PDBsum entry 1bq4

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Isomerase PDB id
Protein chains
234 a.a. *
SO4 ×3
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Saccharomyces cerevisiae phosphoglycerate mutase in complex with benzene hexacarboxylate
Structure: Protein (phosphoglycerate mutase 1). Chain: d, c, a, b. Synonym: phosphoglyceromutase. Ec:
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: s150-gpm::his3. Cellular_location: cytoplasm
Biol. unit: Tetramer (from PQS)
2.50Å     R-factor:   0.204     R-free:   0.254
Authors: D.J.Rigden,S.E.V.Phillips,L.A.Fothergill-Gilmore
Key ref:
D.J.Rigden et al. (1999). Polyanionic inhibitors of phosphoglycerate mutase: combined structural and biochemical analysis. J Mol Biol, 289, 691-699. PubMed id: 10369755 DOI: 10.1006/jmbi.1999.2848
20-Aug-98     Release date:   26-Aug-98    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P00950  (PMG1_YEAST) -  Phosphoglycerate mutase 1
247 a.a.
234 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   4 terms 
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     4 terms  


    Added reference    
DOI no: 10.1006/jmbi.1999.2848 J Mol Biol 289:691-699 (1999)
PubMed id: 10369755  
Polyanionic inhibitors of phosphoglycerate mutase: combined structural and biochemical analysis.
D.J.Rigden, R.A.Walter, S.E.Phillips, L.A.Fothergill-Gilmore.
The effects that the inhibitors inositol hexakisphosphate and benzene tri-, tetra- and hexacarboxylates have on the phosphoglycerate mutases from Saccharomyces cerevisiae and Schizosaccharomyces pombe have been determined. Their Kivalues have been calculated, and the ability of the inhibitors to protect the enzymes against limited proteolysis investigated. These biochemical data have been placed in a structural context by the solution of the crystal structures of S. cerevisiae phosphoglycerate mutase soaked with inositol hexakisphosphate or benzene hexacarboxylate. These large polyanionic compounds bind to the enzyme so as to block the entrance to the active-site cleft. They form multiple interactions with the enzyme, consistent with their low Kivalues, and afford good protection against limited proteolysis of the C-terminal region by thermolysin. The inositol compound is more efficacious because of its greater number of negative charges. The S. pombe phosphoglycerate mutase that is inherently lacking a comparable C-terminal region has higher Kivalues for the compounds tested. Moreover, the S. pombe enzyme is less sensititive to proteolysis, and the presence or absence of the inhibitor molecules has little effect on susceptibility to proteolysis.
  Selected figure(s)  
Figure 1.
Figure 1. (a) A diagram of the S. cerevisiae tetramer. The subunits A to D are labelled, and subunit A is shaded black. The catalytic-site histidine residues, His8 and His181, are drawn in ball and stick representation and labelled in each subunit. The final C-terminal residues for which electron density was seen are indicated by asterisk symbols. (b) Electron density, in final averaged 2Fo - Fc maps, for IHP contoured at 2s. Interactions with protein are shown as dotted lines. Atom colouring: black, carbon; red, oxygen; blue, nitrogen; magenta, phosphorus. Certain atoms of the inhibitor are labelled to indicate the atom nomenclature. The Figure was drawn with Bobscript (Kraulis, 1991; Esnouf, 1999). The initial averaged maps calculated from data derived from IHP-soaked crystals showed significant positive difference density in the active sites of subunits A and D. Contoured at a level of 3s, six large peaks could be seen in each of these active sites. Using an energy-minimised structure of IHP, containing a chair-form inositol ring, good fits between the six phospho groups and these peaks could be obtained in both subunits. The two sulphate molecules per active site seen in the native structure were visible in the other two subunits. (c) Electron density, in final averaged 2Fo - Fc maps, for BHC contoured at 1s. In the BHC soak maps significant positive difference density was seen only in the active site of subunit A. This had a flat disc shape into which a model of BHC could be satisfac- torily inserted. Only the sulphate ion bound near the active-site histidine residues was visible in subunits B, C and D. From these starting points, several rounds of positional and B-factor refinement using X-PLOR and manual rebuilding using O (Jones et al., 1991) were carried out. The B-factor refinement was done by assigning one value each for the side-chain and main-chain of each protein residue, and one value for each sulphate ion. For IHP, one value was assigned to the atoms of the inositol ring and one each for the six phospho groups. Similarly, for BHC the benzene ring and the six carboxylate groups were each assigned a B-factor. The IHP was modelled as being fully ionised. In the case of BHC, the neighbouring carboxylate groups would be expected to affect each other. For this reason, BHC was modelled as semi-ionised, i.e. with three intramolecular hydrogen bonds. This decision was also justified by the slightly improved geometry and B-factors of the semi-ionised BHC model compared to a fully ionised one.
Figure 3.
Figure 3. Comparison of the binding modes of IHP (cyan) and BHC (yellow). A solvent-accessible molecular surface coloured by elec- trostatic potential (positive is blue, negative is red) is shown for the main body of the protein. The helix in the C-terminal region from resi- dues 230-242 (the first part visible in electron density maps, the latter part strongly predicted by the PHD program (Rost & Sander, 1993, 1994; Rost et al., 1994) is shown in magenta. Val240, before which thermolysin cuts, is highlighted in green. The Figure was generated using GRASP (Nicholls et al., 1991).
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 289, 691-699) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19015259 H.Li, and G.Jogl (2009).
Structural and Biochemical Studies of TIGAR (TP53-induced Glycolysis and Apoptosis Regulator).
  J Biol Chem, 284, 1748-1754.  
19919089 S.Das, A.Kokardekar, and C.M.Breneman (2009).
Rapid comparison of protein binding site surfaces with property encoded shape distributions.
  J Chem Inf Model, 49, 2863-2872.  
17579775 M.J.Evans, G.M.Morris, J.Wu, A.J.Olson, E.J.Sorensen, and B.F.Cravatt (2007).
Mechanistic and structural requirements for active site labeling of phosphoglycerate mutase by spiroepoxides.
  Mol Biosyst, 3, 495-506.  
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.  
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
16200062 M.J.Evans, A.Saghatelian, E.J.Sorensen, and B.F.Cravatt (2005).
Target discovery in small-molecule cell-based screens by in situ proteome reactivity profiling.
  Nat Biotechnol, 23, 1303-1307.  
15162493 A.Berchanski, B.Shapira, and M.Eisenstein (2004).
Hydrophobic complementarity in protein-protein docking.
  Proteins, 56, 130-142.  
14635124 A.Berchanski, and M.Eisenstein (2003).
Construction of molecular assemblies via docking: modeling of tetramers with D2 symmetry.
  Proteins, 53, 817-829.  
11114510 H.Erlandsen, E.E.Abola, and R.C.Stevens (2000).
Combining structural genomics and enzymology: completing the picture in metabolic pathways and enzyme active sites.
  Curr Opin Struct Biol, 10, 719-730.  
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