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Search The CSA
PDB ID
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Catalytic Site Atlas

CSA LITERATURE entry for 1pix

E.C. nameglutaconyl-CoA decarboxylase
SpeciesAcidaminococcus fermentans (strain ATCC 25085 / DSM 20731 / VR4)
E.C. Number (IntEnz) 4.1.1.70
CSA Homologues of 1pix3gf3,3gf7,3glm,3gma,
CSA Entries With UniProtID Q06700
CSA Entries With EC Number 4.1.1.70
PDBe Entry 1pix
PDBSum Entry 1pix
MACiE Entry 1pix

Literature Report

IntroductionBacterial 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.
MechansimIn 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.
Reaction

Catalytic Sites for 1pix

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
IleA417418macie:mainChainAmideAs 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
ValA151152macie:mainChainAmideAs part of an oxyanion hole with Gly 194 acts to stabilise the crotonyl coA enolate intermediate, thus facilitating the initial decarboxylation.
AlaA457458macie:mainChainAmideAs 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
GlyA194195macie:mainChainAmideAs part of an oxyanion hole with Val 151 acts to stabilise the crotonyl coA enolate intermediate, thus facilitating the initial decarboxylation.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
IleB417418macie:mainChainAmideAs 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
ValB151152macie:mainChainAmideAs part of an oxyanion hole with Gly 194 acts to stabilise the crotonyl coA enolate intermediate, thus facilitating the initial decarboxylation.
AlaB457458macie:mainChainAmideAs 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
GlyB194195macie:mainChainAmideAs part of an oxyanion hole with Val 151 acts to stabilise the crotonyl coA enolate intermediate, thus facilitating the initial decarboxylation.

Literature References

Notes:
Wendt KS
Crystal structure of the carboxyltransferase subunit of the bacterial sodium ion pump glutaconyl-coenzyme A decarboxylase.
EMBO J 2003 22 3493-3502
PubMed: 12853465
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