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CSA entry for 1pix
Original Entry
Title:
Lyase
Compound:
Glutaconyl-coa decarboxylase a subunit
Mutant:
No
UniProt/Swiss-Prot:
Q06700-GCDA_ACIFE
EC Class:
4.1.1.70
Other CSA Entries:
Overview of all sites for 1pix
Homologues of 1pix
Entries for UniProt/Swiss-Prot: Q06700
Entries for EC: 4.1.1.70
Other Databases:
PDB entry: 1pix
PDBsum entry: 1pix
UniProt/Swiss-Prot: Q06700
IntEnz entry: 4.1.1.70
Literature Report:
Introduction:
Bacterial Glutaconyl-coA decarboxylase is an unusual ion transport holozyme, which uses the free energy released from the decarboxylation of glutaconyl coA to crotonyl coA in order to power the active transport of sodium ions into the periplasm. The carboxyl transferase subunit, Gcdalpha is responsible for the first step in this process whereby the transfer of CO2 to the biotin cofactor on Gcdgamma is carried out. This subunit displays structural homology to the family of crotonases such as methylmalonoyl coA decarboxylase, but little sequence identity, so although it clearly shares a common ancestor, divergence is likely to have occurred a long time in the past.
Mechanism:
In the first stage of the reaction, the decarboxylation of glutaconyl coA occurs spontaneously, forming an enolate intermediate stabilised by an oxyanion hole composed of Gly 194 and Val 151. Protonation of this enolate occurs with biotin acting as the general acid, resulting in the crotonyl coA product and the enolate form of biotin, stabilised by an oxyanion hole composed of Ile 415 and Ala 457. The enolate form of biotin is thus able to act as a nucleophile to attack the CO2 previously liberated thus forming the carboxylated biotin.
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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
VALA 151 152Backbone amide
ElectrostaticTransition state
As part of an oxyanion hole with Gly 194 acts to stabilise the crotonyl coA enolate intermediate, thus facilitating the initial decarboxylation.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12853465 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 12853465 Current protein Structural similarity to homologue of known mechanism

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
GLYA 194 195Backbone amide
ElectrostaticTransition state
As part of an oxyanion hole with Val 151 acts to stabilise the crotonyl coA enolate intermediate, thus facilitating the initial decarboxylation.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12853465 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 12853465 Current protein Structural similarity to homologue of known mechanism

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ILEA 417 418Backbone amide
ElectrostaticCofactor
ElectrostaticTransition state
As part of an oxyanion hole with Ala 457 acts to stabilise the biotin enolate intermediate, thus allowing biotin to donate a proton to crotonyl coA, and to act as a nucleophile towards CO2
Evidence from paper Evidence concerns Evidence type
PubMed ID 12853465 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 12853465 Current protein Structural similarity to homologue of known mechanism

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ALAA 457 458Backbone amide
ElectrostaticTransition state
ElectrostaticCofactor
As part of an oxyanion hole with Ile 417 acts to stabilise the biotin enolate intermediate, thus allowing biotin to donate a proton to crotonyl coA, and to act as a nucleophile towards CO2
Evidence from paper Evidence concerns Evidence type
PubMed ID 12853465 Current protein Structural similarity to homologue of known mechanism
PubMed ID 12853465 Current protein Residue is positioned appropriately (ligand position known)
References:
1
Crystal structure of the carboxyltransferase subunit of the bacterial sodium ion pump glutaconyl-coenzyme A decarboxylase.
K. S. Wendt and I. Schall and R. Huber and W. Buckel and U. Jacob
EMBO J 22, (14) 3493-502, (2003).
12853465
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