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Catalytic Site Atlas Version 2.2.12
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CSA entry for 13pk
Original Entry
Title:
Kinase
Compound:
3-phosphoglycerate kinase
Mutant:
Yes
UniProt/Swiss-Prot:
P07378-PGKC_TRYBB
EC Class:
2.7.2.3
Other CSA Entries:
Overview of all sites for 13pk
Homologues of 13pk
Entries for UniProt/Swiss-Prot: P07378
Entries for EC: 2.7.2.3
Other Databases:
PDB entry: 13pk
PDBsum entry: 13pk
UniProt/Swiss-Prot: P07378
IntEnz entry: 2.7.2.3
Literature Report:
Introduction:
The 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.
Mechanism:
Phosphoglycerate 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.
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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ARGA 39 39Sidechain
ElectrostaticSubstrate
ElectrostaticTransition state
Activates and stabilises phosphoryl group oxygen atom in transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 9384563 Related protein: UniProt P36204 Structural similarity to homologue of known mechanism
PubMed ID 9521762 Current protein Computer modelling
PubMed ID 9384563 Related protein: UniProt P36204 Residue is positioned appropriately (ligand position known)
PubMed ID 9521762 Current protein Residue is positioned appropriately (ligand position hypothetical)
PubMed ID 9384563 Related protein: UniProt P36204 Conservation of residue
PubMed ID 9521762 Current protein Structural similarity to homologue of known mechanism

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
LYSA 219 219Sidechain
ElectrostaticTransition state
Stabilises phosphoryl group oxygen atom in transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 9384563 Related protein: UniProt P36204 Residue is positioned appropriately (ligand position known)
PubMed ID 9521762 Current protein Computer modelling
PubMed ID 9384563 Related protein: UniProt P36204 Conservation of residue
PubMed ID 9521762 Current protein Residue is positioned appropriately (ligand position hypothetical)
PubMed ID 9521762 Current protein Structural similarity to homologue of known mechanism
PubMed ID 9384563 Related protein: UniProt P36204 Structural similarity to homologue of known mechanism

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
GLYA 376 376Backbone amide
ElectrostaticSubstrate
ElectrostaticTransition state
Activates and stabilises phosphoryl group oxygen atom in transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 9384563 Related protein: UniProt P36204 Residue is positioned appropriately (ligand position known)
PubMed ID 9521762 Current protein Computer modelling
PubMed ID 9384563 Related protein: UniProt P36204 Conservation of residue
PubMed ID 9521762 Current protein Structural similarity to homologue of known mechanism
PubMed ID 9384563 Related protein: UniProt P36204 Structural similarity to homologue of known mechanism
PubMed ID 9521762 Current protein Residue is positioned appropriately (ligand position hypothetical)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
GLYA 399 399Backbone amide
ElectrostaticSubstrate
ElectrostaticTransition state
Activates and stabilises phosphoryl group oxygen atom in transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 9384563 Related protein: UniProt P36204 Conservation of residue
PubMed ID 9521762 Current protein Residue is positioned appropriately (ligand position hypothetical)
PubMed ID 9384563 Related protein: UniProt P36204 Residue is positioned appropriately (ligand position known)
PubMed ID 9384563 Related protein: UniProt P36204 Structural similarity to homologue of known mechanism
PubMed ID 9521762 Current protein Computer modelling
PubMed ID 9521762 Current protein Structural similarity to homologue of known mechanism

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
MGA 422 0Sidechain
ElectrostaticSubstrate
ElectrostaticTransition state
Activates and stabilises phosphoryl group oxygen atom in transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 9521762 Current protein Residue is positioned appropriately (ligand position hypothetical)
PubMed ID 9384563 Related protein: UniProt P36204 Residue is positioned appropriately (ligand position known)
PubMed ID 9521762 Current protein Structural similarity to homologue of known mechanism
PubMed ID 9384563 Related protein: UniProt P36204 Structural similarity to homologue of known mechanism
PubMed ID 9521762 Current protein Computer modelling
PubMed ID 9384563 Related protein: UniProt P36204 Conservation of residue
References:
1
Closed structure of phosphoglycerate kinase from Thermotoga maritima reveals the catalytic mechanism and determinants of thermal stability.
G. Auerbach and R. Huber and M. Gr├Ąttinger and K. Zaiss and H. Schurig and R. Jaenicke and U. Jacob
Structure 5, (11) 1475-83, (1997).
9384563
2
Crystal structures of substrates and products bound to the phosphoglycerate kinase active site reveal the catalytic mechanism.
B. E. Bernstein and W. G. Hol
Biochemistry 37, (13) 4429-36, (1998).
9521762
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