PDBsum entry: 1bq3

Isomerase

PDB id: 1bq3

Contents

Protein chains

234 a.a. *

Ligands

SO4 ×4

IHP ×2

* Residue conservation analysis

PDB id:

1bq3

Name:

Isomerase

Title:

Saccharomyces cerevisiae phosphoglycerate mutase in complex with inositol hexakisphosphate

Structure:

Protein (phosphoglycerate mutase 1). Chain: d, c, a, b. Synonym: phosphoglyceromutase. Ec: 5.4.2.1

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: s150-gpm::his3. Cellular_location: cytoplasm

Biol. unit:

Tetramer (from PQS)

Resolution:

2.70Å R-factor: 0.200 R-free: 0.240

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

Date:

20-Aug-98 Release date: 26-Aug-98

Protein chains

P00950  (PMG1_YEAST) -  Phosphoglycerate mutase 1

Seq: 247 a.a.

Struc: 234 a.a.

Enzyme reactions

• Enzyme class: E.C.5.4.2.1 - Phosphoglycerate mutase.
• Reaction: 2-phospho-D-glycerate = 3-phospho-D-glycerate

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

 Gene Ontology (GO) functional annotation 

• Cellular component: mitochondrion (2 terms)
• Biological process: metabolic process (3 terms)
• Biochemical function: catalytic activity (5 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.

ABSTRACT

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.