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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1xa8
Original Entry
Title:
Lyase
Compound:
Crystal structure analysis of glutathione-dependent formaldehy
activating enzyme (gfa)
Mutant:
No
UniProt/Swiss-Prot:
Q51669-GFA_PARDE
EC Class:
4.4.-.-
Other CSA Entries:
Overview of all sites for 1xa8
Homologues of 1xa8
Entries for UniProt/Swiss-Prot: Q51669
Entries for EC: 4.4.-.-
Other Databases:
PDB entry: 1xa8
PDBsum entry: 1xa8
UniProt/Swiss-Prot: Q51669
IntEnz entry: 4.4.-.-
Literature Report:
Introduction:
Glutathione-dependent formaldehyde-activating enzyme (Gfa) is a carbon-sulphur lyase enzyme that catalyses the first step of a pathway that metabolises toxic formaldehyde to yield formate as a product. Gfa catalyses the condensation of formaledhyde and glutathione to form an adduct, S-hydroxymethylglutathione.
Mechanism:
Catalysis uses a zinc redox switch mechanism, in which a zinc molecule moves in a ping-pong fashion between its coordination state and its dislocated state. Formation of a disulphide bond between a glutathione molecule in its oxidised form (GSSG) and a zinc-coordinating thiol (Cys56) releases zinc into its dislocated state. In its dislocated state, zinc exerts its actual catalytic function by activating the coordinated formaldehyde and glutathione (GSH) for nucleophilic addition.

The proposed mechanism involves the GSSG reacting with Cys56, resulting in the formation of a disulphide-bonded Gfa-glutathione intermediate and the displacement of zinc. The zinc-glutathione complex acts as a formaldehyde scavenger.

In this complex, the carbonyl bond of the formaldehyde and the sulfinyl bond of GSH are polarised by zinc and activated for the final nucleophilic addition to form S-hydroxymethylglutathione, relocate zinc into the catalytic site and regenerate GSSG.
Sites:

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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
CYSA 56 54Sidechain
ElectrostaticCofactor
ModifiedCofactor
Cys 56 forms a ligand interaction with zinc and also forms a disulphide bridge with GSSG, which is important in the displacement of zinc forming a highly dynamic zinc redox switch which is crucial for the reaction. Sulphur ligands, such as Cys56, are needed to create an oxidoreductive environment in which the ligands (not the metal) are oxidised and reduced with concomitant release and binding of zinc.
Evidence from paper Evidence concerns Evidence type
PubMed ID 11741920 Current protein pH dependence of reaction
PubMed ID 15548539 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ZNA 200 0
ElectrostaticSubstrate
Zn200 activates formaldehyde and GSH for nucleophilic addition by polarising the carbonyl bond of the formaldehyde and the sulfinyl bond of GSH.
Evidence from paper Evidence concerns Evidence type
PubMed ID 15548539 Current protein Residue is positioned appropriately (ligand position known)
Notes:

References:
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