2c) [LarE]-S-[1-(5-O-phosphono-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium-3-carbonyl]-L-cysteine = [LarE]-dehydroalanine + pyridin-1-ium-3,5-bisthiocarboxylate mononucleotide [RN:R12065]

R12059 R12060 R12061 R12062 R12063 R12064 R12065 R12066

[LarE]-L-cysteine;
pyridin-1-ium-3,5-dicarboxylate mononucleotide [CPD:C21851];
ATP [CPD:C00002];
5-carboxy-1-(5-O-phospho-beta-D-ribofuranosyl)pyridin-1-ium-3-carbonyl adenylate [CPD:C21877];
[LarE]-S-[5-carboxy-1-(5-O-phosphono-beta-D-ribofuranosyl)pyridin-1-ium-3-carbonyl]-L-cysteine;
pyridin-1-ium-3-carboxylate-5-thiocarboxylate mononucleotide [CPD:C21878];
1-(5-O-phospho-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium-3-carbonyl adenylate [CPD:C21879];
[LarE]-S-[1-(5-O-phosphono-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium-3-carbonyl]-L-cysteine

This enzyme, found in Lactobacillus plantarum, is involved in the biosynthesis of a nickel-pincer cofactor. The process starts when one enzyme molecule adenylates pyridinium-3,5-dicarboxylate mononucleotide (P2CMN) and covalently binds the adenylated product to an intrinsic cysteine residue. Next, the enzyme cleaves the carbon-sulfur bond, liberating pyridinium-3-carboxylate-5-thiocarboxylate mononucleotide (PCTMN) and leaving a 2-aminoprop-2-enoate (dehydroalanine) residue attached to the protein. Since the cysteine residue is not regenerated in vivo, the enzyme is inactivated during the process. A second enzyme molecule then repeats the process with PCTMN, adenylating it and covalently binding it to the same cysteine residue, followed by liberation of pyridinium-3,5-bisthiocarboxylate mononucleotide (P2TMN) and the inactivation of the second enzyme molecule.

EC 4.4.1.37 created 2018

1  [PMID:24710389]

Desguin B, Goffin P, Viaene E, Kleerebezem M, Martin-Diaconescu V, Maroney MJ, Declercq JP, Soumillion P, Hols P

Lactate racemase is a nickel-dependent enzyme activated by a widespread maturation system.

Nat Commun 5:3615 (2014)
DOI:10.1038/ncomms4615

[lpl:lp_0109]

2  [PMID:27114550]

Desguin B, Soumillion P, Hols P, Hausinger RP

Nickel-pincer cofactor biosynthesis involves LarB-catalyzed pyridinium carboxylation and LarE-dependent sacrificial sulfur insertion.

Proc Natl Acad Sci U S A 113:5598-603 (2016)
DOI:10.1073/pnas.1600486113

[lpl:lp_0109]

3  [PMID:28784764]

Fellner M, Desguin B, Hausinger RP, Hu J

Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE.

Proc Natl Acad Sci U S A 114:9074-9079 (2017)
DOI:10.1073/pnas.1704967114

[lpl:lp_0109]