KEGG ENZYME: 4.4.1.45

ENZYME: 4.4.1.45

Entry

EC 4.4.1.45                 Enzyme

Name

extrinsic cysteine-dependent pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase;
larE (gene name)

Class

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

Sysname

pyridin-1-ium-3,5-bisthiocarboxylate mononucleotide sufo-lyase

Reaction(IUBMB)

(1) a [4Fe-5S] iron-sulfur cluster linked by 3 L-cysteine residues + pyridin-1-ium-3,5-dicarboxylate mononucleotide + ATP + reduced acceptor = a [4Fe-4S] iron-sulfur cluster linked by 3 L-cysteine residues + pyridin-1-ium-3-carboxylate-5-thiocarboxylate mononucleotide + AMP + diphosphate + acceptor (overall reaction) [RN:R13530];
(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) a [4Fe-5S] iron-sulfur cluster linked by 3 L-cysteine residues + 5-carboxy-1-(5-O-phospho-beta-D-ribofuranosyl)pyridin-1-ium-3-carbonyl adenylate + reduced acceptor = a [4Fe-4S] iron-sulfur cluster linked by 3 L-cysteine residues + pyridin-1-ium-3-carboxylate-5-thiocarboxylate mononucleotide + AMP + acceptor [RN:R13531];
(2) a [4Fe-5S] iron-sulfur cluster linked by 3 L-cysteine residues + pyridin-1-ium-3-carboxylate-5-thiocarboxylate mononucleotide + ATP + reduced acceptor = a [4Fe-4S] iron-sulfur cluster linked by 3 L-cysteine residues + pyridin-1-ium-3,5-bisthiocarboxylate mononucleotide + AMP + diphosphate + acceptor (overall reaction) [RN:R13532];
(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) a [4Fe-5S] iron-sulfur cluster linked by 3 L-cysteine residues + 1-(5-O-phospho-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium-3-carbonyl adenylate + reduced acceptor = a [4Fe-4S] iron-sulfur cluster linked by 3 L-cysteine residues + pyridin-1-ium-3,5-bisthiocarboxylate mononucleotide + AMP + acceptor [RN:R13533]

Reaction(KEGG)

R12059 R12063 R13530 R13531 R13532 R13533

Substrate

[4Fe-5S] iron-sulfur cluster linked by 3 L-cysteine residues;
pyridin-1-ium-3,5-dicarboxylate mononucleotide [CPD:C21851];
ATP [CPD:C00002];
reduced acceptor [CPD:C00030];
5-carboxy-1-(5-O-phospho-beta-D-ribofuranosyl)pyridin-1-ium-3-carbonyl adenylate [CPD:C21877];
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]

Product

[4Fe-4S] iron-sulfur cluster linked by 3 L-cysteine residues;
pyridin-1-ium-3-carboxylate-5-thiocarboxylate mononucleotide [CPD:C21878];
AMP [CPD:C00020];
diphosphate [CPD:C00013];
acceptor [CPD:C00028];
5-carboxy-1-(5-O-phospho-beta-D-ribofuranosyl)pyridin-1-ium-3-carbonyl adenylate [CPD:C21877];
pyridin-1-ium-3,5-bisthiocarboxylate mononucleotide [CPD:C21767];
1-(5-O-phospho-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium-3-carbonyl adenylate [CPD:C21879]

Comment

This enzyme, found in the bacterium Thermotoga maritima, catalyses two complex reactions during the biosynthesis of a nickel-pincer cofactor. The process starts with the adenylation of pyridin-1-ium-3,5-dicarboxylate mononucleotide (P2CMN), which is covalently bound to an intrinsic cysteine residue. Next, a [4Fe-4S] iron-sulfur cluster receives a sulfane sulfur from free L-cysteine via the action of EC 2.8.1.7, cysteine desulfurase, forming a temporary [4Fe-5S] cluster. The sulfur atom then attacks the activated substrate, resulting in formation of pyridin-1-ium-3-carboxylate-5-thiocarboxylate mononucleotide (PCTMN). The process repeats twice, with pyridin-1-ium-3,5-bisthiocarboxylate mononucleotide (P2TMN) being the final product. cf. EC 4.4.1.37, intrinsic cysteine-dependent pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase.

History

EC 4.4.1.45 created 2025

Reference

1 [PMID:35700827]

Authors

Chatterjee S, Parson KF, Ruotolo BT, McCracken J, Hu J, Hausinger RP.

Title

Characterization of a [4Fe-4S]-dependent LarE sulfur insertase that facilitates nickel-pincer nucleotide cofactor biosynthesis in Thermotoga maritima.

Journal

J Biol Chem 298:102131 (2022)
DOI:10.1016/j.jbc.2022.102131

Sequence

[tmm:Tmari_0968]

Reference

2 [PMID:38100250]

Authors

Zecchin P, Pecqueur L, Oltmanns J, Velours C, Schunemann V, Fontecave M, Golinelli-Pimpaneau B.

Title

Structure-based insights into the mechanism of [4Fe-4S]-dependent sulfur insertase LarE.

Journal

Protein Sci 33:e4874 (2024)
DOI:10.1002/pro.4874