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Catalytic Site Atlas

CSA LITERATURE entry for 1al6

E.C. namecitrate (Si)-synthase
SpeciesGallus gallus (Chicken)
E.C. Number (IntEnz) 2.3.3.1
CSA Homologues of 1al6There are 36 Homologs
CSA Entries With UniProtID P23007
CSA Entries With EC Number 2.3.3.1
PDBe Entry 1al6
PDBSum Entry 1al6
MACiE Entry M0078

Literature Report

IntroductionCitrate synthase catalyses the condensation between the carbonyl of oxaloacetate and the acetyl methyl group of acetyl CoA. The product of this reaction, citryl-CoA, remains tightly bound to the enzyme and is hydrolysed to citrate and CoA in a separate chemical step that nevertheless uses the same catalytic residues. Conformational changes of the enzyme during the reaction are believed to be important in the catalytic mechanism.
MechansimThe condensation reaction occurs via formation of an enolate intermediate that is produced on removal of a proton from the methyl group of acetyl CoA by Asp 375. Accumulation of negative charge on the carbonyl oxygen during formation of the enolate is stabilised by donation of hydrogen bonds from His 274 and from a water molecule. The enolate now acts as a nucleophile to attack the C2 carbonyl of oxaloacetate, with His 230 acting as a hydrogen bond donor to stabilise accumulation of negative charge on the C2 carbonyl oxygen during the attack.
Cleavage of the citryl CoA intermediate involves Asp 375 and His 274, with the latter functioning to stabilise negative charge on the thioester carbonyl of citryl CoA during the hydrolysis.
Reaction

Catalytic Sites for 1al6

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AspA375375macie:sideChainRemoves a proton from the methyl group of acetyl CoA during formation of the enolate intermediate. Is also involved in the hydrolysis of citryl CoA.
HisA274274macie:sideChainActs as a hydrogen bond donor to stabilise accumulation of negative charge on the carbonyl of acetyl CoA during formation of the enolate intermediate. Later stabilises accumulation of negative charge on the same carbonyl oxygen atom during hydrolysis of citryl CoA.
HisA320320macie:sideChainActs as a hydrogen bond donor to polarise the C2 carbony of oxaloacetate and stabilise accumulation of negative charge on the carbonyl oxygen during attack by the enolate of acetyl CoA.
SerA244244macie:sideChainActs as a hydrogen bond donor to His 274, increasing the acidity and hydrogen-bond donor ability of this residue towards the enolate intermediate.

Literature References

Notes:1. The details of the mechanism for hydrolysis of citryl CoA are not entirely clear. 2. There has been some debate regarding whether an enolate or a neutral enol is the intermediate in the reaction. The description given here assumes an enolate, as is suggested by recent theoretical calculations.
W. Yang
Computational Study of the Citrate Synthase Catalyzed Deprotonation of Acetyl-Coenzyme A and Fluoroacetyl-Coenzyme A: Demonstration of a Layered Quantum Mechanical Approach
J Phys Chem B 2003 107 5986-5994
PubMed: Yang2003
Usher KC
A very short hydrogen bond provides only moderate stabilization of an enzyme-inhibitor complex of citrate synthase.
Biochemistry 1994 33 7753-7759
PubMed: 8011640
Kurz LC
Effects of changes in three catalytic residues on the relative stabilities of some of the intermediates and transition states in the citrate synthase reaction.
Biochemistry 1998 37 9724-9737
PubMed: 9657685
Evans CT
Active site mutants of pig citrate synthase: effects of mutations on the enzyme catalytic and structural properties.
Biochemistry 1996 35 10661-10672
PubMed: 8718855
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