PDBsum entry 1tzc

Isomerase

PDB id: 1tzc

Contents

Protein chains

301 a.a. *

Ligands

SO4 ×5

PA5 ×2

GOL ×2

Waters ×439

* Residue conservation analysis

PDB id:

1tzc

Name:

Isomerase

Title:

Crystal structure of phosphoglucose/phosphomannose isomerase from pyrobaculum aerophilum in complex with 5-phosphoarabinonate

Structure:

Glucose-6-phosphate isomerase, conjectural. Chain: a, b. Engineered: yes

Source:

Pyrobaculum aerophilum. Organism_taxid: 178306. Strain: str. Im2. Gene: pae1610. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.45Å R-factor: 0.170 R-free: 0.192

Authors:

M.K.Swan,T.Hansen,P.Schoenheit,C.Davies

Key ref:

M.K.Swan et al. (2004). A novel phosphoglucose isomerase (PGI)/phosphomannose isomerase from the crenarchaeon Pyrobaculum aerophilum is a member of the PGI superfamily: structural evidence at 1.16-A resolution. J Biol Chem, 279, 39838-39845. PubMed id: 15252053 DOI: 10.1074/jbc.M406855200

Date:

09-Jul-04 Release date: 20-Jul-04

Protein chains

Q8ZWV0  (PGMI_PYRAE) -  Bifunctional phosphoglucose/phosphomannose isomerase from Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2)

Seq: 302 a.a.

Struc: 301 a.a.

Enzyme reactions

• Enzyme class 1: E.C.5.3.1.8 - mannose-6-phosphate isomerase.
• Pathway: GDP-L-Fucose and GDP-mannose Biosynthesis
• Reaction: D-mannose 6-phosphate = D-fructose 6-phosphate

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

• Cofactor: Zn(2+)
• Enzyme class 2: 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

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1074/jbc.M406855200

J Biol Chem 279:39838-39845 (2004)

PubMed id: 15252053

A novel phosphoglucose isomerase (PGI)/phosphomannose isomerase from the crenarchaeon Pyrobaculum aerophilum is a member of the PGI superfamily: structural evidence at 1.16-A resolution.

M.K.Swan, T.Hansen, P.Schönheit, C.Davies.

ABSTRACT

The crystal structure of a dual specificity phosphoglucose isomerase (PGI)/phosphomannose isomerase from Pyrobaculum aerophilum (PaPGI/PMI) has been determined in native form at 1.16-A resolution and in complex with the enzyme inhibitor 5-phosphoarabinonate at 1.45-A resolution. The similarity of its fold, with the inner core structure of PGIs from eubacterial and eukaryotic sources, confirms this enzyme as a member of the PGI superfamily. The almost total conservation of amino acids in the active site, including the glutamate base catalyst, shows that PaPGI/PMI uses the same catalytic mechanisms for both ring opening and isomerization for the interconversion of glucose 6-phosphate (Glc-6-P) to fructose 6-phosphate (Fru-6-P). The lack of structural differences between native and inhibitor-bound enzymes suggests this activity occurs without any of the conformational changes that are the hallmark of the well characterized PGI family. The lack of a suitable second base in the active site of PaPGI/PMI argues against a PMI mechanism involving a trans-enediol intermediate. Instead, PMI activity may be the result of additional space in the active site imparted by a threonine, in place of a glutamine in other PGI enzymes, which could permit rotation of the C-2-C-3 bond of mannose 6-phosphate.

Selected figure(s)

Figure 1.
FIG. 1. Fischer projections of the three substrates for PGI/PMI from P. aerophilum, Glc-6-P, Fru-6-P, and Man-6-P, as well as the PGI inhibitor used in this study, PAB.

Figure 6.
FIG. 6. The structure of PGI/PMI from P. aerophilum in complex with PAB at 1.45-Å resolution. a, a stereo view showing PAB bound to the active site region. Shown is the active site from subunit B but the contacts are essentially identical in subunit A. The electron density shown around the inhibitor in blue is an unbiased (|F[o]| -|F[c]|) difference map, calculated from the final coordinates refined in the absence of ligand. The side chains of those residues surrounding the ligand are shown in bond form in which carbon, oxygen, and nitrogen are yellow, red, and blue, respectively, except for His-219 which is colored orange to indicate it is part of subunit A. PAB is colored with green bonds. Water molecules are shown as red spheres. Important contacts are shown as dashed lines. The figure was produced using PYMOL (40). b, a diagram of the distances (in Å) between atoms of PAB (colored green) and of amino acids in the active site (colored black).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 39838-39845) copyright 2004.

Figures were selected by an automated process.