PDBsum entry 2wzc

Transferase

PDB id: 2wzc

Contents

Protein chain

405 a.a. *

Ligands

ALF-ADP-3PG

Metals

_MG

_CL

Waters ×473

* Residue conservation analysis

PDB id:

2wzc

Name:

Transferase

Title:

The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with adp, 3pg and aluminium tetrafluoride

Structure:

Phosphoglycerate kinase 1. Chain: a. Fragment: residues 2-417. Synonym: primer recognition protein 2, prp 2, cell migration-inducing gene 10 protein. Engineered: yes. Other_details: complexed with adp, 3pg and aluminium fluoride

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

1.50Å R-factor: 0.166 R-free: 0.198

Authors:

M.W.Bowler,M.J.Cliff,J.P.M.Marston,N.J.Baxter,A.M.H.Hownslow, A.V.Varga,J.Szabo,M.Vas,G.M.Blackburn,J.P.Waltho

Key ref:

M.J.Cliff et al. (2010). Transition state analogue structures of human phosphoglycerate kinase establish the importance of charge balance in catalysis. J Am Chem Soc, 132, 6507-6516. PubMed id: 20397725

Date:

27-Nov-09 Release date: 14-Apr-10

Protein chain

P00558  (PGK1_HUMAN) -  Phosphoglycerate kinase 1 from Homo sapiens

Seq: 417 a.a.

Struc: 405 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.2.3 - phosphoglycerate kinase.
• Pathway: Calvin Cycle (carbon fixation stages)
• Reaction: (2R)-3-phosphoglycerate + ATP = (2R)-3-phospho-glyceroyl phosphate + ADP

(2R)-3-phosphoglycerate + ATP = (2R)-3-phospho-glyceroyl phosphate + ADP (Bound ligand (Het Group name = ADP) corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

J Am Chem Soc 132:6507-6516 (2010)

PubMed id: 20397725

Transition state analogue structures of human phosphoglycerate kinase establish the importance of charge balance in catalysis.

M.J.Cliff, M.W.Bowler, A.Varga, J.P.Marston, J.Szabó, A.M.Hounslow, N.J.Baxter, G.M.Blackburn, M.Vas, J.P.Waltho.

ABSTRACT

Transition state analogue (TSA) complexes formed by phosphoglycerate kinase (PGK) have been used to test the hypothesis that balancing of charge within the transition state dominates enzyme-catalyzed phosphoryl transfer. High-resolution structures of trifluoromagnesate (MgF(3)(-)) and tetrafluoroaluminate (AlF(4)(-)) complexes of PGK have been determined using X-ray crystallography and (19)F-based NMR methods, revealing the nature of the catalytically relevant state of this archetypal metabolic kinase. Importantly, the side chain of K219, which coordinates the alpha-phosphate group in previous ground state structures, is sequestered into coordinating the metal fluoride, thereby creating a charge environment complementary to the transferring phosphoryl group. In line with the dominance of charge balance in transition state organization, the substitution K219A induces a corresponding reduction in charge in the bound aluminum fluoride species, which changes to a trifluoroaluminate (AlF(3)(0)) complex. The AlF(3)(0) moiety retains the octahedral geometry observed within AlF(4)(-) TSA complexes, which endorses the proposal that some of the widely reported trigonal AlF(3)(0) complexes of phosphoryl transfer enzymes may have been misassigned and in reality contain MgF(3)(-).