PDBsum entry 1hm5

Isomerase

PDB id: 1hm5

Contents

Protein chains

556 a.a. *

Waters ×926

* Residue conservation analysis

PDB id:

1hm5

Name:

Isomerase

Title:

Crystal structure analysis of the rabbit d-glucose 6-phosphate isomerase (no ligand bound)

Structure:

Phosphoglucose isomerase. Chain: a, b. Synonym: d-glucose 6-phosphate isomerase. Ec: 5.3.1.9

Source:

Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986. Other_details: rabbit skeletal muscle tissue

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.183 R-free: 0.212

Authors:

D.A.Arsenieva,C.J.Jeffery,R.Hardre,L.Salmon

Key ref:

D.Arsenieva and C.J.Jeffery (2002). Conformational changes in phosphoglucose isomerase induced by ligand binding. J Mol Biol, 323, 77-84. PubMed id: 12368100 DOI: 10.1016/S0022-2836(02)00892-6

Date:

04-Dec-00 Release date: 27-Sep-02

Protein chains

Q9N1E2  (G6PI_RABIT) -  Glucose-6-phosphate isomerase from Oryctolagus cuniculus

Seq: 558 a.a.

Struc: 556 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.5.3.1.9 - glucose-6-phosphate isomerase.
• Reaction: alpha-D-glucose 6-phosphate = beta-D-fructose 6-phosphate

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

Added reference

DOI no: 10.1016/S0022-2836(02)00892-6

J Mol Biol 323:77-84 (2002)

PubMed id: 12368100

Conformational changes in phosphoglucose isomerase induced by ligand binding.

D.Arsenieva, C.J.Jeffery.

ABSTRACT

Phosphoglucose isomerase (PGI; EC 5.3.1.9) is the second enzyme in glycolysis, where it catalyzes the isomerization of D-glucose-6-phosphate to D-fructose-6-phosphate. It is the same protein as autocrine motility factor, differentiation and maturation mediator, and neuroleukin. Here, we report a new X-ray crystal structure of rabbit PGI (rPGI) without ligands bound in its active site. The structure was solved at 1.8A resolution by isomorphous phasing with a previously solved X-ray crystal structure of the rPGI dimer containing 6-phosphogluconate in its active site. Comparison of the new structure to previously reported structures enables identification of conformational changes that occur during binding of substrate or inhibitor molecules. Ligand binding causes an induced fit of regions containing amino acid residues 209-215, 245-259 and 385-389. This conformational change differs from the change previously reported to occur between the ring-opening and isomerization steps, in which the helix containing residues 513-521 moves toward the bound substrate. Differences between the liganded and unliganded structures are limited to the region within and close to the active-site pocket.

Selected figure(s)

Figure 1.
Figure 1. Conformational changes in the active site of rPGI during catalysis. The unliganded structure is shown in blue. The enzyme in complex with F6P is shown in green. The complex with 5PAH is shown in red. Ordered water molecules are indicated by a number accompanied by the letter W. (a) Active site of unliganded rPGI. An electron density map calculated with coefficients |2F[o] -F[c]| is shown with a 1s contour level (gray). The active site is filled with ordered water molecules. (b) Movements in the active site induced by substrate binding. A partial alpha carbon trace indicates regions that move upon F6P binding. (Alpha carbon atoms of amino acid residues 1-555 were superposed, only the regions that move are shown.) The F6P ligand is in dark green, and water molecules displaced by F6P are labeled in blue. (c) Conformational changes in the active site between the ring opening and isomerization steps. An alpha carbon trace indicates the helix containing amino acid residues 513-521 that shifts after the ring opening step but before the isomerization step. That movement is different from the movement of regions induced by F6P binding. This Figure and Figure 2 were made using the program BOBSCRIPT.42

Figure 3.
Figure 3. Surface shape and potential of rPGI with and without bound ligands. The molecular surface shape and charge distribution do not change significantly upon ligand binding, except in the region of the active site. The protein is oriented similarly in all four panels. The surface is colored according to charge: positively charged groups are blue, negatively charged groups are red, and uncharged groups are gray. In (a), unliganded rPGI, the black rectangle indicates the active-site pocket. The active site is filled in (b) the rPGI/F6P complex, (c) the rPGI/5PAH complex, and (d) the rPGI/6PGA complex.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 323, 77-84) copyright 2002.

Figures were selected by the author.