PDBsum entry: 1e58

Isomerase

PDB id: 1e58

Contents

Protein chain

247 a.a. *

Ligands

SO4 ×2

Metals

_CL

Waters ×425

* Residue conservation analysis

PDB id:

1e58

Name:

Isomerase

Title:

E.Coli cofactor-dependent phosphoglycerate mutase

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.

Resolution:

1.25Å R-factor: 0.120 R-free: 0.168

Authors:

C.S.Bond,W.N.Hunter

Key ref:

C.S.Bond et al. (2001). High resolution structure of the phosphohistidine-activated form of Escherichia coli cofactor-dependent phosphoglycerate mutase. J Biol Chem, 276, 3247-3253. PubMed id: 11038361 DOI: 10.1074/jbc.M007318200

Date:

19-Jul-00 Release date: 20-Mar-01

Protein chain

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

Seq: 250 a.a.

Struc: 247 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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 (4 terms)

Added reference

DOI no: 10.1074/jbc.M007318200

J Biol Chem 276:3247-3253 (2001)

PubMed id: 11038361

High resolution structure of the phosphohistidine-activated form of Escherichia coli cofactor-dependent phosphoglycerate mutase.

C.S.Bond, M.F.White, W.N.Hunter.

ABSTRACT

The active conformation of the dimeric cofactor-dependent phosphoglycerate mutase (dPGM) from Escherichia coli has been elucidated by crystallographic methods to a resolution of 1.25 A (R-factor 0.121; R-free 0.168). The active site residue His(10), central in the catalytic mechanism of dPGM, is present as a phosphohistidine with occupancy of 0.28. The structural changes on histidine phosphorylation highlight various features that are significant in the catalytic mechanism. The C-terminal 10-residue tail, which is not observed in previous dPGM structures, is well ordered and interacts with residues implicated in substrate binding; the displacement of a loop adjacent to the active histidine brings previously overlooked residues into positions where they may directly influence catalysis. E. coli dPGM, like the mammalian dPGMs, is a dimer, whereas previous structural work has concentrated on monomeric and tetrameric yeast forms. We can now analyze the sequence differences that cause this variation of quaternary structure.

Selected figure(s)

Figure 4.
Fig. 4. a, the surface of dPGM ( semitransparent gray) is cut away to reveal the network of hydrogen bonds linking the catalytic machinery and substrate binding residues to the active site entrance. The sulfate binding sites E1 and E2 are labeled. GRASP (38), Molscript (32), GL_render (L. Esser and J. Deisenhofer, personal communication), and POVRAY were used to prepare this figure. b, the chemical environment of the phosphohistidine. Red spheres represent oxygens, blue spheres represent nitrogens, and yellow spheres represent sulfurs. The phosphohistidine is represented by green bonds, and sulfate is represented by yellow. Residues are represented as follows: blue, basic; red, acidic; gray, apolar; magenta, polar. Hydrogen bonds are shown as cyan dashed lines.

Figure 5.
Fig. 5. The C-terminal tail of E. coli dPGM with 1 2F[o] F[c] [calc] electron density (blue). Hydrogen bonding interactions with residues elsewhere on the structure are labeled.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 3247-3253) copyright 2001.

Figures were selected by the author.