PDBsum entry 1x7n

Isomerase

PDB id: 1x7n

Contents

Protein chain

189 a.a. *

Ligands

PA5

Metals

_MN

Waters ×205

* Residue conservation analysis

PDB id:

1x7n

Name:

Isomerase

Title:

The crystal structure of pyrococcus furiosus phosphoglucose isomerase with bound 5-phospho-d-arabinonate and manganese

Structure:

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

Source:

Pyrococcus furiosus. Organism_taxid: 2261. Gene: pgia. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.89Å R-factor: 0.144 R-free: 0.212

Authors:

J.M.Berrisford,J.Akerboom,S.Brouns,S.E.Sedelnikova,A.P.Turnbull,J.Van Der Oost,L.Salmon,R.Hardre,I.A.Murray,G.M.Blackburn,D.W.Rice, P.J.Baker

Key ref:

J.M.Berrisford et al. (2004). The structures of inhibitor complexes of Pyrococcus furiosus phosphoglucose isomerase provide insights into substrate binding and catalysis. J Mol Biol, 343, 649-657. PubMed id: 15465052 DOI: 10.1016/j.jmb.2004.08.061

Date:

16-Aug-04 Release date: 12-Oct-04

Protein chain

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

Seq: 189 a.a.

Struc: 189 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: 10.1016/j.jmb.2004.08.061

J Mol Biol 343:649-657 (2004)

PubMed id: 15465052

The structures of inhibitor complexes of Pyrococcus furiosus phosphoglucose isomerase provide insights into substrate binding and catalysis.

J.M.Berrisford, J.Akerboom, S.Brouns, S.E.Sedelnikova, A.P.Turnbull, J.van der Oost, L.Salmon, R.Hardré, I.A.Murray, G.M.Blackburn, D.W.Rice, P.J.Baker.

ABSTRACT

Pyrococcus furiosus phosphoglucose isomerase (PfPGI) is a metal-containing enzyme that catalyses the interconversion of glucose 6-phosphate (G6P) and fructose 6-phosphate (F6P). The recent structure of PfPGI has confirmed the hypothesis that the enzyme belongs to the cupin superfamily and identified the position of the active site. This fold is distinct from the alphabetaalpha sandwich fold commonly seen in phosphoglucose isomerases (PGIs) that are found in bacteria, eukaryotes and some archaea. Whilst the mechanism of the latter family is thought to proceed through a cis-enediol intermediate, analysis of the structure of PfPGI in the presence of inhibitors has led to the suggestion that the mechanism of this enzyme involves the metal-dependent direct transfer of a hydride between C1 and C2 atoms of the substrate. To gain further insight in the reaction mechanism of PfPGI, the structures of the free enzyme and the complexes with the inhibitor, 5-phospho-d-arabinonate (5PAA) in the presence and absence of metal have been determined. Comparison of these structures with those of equivalent complexes of the eukaryotic PGIs reveals similarities at the active site in the disposition of possible catalytic residues. These include the presence of a glutamic acid residue, Glu97 in PfPGI, which occupies the same position relative to the inhibitor as that of the glutamate that is thought to function as the catalytic base in the eukaryal-type PGIs. These similarities suggest that aspects of the catalytic mechanisms of these two structurally unrelated PGIs may be similar and based on an enediol intermediate.

Selected figure(s)

Figure 1.
Figure 1. A schematic representation of the PfPGI dimer viewed down the 2-fold axis. One subunit of the dimer is shown in blue and red (strands and helices, respectively) and the other in orange. The N-terminal strand can be seen to interact with the adjacent symmetry-related strand from the other subunit in the biological dimer.

Figure 2.
Figure 2. A stereo diagram of the active site of PfPGI showing the 2F[O] -F[C] map, contoured at 1s (blue) and 4s (red), electron density assigned to 5PAA in the PfPGI/5PAA metal-free complex and its interaction with Glu97. A blue line shows the potential hydrogen bond between the carboxyl of Glu97 and the carboxyl of 5PAA.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 343, 649-657) copyright 2004.

Figures were selected by an automated process.