PDBsum entry 2b5v

Oxidoreductase

PDB id: 2b5v

Contents

Protein chain

355 a.a.

Ligands

NAP

Waters ×146

References listed in PDB file

Key reference

Title

Analysis of protein solvent interactions in glucose dehydrogenase from the extreme halophile haloferax mediterranei.

Authors

K.L.Britton, P.J.Baker, M.Fisher, S.Ruzheinikov, D.J.Gilmour, M.J.Bonete, J.Ferrer, C.Pire, J.Esclapez, D.W.Rice.

Ref.

Proc Natl Acad Sci U S A, 2006, 103, 4846-4851. [DOI no: 10.1073/pnas.0508854103]

PubMed id

16551747

Abstract

The structure of glucose dehydrogenase from the extreme halophile Haloferax mediterranei has been solved at 1.6-A resolution under crystallization conditions which closely mimic the "in vivo" intracellular environment. The decoration of the enzyme's surface with acidic residues is only partially neutralized by bound potassium counterions, which also appear to play a role in substrate binding. The surface shows the expected reduction in hydrophobic character, surprisingly not from changes associated with the loss of exposed hydrophobic residues but rather arising from a loss of lysines consistent with the genome wide-reduction of this residue in extreme halophiles. The structure reveals a highly ordered, multilayered solvation shell that can be seen to be organized into one dominant network covering much of the exposed surface accessible area to an extent not seen in almost any other protein structure solved. This finding is consistent with the requirement of the enzyme to form a protective shell in a dehydrating environment.

Figure 1.
Fig. 1. The Hm GlcDH structure. (A) The molecular surface of the dimer of Hm GlcDH to show the electrostatic potential calculated at 0 M salt concentration, prepared by using the program GRASP (17, 18). Red corresponds to a surface potential less than –10 kcal(mol·electron)^–1; blue corresponds to a potential greater than +10 kcal(mol·electron)^–1. (B) Stereo view of the location of two of the potassium ions (lilac spheres). Individual residues are shown in atom colors if they lie within 3.5 Å of each potassium ion. The remainder of the polypeptide chain is shown as an alpha carbon trace, whereas water molecules are depicted as red spheres. The bound cofactor, NADP, can be seen to lie close to a cation cluster involving two bound counterions. (C) A close up stereo view, using standard atom coloring for the protein, to show two fused pentagonal rings suspended above the hydrophobic chain of proline 21 and anchored by hydrogen-bonding interactions to the surrounding water molecules and polar protein atoms.

Figure 2.
Fig. 2. Comparison of the water structure around Hm GlcDH to that surrounding other proteins. (A) The dependence of the water to protein residue ratio (ordinate) against the resolution in Š(abscissa) for the structure determinations of all proteins solved between 3.5- and 0.5-Šresolution. Only the points in the lower 5% and above 95% are shown. The lower dashes, crosses, and upper dashes mark the 10, 50, and 90% boundaries for the data, respectively. The data point, corresponding to the Hm GlcDH, is shown by a large diamond. (B) A least squares line drawn through points that represent the B factors of the water structure normalized by the average B factor of the protein atoms (ordinate) plotted against the ratio of the number of water molecules to the number of protein atoms in a given structure (abscissa). The plot covers the 263 structures determined in the resolution range 1.55–1.65 Šfor proteins that are of equivalent or greater size to Hm GlcDH. Each structure is represented on the plot by a diamond, except for the GlcDH structure, which is shown as a square. (C) A comparison of the distribution of the distance of the water molecules from the protein surface between the Hm GlcDH structure (black) and that of the average of the subset of 263 structures (hatched) as defined in B. The histogram shows the number of water molecules per residue that fall into specific distance bands from the protein surface. The abscissa is labeled with the midpoint of each range. Waters with partial occupancy were not included in the analysis.

Secondary reference #1

Title

Crystallization and preliminary X-Ray analysis of glucose dehydrogenase from haloferax mediterranei.

Authors

J.Ferrer, M.Fisher, J.Burke, S.E.Sedelnikova, P.J.Baker, D.J.Gilmour, M.J.Bonete, C.Pire, J.Esclapez, D.W.Rice.

Ref.

Acta Crystallogr D Biol Crystallogr, 2001, 57, 1887-1889. [DOI no: 10.1107/S0907444901015189]

PubMed id

11717506

Figure 1.
Figure 1 X-ray diffraction images recorded at room temperature on a MAR345 image plate of the form I (a) and form II (b) GlcDH crystals. The diffraction limit to the edge of the images is 3.2 and 1.8 Å, respectively.

The above figure is reproduced from the cited reference with permission from the IUCr