PDBsum entry 1qxr

Isomerase

PDB id: 1qxr

Contents

Protein chains

187 a.a. *

Ligands

PA5 ×2

Metals

_NI ×2

Waters ×126

* Residue conservation analysis

PDB id:

1qxr

Name:

Isomerase

Title:

Crystal structure of phosphoglucose isomerase from pyrococcus furiosus in complex with 5-phosphoarabinonate

Structure:

Glucose-6-phosphate isomerase. Chain: a, b. Synonym: gpi, phosphoglucose isomerase, pgi, phosphohexose isomerase, phi. Engineered: yes

Source:

Pyrococcus furiosus. Organism_taxid: 2261. Gene: pgia or pf0196. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Dimer (from PQS)

Resolution:

1.70Å R-factor: 0.223 R-free: 0.264

Authors:

M.K.Swan,J.T.G.Solomons,C.C.Beeson,P.Hansen,P.Schonheit,C.Davies

Key ref:

M.K.Swan et al. (2003). Structural evidence for a hydride transfer mechanism of catalysis in phosphoglucose isomerase from Pyrococcus furiosus. J Biol Chem, 278, 47261-47268. PubMed id: 12970347 DOI: 10.1074/jbc.M308603200

Date:

08-Sep-03 Release date: 09-Dec-03

Protein chains

P83194  (G6PI_PYRFU) -  Glucose-6-phosphate isomerase from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 189 a.a.

Struc: 187 a.a.

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

alpha-D-glucose 6-phosphate (Bound ligand (Het Group name = PA5) matches with 82.35% similarity) = beta-D-fructose 6-phosphate

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

Added reference

DOI no: 10.1074/jbc.M308603200

J Biol Chem 278:47261-47268 (2003)

PubMed id: 12970347

Structural evidence for a hydride transfer mechanism of catalysis in phosphoglucose isomerase from Pyrococcus furiosus.

M.K.Swan, J.T.Solomons, C.C.Beeson, T.Hansen, P.Schönheit, C.Davies.

ABSTRACT

In the Euryarchaeota species Pyrococcus furiosus and Thermococcus litoralis, phosphoglucose isomerase (PGI) activity is catalyzed by an enzyme unrelated to the well known family of PGI enzymes found in prokaryotes, eukaryotes, and some archaea. We have determined the crystal structure of PGI from Pyrococcus furiosus in native form and in complex with two active site ligands, 5-phosphoarabinonate and gluconate 6-phosphate. In these structures, the metal ion, which in vivo is presumed to be Fe2+, is located in the core of the cupin fold and is immediately adjacent to the C1-C2 region of the ligands, suggesting that Fe2+ is involved in catalysis rather than serving a structural role. The active site contains a glutamate residue that contacts the substrate, but, because it is also coordinated to the metal ion, it is highly unlikely to mediate proton transfer in a cis-enediol mechanism. Consequently, we propose a hydride shift mechanism of catalysis. In this mechanism, Fe2+ is responsible for proton transfer between O1 and O2, and the hydride shift between C1 and C2 is favored by a markedly hydrophobic environment in the active site. The absence of any obvious enzymatic machinery for catalyzing ring opening of the sugar substrates suggests that pyrococcal PGI has a preference for straight chain substrates and that metabolism in extreme thermophiles may use sugars in both ring and straight chain forms.

Selected figure(s)

Figure 4.
FIG. 4. The structure of the PfPGI in complex with PAB at 1.7 Å resolution. a, stereo view showing PAB bound to the active site region of PfPGI. Monomer B of the dimer is shown, but the contacts are essentially the same in monomer A. The electron density is a F[o] - F[c] difference map calculated from the final coordinates refined in the absence of ligand and thus represents unbiased density of PAB. The side chains of those residues surrounding the ligand are shown in ball-and-stick form in which carbons are yellow, oxygens are red, and nitrogens are blue. The metal ion atom, denoted M, is shown as an orange sphere, and water molecules are shown as red spheres. Potential hydrogen bonding and coordination contacts are shown as dashed lines. The figure was produced using PyMOL (www.pymol.org) (32). b, diagram of the contacts made between PAB and the enzyme in which the distances are shown in Ångstroms. The inhibitor is colored green.

Figure 7.
FIG. 7. A catalytic mechanism for phosphoglucose isomerase from P. furiosus, shown here in the glucose 6-phosphate to fructose 6-phosphate direction. The substrate binds as the straight form of G6P, and O1 and O2 displace both water molecules from the coordination shell around Fe^2+. By withdrawing electron density from O2, Fe^2+ facilitates the movement of a proton from O2 to O1, creating a carbocation at C1. An atom of hydrogen in the form of a hydride then shifts from C2 to C1. A lone pair of electrons from O2 moves to form a double bond between O2 and C2, thus creating F6P. When the product leaves the active site, water molecules again occupy the coordination positions left vacant by O1 and O2. Note that, although Glu-97 is shown in this diagram, it does not play a direct role in this proposed mechanism of catalysis. Its role appears to be to counteract the positive charge of the inferred Fe^2+ ion and it does not mediate proton transfer.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 47261-47268) copyright 2003.

Figures were selected by an automated process.