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Catalytic Site Atlas

CSA LITERATURE entry for 1n2t

E.C. nameL-CYSTEINE-CYSTINE LYASE C-DES
SpeciesSynechocystis sp. pcc 6714 ()
E.C. Number (IntEnz) 4.4.-.-
CSA Homologues of 1n2t
CSA Entries With UniProtID
CSA Entries With EC Number 4.4.-.-
PDBe Entry 1n2t
PDBSum Entry 1n2t
MACiE Entry 1n2t

Literature Report

IntroductionCyst(e)ine C-S lyase (C-DES), isolated from Synechocystis sp. PCC 6714, is a pyridoxal 5'-phosphate (PLP)-dependent enzyme. It catalyses the conversion of cystine to cysteine persulfide, pyruvate and ammonia. The enzyme can also use cysteine, but to a lesser extent. C-DES is an important enzyme in sulfur mobilisation and Fe-S cluster assembly.
MechansimPLP is covalently bound to the enzyme through Lys223; this is the internal aldimine. One of the amino groups of cystine is deprotonated by His114 and this causes transaldimination via a gem-diamine to form an external aldimine. Lys223 abstracts the C-alpha proton of the substrate and PLP acts as an electron sink. This is followed by beta-lysis, forming cysteine persulfide and an aminoacrylate intermediate. There is another transaldimination reaction involving Lys223 and the released product is hydrolysed to pyruvate and ammonia.

Catalytic Sites for 1n2t

Annotated By Reference To The Literature - Site 5 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AlaA199199macie:sideChainAla199 interacts with the pyridine ring of PLP, stabilising the electronic distributions that form in the ring during the reaction.
AlaA223223macie:sideChainLys223 forms an internal aldimine complex with PLP. It is the leaving group during transaldimination. It deprotonates C-alpha of this intermediate and then protonates the cysteine persulfide leaving group. It then forms another internal aldimine complex with PLP so that the product can be released.
HisA114114macie:sideChainHis114 deprotonates the amine group of the substrate so that it can act as a nucleophile for attack on the enzyme-bound PLP. The imidazole ring interacts with the pyridine ring of PLP, stabilising the electronic distributions that form in the ring during the reaction.
GlnA200200macie:sideChainGln200 hydrogen bonds to the C3 hydroxyl group of PLP. This stabilises the electronic distributions that form in the ring during the reaction.
ArgA360360macie:sideChainUpon formation of the external aldimine, Arg360 and the carboxylate of the substrate rearrange relative to each other and form electrostatic interactions. This induces strain in the substrate and is necessary for C-S cleavage.
AspA197197macie:sideChainAsp197 forms a salt bridge with the nitrogen of the pyridine ring of PLP. This stabilises the electronic distributions that form in the ring during the reaction.

Annotated By Reference To The Literature - Site 6 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AlaB199199macie:sideChainAla199 interacts with the pyridine ring of PLP, stabilising the electronic distributions that form in the ring during the reaction.
HisB114114macie:sideChainHis114 deprotonates the amine group of the substrate so that it can act as a nucleophile for attack on the enzyme-bound PLP. The imidazole ring interacts with the pyridine ring of PLP, stabilising the electronic distributions that form in the ring during the reaction.
GlnB200200macie:sideChainGln200 hydrogen bonds to the C3 hydroxyl group of PLP. This stabilises the electronic distributions that form in the ring during the reaction.
AlaB223223macie:sideChainLys223 forms an internal aldimine complex with PLP. It is the leaving group during transaldimination. It deprotonates C-alpha of this intermediate and then protonates the cysteine persulfide leaving group. It then forms another internal aldimine complex with PLP so that the product can be released.
ArgB360360macie:sideChainUpon formation of the external aldimine, Arg360 and the carboxylate of the substrate rearrange relative to each other and form electrostatic interactions. This induces strain in the substrate and is necessary for C-S cleavage.
AspB197197macie:sideChainAsp197 forms a salt bridge with the nitrogen of the pyridine ring of PLP. This stabilises the electronic distributions that form in the ring during the reaction.

Literature References

Notes:
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