PDBsum entry 2wzb

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protein ligands metals links
Transferase PDB id
Protein chain
405 a.a. *
Waters ×617
* Residue conservation analysis
PDB id:
Name: Transferase
Title: The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with adp, 3pg and magnesium trifluoride
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 magnesium fluori
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 511693.
1.47Å     R-factor:   0.162     R-free:   0.186
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 DOI: 10.1021/ja100974t
27-Nov-09     Release date:   14-Apr-10    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00558  (PGK1_HUMAN) -  Phosphoglycerate kinase 1
417 a.a.
405 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Phosphoglycerate kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Calvin Cycle (carbon fixation stages)
      Reaction: ATP + 3-phospho-D-glycerate = ADP + 3-phospho-D-glyceroyl phosphate
Bound ligand (Het Group name = 3PG)
corresponds exactly
Bound ligand (Het Group name = ADP)
corresponds exactly
+ 3-phospho-D-glyceroyl phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   3 terms 
  Biological process     small molecule metabolic process   7 terms 
  Biochemical function     nucleotide binding     6 terms  


DOI no: 10.1021/ja100974t 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.
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)(-).

Literature references that cite this PDB file's key reference

  PubMed id Reference
21409189 S.Y.Lu, Y.J.Jiang, J.W.Zou, and T.X.Wu (2011).
Dissection of the difference between the group I metal ions in inhibiting GSK3β: a computational study.
  Phys Chem Chem Phys, 13, 7014-7023.  
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