PDBsum entry: 1e59

Isomerase

PDB id: 1e59

Contents

Protein chain

239 a.a. *

Ligands

VO3

Metals

_CL

Waters ×264

* Residue conservation analysis

PDB id:

1e59

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)

Resolution:

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

Date:

19-Jul-00 Release date: 05-Feb-02

Protein chain

P62707  (GPMA_ECOLI) -  2,3-bisphosphoglycerate-dependent phosphoglycerate mutase

Seq: 250 a.a.

Struc: 239 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: cytoplasm (1 term)
• Biological process: metabolic process (2 terms)
• Biochemical function: catalytic activity (6 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.

ABSTRACT

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.