L-cysteine/cystine lyase

 

Cyst(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 and directs FeS cluster insertion into Synechocystis apoferridoxin in vivo.

The observation of a persulfidic intermediate mimics the NifS PLP dependent L-Cysteine desulphurase, although C-DES is missing the largely conserved active site cysteine associated with NifS enzymes. The mechanism for C-DES persulphide formation offers an alternative pathway for the formation of S(0), although the mode of transport of the elemental sulfur has yet to be determined.

 

Reference Protein and Structure

Sequence
Q9ZHG9 UniProt IPR000192 (Sequence Homologues) (PDB Homologues)
Biological species
Synechocystis sp. PCC 6714 (Bacteria) Uniprot
PDB
1elu - COMPLEX BETWEEN THE CYSTINE C-S LYASE C-DES AND ITS REACTION PRODUCT CYSTEINE PERSULFIDE. (1.55 Å) PDBe PDBsum 1elu
Catalytic CATH Domains
3.40.640.10 CATHdb 3.90.1150.10 CATHdb (see all for 1elu)
Cofactors
Pyridoxal 5'-phosphate(2-) (1)
Click To Show Structure

Enzyme Reaction (EC:4.4.1.35)

L-cystine zwitterion
CHEBI:35491ChEBI
+
water
CHEBI:15377ChEBI
→
pyruvate
CHEBI:15361ChEBI
+
ammonium
CHEBI:28938ChEBI
+
3-disulfanyl-L-alanine zwitterion
CHEBI:58591ChEBI
Alternative enzyme names: CORI3 (gene name),

Enzyme Mechanism

Introduction

PLP 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 PLP-amino acrylate intermediate. There is another transaldimination reaction involving Lys223 and the released product is hydrolysed to pyruvate and ammonia. Stabilisation of the reactive persulphide group by controlling the electrostatics within the active site allows the enzyme to act as an activated sulfur source.

Catalytic Residues Roles

UniProt PDB* (1elu)
Lys223 Lys223(220)A Lys223 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. covalent catalysis, proton shuttle (general acid/base)
Arg360 Arg360(357)A Upon 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. steric role
Ala199 Ala199(196)A Ala199 interacts with the pyridine ring of PLP, stabilising the electronic distributions that form in the ring during the reaction. electrostatic stabiliser
His114 His114(111)A His114 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. proton shuttle (general acid/base)
Asp197 Asp197(194)A Asp197 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. electrostatic stabiliser
Gln200 Gln200(197)A Gln200 hydrogen bonds to the C3 hydroxyl group of PLP. This stabilises the electronic distributions that form in the ring during the reaction. electrostatic stabiliser
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

References

  1. Campanini B et al. (2006), J Biol Chem, 281, 38769-38780. Sulfur Mobilization in Cyanobacteria: THE CATALYTIC MECHANISM OF L-CYSTINE C-S LYASE (C-DES) FROM SYNECHOCYSTIS. DOI:10.1074/jbc.m607098200. PMID:17020883.
  2. Kaiser JT et al. (2003), J Biol Chem, 278, 357-365. Snapshots of the Cystine Lyase C-DES during Catalysis. STUDIES IN SOLUTION AND IN THE CRYSTALLINE STATE. DOI:10.1074/jbc.m209862200. PMID:12386155.
  3. Clausen T et al. (2000), Proc Natl Acad Sci U S A, 97, 3856-3861. Crystal structure of the cystine C-S lyase from Synechocystis: Stabilization of cysteine persulfide for FeS cluster biosynthesis. DOI:10.1073/pnas.97.8.3856. PMID:10760256.
  4. Kaiser JT et al. (2000), J Mol Biol, 297, 451-464. Crystal structure of a NifS-like protein from Thermotoga maritima: implications for iron sulphur cluster assembly. DOI:10.1006/jmbi.2000.3581. PMID:10715213.

Step 1.

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Catalytic Residues Roles

Residue Roles
Lys223(220)A covalent catalysis, proton shuttle (general acid/base)
Arg360(357)A steric role
Asp197(194)A electrostatic stabiliser
Ala199(196)A electrostatic stabiliser
Gln200(197)A electrostatic stabiliser
His114(111)A proton shuttle (general acid/base)

Chemical Components

Step 1.

Contributors

James W. Murray, Craig Porter, Gemma L. Holliday