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Catalytic Site Atlas

CSA LITERATURE entry for 13pk

E.C. namephosphoglycerate kinase
SpeciesTrypanosoma brucei (Trypanosome)
E.C. Number (IntEnz) 2.7.2.3
CSA Homologues of 13pkThere are 23 Homologs
CSA Entries With UniProtID P07378
CSA Entries With EC Number 2.7.2.3
PDBe Entry 13pk
PDBSum Entry 13pk
MACiE Entry M0040

Literature Report

IntroductionThe first energy-producing reaction of glycolysis is catalysed by phosphoglycerate kinase (PGK). This enzyme is unusual among kinases in that, biologically, it functions mainly in the reverse direction to phosphorylate ADP. This important energy saving feature makes it fairly ubiquitous. In all known cases it also requires an Mg(2+) ion to enable the negatively charged phosphate groups to interact.
MechansimPhosphoglycerate kinase catalyses the reversible phosphoryl transfer between 1,3-bisphosphoglycerate and ADP to form 3-phosphoglycerate and ATP, in the presence of magnesium. Phosphoryl transfer occurs by a single step in-line mechanism, or SN2-reaction mechanism, with nucleophilic attack by the ADP-beta-phosphate oxygen atom at the 1-phosphate group of 1,3-BPG. This reaction involves an inversion of configuration at the gamma phosphorous atom. The main role of the enzyme is to orientate the two compounds favourably with respect to each other and to stabilise the pentacoordinate transition state. The protein undergoes a conformational change after binding substrate to exclude water from the active site; in the closed formation, the Lys219 side chain moves into position to assist the main chain amides of two residues, Gly376 and Gly399, the Mg(2+) ion and the Arg39 side chain in transition state stabilisation.
Reaction

Catalytic Sites for 13pk

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GlyA376376macie:mainChainAmideActivates and stabilises phosphoryl group oxygen atom in transition state.
ArgA3939macie:sideChainActivates and stabilises phosphoryl group oxygen atom in transition state.
LysA219219macie:sideChainStabilises phosphoryl group oxygen atom in transition state.
GlyA399399macie:mainChainAmideActivates and stabilises phosphoryl group oxygen atom in transition state.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GlyB376376macie:mainChainAmideActivates and stabilises phosphoryl group oxygen atom in transition state.
ArgB3939macie:sideChainActivates and stabilises phosphoryl group oxygen atom in transition state.
LysB219219macie:sideChainStabilises phosphoryl group oxygen atom in transition state.
GlyB399399macie:mainChainAmideActivates and stabilises phosphoryl group oxygen atom in transition state.

Annotated By Reference To The Literature - Site 3 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GlyC376376macie:mainChainAmideActivates and stabilises phosphoryl group oxygen atom in transition state.
ArgC3939macie:sideChainActivates and stabilises phosphoryl group oxygen atom in transition state.
LysC219219macie:sideChainStabilises phosphoryl group oxygen atom in transition state.
GlyC399399macie:mainChainAmideActivates and stabilises phosphoryl group oxygen atom in transition state.

Annotated By Reference To The Literature - Site 4 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GlyD376376macie:mainChainAmideActivates and stabilises phosphoryl group oxygen atom in transition state.
ArgD3939macie:sideChainActivates and stabilises phosphoryl group oxygen atom in transition state.
LysD219219macie:sideChainStabilises phosphoryl group oxygen atom in transition state.
GlyD399399macie:mainChainAmideActivates and stabilises phosphoryl group oxygen atom in transition state.

Literature References

Notes:
Bernstein BE
Crystal structures of substrates and products bound to the phosphoglycerate kinase active site reveal the catalytic mechanism.
Biochemistry 1998 37 4429-4436
PubMed: 9521762
Auerbach G
Closed structure of phosphoglycerate kinase from Thermotoga maritima reveals the catalytic mechanism and determinants of thermal stability.
Structure 1997 5 1475-1483
PubMed: 9384563
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