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Catalytic Site Atlas

CSA LITERATURE entry for 1gim

E.C. nameadenylosuccinate synthase
SpeciesEscherichia coli (Bacteria)
E.C. Number (IntEnz) 6.3.4.4
CSA Homologues of 1gimThere are 27 Homologs
CSA Entries With UniProtID P0A7D4
CSA Entries With EC Number 6.3.4.4
PDBe Entry 1gim
PDBSum Entry 1gim
MACiE Entry M0065

Literature Report

IntroductionAdenylosuccinate synthetase is an essential enzyme in Escherichia coli and many other forms of life, catalysing the first committed step in de novo biosyntheses of AMP: The catalytic mechanism proceeds with the initial formation of 6-phosphoryl-IMP by nucleophilic attack of the 6-oxo group of IMP on the gamma-phosphorus atom of GTP, followed by the nucleophilic displacement of the 6-phosphoryl group by L -aspartate to form adenylosuccinate.
MechansimThere is a two-step nature of the reaction. Four residues are essential for the reaction: Asp13, His41 and Gln224 and Lys16 . Asp13 acts first as a catalytic base, removing a proton from the N1 atom of IMP, while His41 acts as an acid, protonating the beta-phosphoryl group of GTP which then becomes the leaving group. It is suggested that once the IMP-6-phosphoryl intermediate is formed, as a response to binding aspartate the active site alters: Asp13 moves to be co-ordinated by the Mg2+ ion, transforming it into an acid, while His41 rotates to interact with the 6-phosphoryl group instead of the GDP phosphate. Both of these changes facilitate the displacement of phosphate by aspartate. Throughout the reaction Gln224 is positioned to H-bond to the 6-0 atom of IMP, stabilising the negative charge that develops on it. Similarly Lys16 hydrogen bonds with the 6-phosphoryl group of the intermediate.
Reaction

Catalytic Sites for 1gim

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AspA1314macie:sideChainAsp13 acts as a base in phosphorylation abstracting a proton from N1 of IMP. In the formation of 6-phosphoryl-IMP, the active site could alter as to permit the coordination of protonated Asp13 to Mg2+ which transforms the side chain into a potent catalytic acid. Then the now catalytic Asp13 acid to induce forced protonation of N1 makes C6 more electrophilic in the nucleophilic displacement of 6-phosphoryl group.
HisA4142macie:sideChainHis41 acts as a catalytic acid in the phosphorylation, by proton donation to the leaving group GDP via binding to beta-phosphoryl group of GTP. Then again as an acid in the phosphoryl displacement by donating a proton to the phosphate group. The conformation change during the second step is thought to be triggered by the association of L-aspartate. Note it also acts throughout the reaction to stabilise the intermediate, as the NE2 of His41 hydrogen bonds with the 6-phosphoryl group of the intermediate.
GlnA224225macie:sideChainGln224 works in concert with asp13 to stabilise the 6-oxyanion of IMP via hydrogen bonding.
LysA1617macie:sideChainys16 hydrogen bonds with the 6-phosphoryl group of the intermediate to stabilise it and also, perhaps with beta-phosphoryl group of GDP.

Literature References

Notes:Lys16 has a less significant role than the other 3 residues.
Poland BW
Entrapment of 6-thiophosphoryl-IMP in the active site of crystalline adenylosuccinate synthetase from Escherichia coli.
J Biol Chem 1997 272 15200-15205
PubMed: 9182542
Choe JY
Mechanistic implications from crystalline complexes of wild-type and mutant adenylosuccinate synthetases from Escherichia coli.
Biochemistry 1999 38 6953-6961
PubMed: 10346917
Wang W
Relationship of conserved residues in the IMP binding site to substrate recognition and catalysis in Escherichia coli adenylosuccinate synthetase.
J Biol Chem 1997 272 16911-16916
PubMed: 9202000
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