PDBsum entry: 1o99

Isomerase

PDB id: 1o99

Contents

Protein chain

510 a.a. *

Ligands

2PG

SO4 ×6

Metals

_MN

Waters ×120

* Residue conservation analysis

PDB id:

1o99

Name:

Isomerase

Title:

Crystal structure of the s62a mutant of phosphoglycerate mutase from bacillus stearothermophilus complexed with 2-phosphoglycerate

Structure:

2,3-bisphosphoglycerate-independent phosphoglycerate mutase. Chain: a. Synonym: phosphoglycerate mutase. Engineered: yes. Mutation: yes

Source:

Bacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.65Å R-factor: 0.199 R-free: 0.242

Authors:

D.J.Rigden,E.Lamani,J.E.Littlejohn,M.J.Jedrzejas

Key ref:

D.J.Rigden et al. (2003). Insights into the catalytic mechanism of cofactor-independent phosphoglycerate mutase from X-ray crystallography, simulated dynamics and molecular modeling. J Mol Biol, 328, 909-920. PubMed id: 12729763 DOI: 10.1016/S0022-2836(03)00350-4

Date:

11-Dec-02 Release date: 23-Dec-02

Protein chain

Q9X519  (GPMI_GEOSE) -  2,3-bisphosphoglycerate-independent phosphoglycerate mutase

Seq: 511 a.a.

Struc: 510 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

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

2-phospho-D-glycerate (Bound ligand (Het Group name = 2PG) corresponds exactly) = 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 (3 terms)
• Biochemical function: catalytic activity (5 terms)

Added reference

DOI no: 10.1016/S0022-2836(03)00350-4

J Mol Biol 328:909-920 (2003)

PubMed id: 12729763

Insights into the catalytic mechanism of cofactor-independent phosphoglycerate mutase from X-ray crystallography, simulated dynamics and molecular modeling.

D.J.Rigden, E.Lamani, L.V.Mello, J.E.Littlejohn, M.J.Jedrzejas.

ABSTRACT

Phosphoglycerate mutases catalyze the isomerization of 2 and 3-phosphoglycerates, and are essential for glucose metabolism in most organisms. Here, we further characterize the 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (iPGM) from Bacillus stearothermophilus by determination of a high-resolution (1.4A) crystal structure of the wild-type enzyme and the crystal structure of its S62A mutant. The mutant structure surprisingly showed the replacement of one of the two catalytically essential manganese ions with a water molecule, offering an additional possible explanation for its lack of catalytic activity. Crystal structures invariably show substrate phosphoglycerate to be entirely buried in a deep cleft between the two iPGM domains. Flexibility analyses were therefore employed to reveal the likely route of substrate access to the catalytic site through an aperture created in the enzyme's surface during certain stages of the catalytic process. Several conserved residues lining this aperture may contribute to orientation of the substrate as it enters. Factors responsible for the retention of glycerate within the phosphoenzyme structure in the proposed mechanism are identified by molecular modeling of the glycerate complex of the phosphoenzyme. Taken together, these results allow for a better understanding of the mechanism of action of iPGMs. Many of the results are relevant to a series of evolutionarily related enzymes. These studies will facilitate the development of iPGM inhibitors which, due to the demonstrated importance of this enzyme in many bacteria, would be of great potential clinical significance.

Selected figure(s)

Figure 5.
Figure 5. Comparison of crystal (white) and eigenvector 3 maximum projection (purple) structures showing the greater distance between the two domains in the latter. Substrate 2PGA (cyan) and the manganese ions (larger violet isolated spheres) are shown for orientation purposes. The Figure was made with PYMOL.

Figure 7.
Figure 7. Stereo view of the catalytic site of the phospho-iPGM-glycerate model. Glycerate is shown with white carbon and orange oxygen atoms. The aperture through which the substrate enters is towards the top of the structure, in this orientation, between residues Arg153 and Glu335. The Figure was made with PYMOL.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 328, 909-920) copyright 2003.

Figures were selected by an automated process.