PDBsum entry 1x9h

Isomerase

PDB id: 1x9h

Contents

Protein chains

301 a.a.

Ligands

SO4 ×5

F6R ×2

GOL ×4

Waters ×403

References listed in PDB file

Key reference

Title

Structural basis for phosphomannose isomerase activity in phosphoglucose isomerase from pyrobaculum aerophilum: a subtle difference between distantly related enzymes.

Authors

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

Ref.

Biochemistry, 2004, 43, 14088-14095. [DOI no: 10.1021/bi048608y]

PubMed id

15518558

Abstract

The crystal structure of a dual-specificity phosphoglucose/phosphomannose isomerase from the crenarchaeon Pyrobaculum aerophilum (PaPGI/PMI) has been determined in complex with glucose 6-phosphate at 1.16 A resolution and with fructose 6-phosphate at 1.5 A resolution. Subsequent modeling of mannose 6-phosphate (M6P) into the active site of the enzyme shows that the PMI activity of this enzyme may be due to the additional space imparted by a threonine. In PGIs from bacterial and eukaryotic sources, which cannot use M6P as a substrate, the equivalent residue is a glutamine. The increased space may permit rotation of the C2-C3 bond in M6P to facilitate abstraction of a proton from C2 by Glu203 and, after a further C2-C3 rotation of the resulting cis-enediolate, re-donation of a proton to C1 by the same residue. A proline residue (in place of a glycine in PGI) may also promote PMI activity by positioning the C1-O1 region of M6P. Thus, the PMI reaction in PaPGI/PMI probably uses a cis-enediol mechanism of catalysis, and this activity appears to arise from a subtle difference in the architecture of the enzyme, compared to bacterial and eukaryotic PGIs.

Secondary reference #1

Title

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.

Authors

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

Ref.

J Biol Chem, 2004, 279, 39838-39845. [DOI no: 10.1074/jbc.M406855200]

PubMed id

15252053

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a percentage match of 93%.

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 reproduced from the cited reference with permission from the ASBMB

Secondary reference #2

Title

Crystallization and preliminary X-Ray diffraction analysis of phosphoglucose/phosphomannose isomerase from pyrobaculum aerophilum.

Authors

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

Ref.

Acta Crystallogr D Biol Crystallogr, 2004, 60, 1481-1483. [DOI no: 10.1107/S0907444904014052]

PubMed id

15272183

Figure 2.
Figure 2 Crystals of phosphoglucose isomerase/phosphomannose isomerase from P. aerophilum grown using the hanging-drop method with polyethylene glycol 8000 as a precipitant. Their approximate dimensions are 0.20 × 0.15 × 0.05 mm.

Figure 3.
Figure 3 A diffraction image collected from crystals of PGI/PMI from P. aerophilum. The edge of the plate corresponds to 1.7 Å resolution.

The above figures are reproduced from the cited reference with permission from the IUCr