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Search The CSA
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Catalytic Site Atlas

CSA LITERATURE entry for 2qf7

E.C. namepyruvate carboxylase
SpeciesRhizobium etli (Bacteria)
E.C. Number (IntEnz) 6.4.1.1
CSA Homologues of 2qf7
CSA Entries With UniProtID Q2K340
CSA Entries With EC Number 6.4.1.1
PDBe Entry 2qf7
PDBSum Entry 2qf7
MACiE Entry M0223

Literature Report

IntroductionPyruvate carboxylase, isolated from Rhizobium etli, is a biotin-dependent enzyme. It catalyses the carboxylation of pyruvate to oxaloacetate using bicarbonate and coupled to the hydrolysis of ATP to ADP and phosphate. This reaction occurs in two major steps: the carboxylation of biotin by ATP and bicarbonate in the biotin carboxylase (BC) domain, and the carboxylation of pyruvate in the carboxyltransferase (CT) domain. The biotin is bound to the biotin carboxyl carrier protein (BCCP) domain, which moves between the BC domain of one subunit and the CT domain of a neighbouring subunit.
MechansimBC domain: The bicarbonate is deprotonated by an unknown base and then acts as the nucleophile for attack on ATP to form ADP and phosphorylated bicarbonate. The latter undergoes spontaneous decarboxylation to form carbon dioxide and phosphate. The phosphate removes a proton from biotin to produce the biotin amidate. The carbonyl of biotin reforms and the activated biotin acts as a nucleophile through its nitrogen to attack the carbon dioxide to form carboxylbiotin.
CT domain: Pyruvate binds to the zinc ion through the oxygen of the carbonyl group. Asp549 removes a proton from pyruvate to form the enolate. The enolate then attacks the carboxylate of carboxylbiotin in a nucleophilic substitution. This produces oxaloacetate and the biotin amidate, which is stabilised by accepting a proton from Lys718 to produce the isourea form of biotin. Lys718 then removes this proton and biotin returns to the ureido form by accepting a proton from Asp549.
Reaction

Catalytic Sites for 2qf7

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AspA655655macie:sideChainAsp655 coordinates to the zinc ion, activating it to stabilise the formation of the pyruvate enolate.
KcxA718718macie:ptmLys718 acts as an acid during the formation of the enol form of biotin in the PC reaction. It then acts as a base and removes this proton so that the enolate form of biotin can act as a nucleophile.
AspA549549macie:sideChainAsp549 acts as a base to produce the enolate form of pyruvate. Later it acts as an acid to return biotin to its ureido form.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AspB655655macie:sideChainAsp655 coordinates to the zinc ion, activating it to stabilise the formation of the pyruvate enolate.
AspB549549macie:sideChainAsp549 acts as a base to produce the enolate form of pyruvate. Later it acts as an acid to return biotin to its ureido form.

Literature References

Notes:
St Maurice M
Domain architecture of pyruvate carboxylase, a biotin-dependent multifunctional enzyme.
Science 2007 317 1076-1079
PubMed: 17717183
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