PDBsum entry 1e59

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Isomerase PDB id
Protein chain
239 a.a. *
Waters ×264
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: E.Coli cofactor-dependent phosphoglycerate mutase complexed with vanadate
Structure: Phosphoglycerate mutase. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: pgm1. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Homo-Dimer (from PDB file)
1.30Å     R-factor:   0.159     R-free:   0.213
Authors: C.S.Bond,W.N.Hunter
Key ref:
C.S.Bond et al. (2002). Mechanistic implications for Escherichia coli cofactor-dependent phosphoglycerate mutase based on the high-resolution crystal structure of a vanadate complex. J Mol Biol, 316, 1071-1081. PubMed id: 11884145 DOI: 10.1006/jmbi.2002.5418
19-Jul-00     Release date:   05-Feb-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P62707  (GPMA_ECOLI) -  2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
250 a.a.
239 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Phosphoglycerate mutase (2,3-diphosphoglycerate-dependent).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate
= 3-phospho-D-glycerate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     5 terms  


    Added reference    
DOI no: 10.1006/jmbi.2002.5418 J Mol Biol 316:1071-1081 (2002)
PubMed id: 11884145  
Mechanistic implications for Escherichia coli cofactor-dependent phosphoglycerate mutase based on the high-resolution crystal structure of a vanadate complex.
C.S.Bond, M.F.White, W.N.Hunter.
The structure of Escherichia coli cofactor-dependent phosphoglycerate mutase (dPGM), complexed with the potent inhibitor vanadate, has been determined to a resolution of 1.30 A (R-factor 0.159; R-free 0.213). The inhibitor is present in the active site, principally as divanadate, but with evidence of additional vanadate moieties at either end, and representing a different binding mode to that observed in the structural homologue prostatic acid phosphatase. The analysis reveals the enzyme-ligand interactions involved in inhibition of the mutase activity by vanadate and identifies a water molecule, observed in the native E.coli dPGM structure which, once activated by vanadate, may dephosphorylate the active protein. Rather than reflecting the active conformation previously observed for E.coli dPGM, the inhibited protein's conformation resembles that of the inactive dephosphorylated Saccharomyces cerevisiae dPGM. The provision of a high-resolution structure of both active and inactive forms of dPGM from a single organism, in conjunction with computational modelling of substrate molecules in the active site provides insight into the binding of substrates and the specific interactions necessary for three different activities, mutase, synthase and phosphatase, within a single active site. The sequence similarity of E.coli and human dPGMs allows us to correlate structure with clinical pathology.
  Selected figure(s)  
Figure 2.
Figure 2. Inhibitor binding. (a) 1.75s 2F[o] - F[c] s[A]-weighted[53] electron density (orange) covering tetravanadate and the nearby residues Thr22 and Tyr91. Grey balls-and-sticks represent oxygen atoms modelled with zero occupancy. (b) Schematic of hydrogen bonding interactions between tetravanadate and the protein. (c) Schematic of sulphate binding positions in native dPGM structures. The Figure was prepared using MOLSCRIPT, [54] O [43] and RASTER3D. [55]
Figure 3.
Figure 3. Comparison of vanadate-binding of (a) dPGM and (b) rat prostatic acid phosphatase. Vanadate shown as red and grey ball-and-stick. Selected residues are shown as ball-and-stick side-chains. Regions of structural homology are depicted in dark blue, while regions that differ are shown in (a) green and (b) cyan. Grey shading indicates the protein surface cut away to reveal the active site shape.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 316, 1071-1081) copyright 2002.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21187861 J.M.Foster, P.J.Davis, S.Raverdy, M.H.Sibley, E.A.Raleigh, S.Kumar, and C.K.Carlow (2010).
Evolution of bacterial phosphoglycerate mutases: non-homologous isofunctional enzymes undergoing gene losses, gains and lateral transfers.
  PLoS One, 5, e13576.  
20067525 K.van Eunen, J.Bouwman, P.Daran-Lapujade, J.Postmus, A.B.Canelas, F.I.Mensonides, R.Orij, I.Tuzun, J.van den Brink, G.J.Smits, W.M.van Gulik, S.Brul, J.J.Heijnen, Winde, Mattos, C.Kettner, J.Nielsen, H.V.Westerhoff, and B.M.Bakker (2010).
