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Catalytic Site Atlas

CSA LITERATURE entry for 1o98

E.C. namephosphoglycerate mutase
SpeciesBacillus stearothermophilus (Bacteria)
E.C. Number (IntEnz) 5.4.2.1
CSA Homologues of 1o981ejj,1eqj,1lno,1o99,2ify,3igy,3igz,
CSA Entries With UniProtID Q9X519
CSA Entries With EC Number 5.4.2.1
PDBe Entry 1o98
PDBSum Entry 1o98
MACiE Entry 1o98

Literature Report

IntroductionPhosphoglycerate mutase catalyses a number of reactions, the most biologically relevant being the interconversion of glycerate-3-phosphate and glycerate-2-phosphate in the glycolysis and gluconeogenesis pathways.
MechansimThe active site contains two Mn2+ ions. Mn1 and Arg 261 coordinate the substrate; this stabilises the negative charge of the substrate and transition states, and increases the electrophilicity of the phosphorus atom. The transfer of the phosphate group between the oxygen atom on C3 and the oxygen atom on C2 on glycerate is facilitated by the hydroxyl group of Ser 62 (activated by Mn2), which attacks the phosphorus centre and causes the glycerate-phosphate bond to break in an two-step addition-elimination reaction. This creates a phospho-serine intermediate. Asp 154 deprotonates the C2 hydroxyl group of the glycerate substrate, which can move in the active site so that this newly deprotonated hydroxyl can attack the phosphorus centre, and break the phospho-serine bond in another addition-elimination reaction. This regenerates Ser 62. A water molecule, activated by Mn1, acts as a specific acid to neutralise the C3 hydroxide group and to release the product from coordination to Mn1.
Reaction

Catalytic Sites for 1o98

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
SerA6262macie:sideChainSer 62 is nucleophilic (activated by Mn2) and attacks the phosphate group of glycerate-3-phosphate. This breaks the glycerate-phosphate bond in an addition-elimination mechanism, and forms a phospho-enzyme intermediate. Ser 62 is regenerated when the substrate's C2 hydroxide group attacks the phospho-enzyme intermediate in an addition-elimination reaction.
AspA154154macie:sideChainAsp 154 deprotonates the C2 hydroxyl group of the substrate, making it nucleophilic enough to attack the phospho-enzyme intermediate.
ArgA261261macie:sideChainArg 261 coordinates the phosphate group throughout the reaction, stabilising the intermediates and transition states, and increasing the electrophilicity of the phosphate group.

Literature References

Notes:Coenzyme-independent phosphoglycerate mutases (iPGMs) exhibit partial sequence homology to the alkaline phosphatase family of enzymes.
Jedrzejas MJ
Structure and mechanism of action of a novel phosphoglycerate mutase from Bacillus stearothermophilus.
EMBO J 2000 19 1419-1431
PubMed: 10747010
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