Measuring enzyme activities under standardized in vivo-like conditions for systems biology.
  FEBS J, 277, 749-760.  
19284550 G.Kastenmuller, M.E.Schenk, J.Gasteiger, and H.W.Mewes (2009).
Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes.
  Genome Biol, 10, R28.  
19154134 J.Dai, L.Finci, C.Zhang, S.Lahiri, G.Zhang, E.Peisach, K.N.Allen, and D.Dunaway-Mariano (2009).
Analysis of the structural determinants underlying discrimination between substrate and solvent in beta-phosphoglucomutase catalysis.
  Biochemistry, 48, 1984-1995.
PDB code: 3fm9
19594426 P.J.Myler, R.Stacy, L.Stewart, B.L.Staker, W.C.Van Voorhis, G.Varani, and G.W.Buchko (2009).
The Seattle Structural Genomics Center for Infectious Disease (SSGCID).
  Infect Disord Drug Targets, 9, 493-506.  
17348005 L.Davies, I.P.Anderson, P.C.Turner, A.D.Shirras, H.H.Rees, and D.J.Rigden (2007).
An unsuspected ecdysteroid/steroid phosphatase activity in the key T-cell regulator, Sts-1: surprising relationship to insect ecdysteroid phosphate phosphatase.
  Proteins, 67, 720-731.  
17468884 L.Song, Z.Xu, and X.Yu (2007).
Molecular cloning and characterization of a phosphoglycerate mutase gene from Clonorchis sinensis.
  Parasitol Res, 101, 709-714.  
17576516 U.Johnsen, and P.Schönheit (2007).
Characterization of cofactor-dependent and cofactor-independent phosphoglycerate mutases from Archaea.
  Extremophiles, 11, 647-657.  
16545112 K.A.Snyder, H.J.Feldman, M.Dumontier, J.J.Salama, and C.W.Hogue (2006).
Domain-based small molecule binding site annotation.
  BMC Bioinformatics, 7, 152.  
16937252 T.K.Sigdel, R.Cilliers, P.R.Gursahaney, P.Thompson, J.A.Easton, and M.W.Crowder (2006).
Probing the adaptive response of Escherichia coli to extracellular Zn(II).
  Biometals, 19, 461-471.  
17052986 Y.Wang, L.Liu, Z.Wei, Z.Cheng, Y.Lin, and W.Gong (2006).
Seeing the process of histidine phosphorylation in human bisphosphoglycerate mutase.
  J Biol Chem, 281, 39642-39648.
PDB codes: 2a9j 2f90 2h4x 2h4z 2h52 2hhj
15735341 P.Müller, M.R.Sawaya, I.Pashkov, S.Chan, C.Nguyen, Y.Wu, L.J.Perry, and D.Eisenberg (2005).
The 1.70 angstroms X-ray crystal structure of Mycobacterium tuberculosis phosphoglycerate mutase.
  Acta Crystallogr D Biol Crystallogr, 61, 309-315.
PDB code: 1rii
15096219 D.G.Guerra, D.Vertommen, L.A.Fothergill-Gilmore, F.R.Opperdoes, and P.A.Michels (2004).
Characterization of the cofactor-independent phosphoglycerate mutase from Leishmania mexicana mexicana. Histidines that coordinate the two metal ions in the active site show different susceptibilities to irreversible chemical modification.
  Eur J Biochem, 271, 1798-1810.  
15388943 Y.Wang, Z.Cheng, L.Liu, Z.Wei, M.Wan, and W.Gong (2004).
Cloning, purification, crystallization and preliminary crystallographic analysis of human phosphoglycerate mutase.
  Acta Crystallogr D Biol Crystallogr, 60, 1893-1894.  
15258155 Y.Wang, Z.Wei, Q.Bian, Z.Cheng, M.Wan, L.Liu, and W.Gong (2004).
Crystal structure of human bisphosphoglycerate mutase.
  J Biol Chem, 279, 39132-39138.
PDB code: 1t8p
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.