PDBsum entry: 1qbi

Oxidoreductase

PDB id: 1qbi

Contents

Protein chains

434 a.a. *

Ligands

GOL

Metals

_CA ×6

_PT ×2

Waters ×1233

* Residue conservation analysis

PDB id:

1qbi

Name:

Oxidoreductase

Title:

Soluble quinoprotein glucose dehydrogenase from acinetobacte calcoaceticus

Structure:

Soluble quinoprotein glucose dehydrogenase. Chain: a, b. Engineered: yes

Source:

Acinetobacter calcoaceticus. Organism_taxid: 471. Cellular_location: periplasm. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

1.72Å R-factor: 0.166 R-free: 0.208

Authors:

A.Oubrie,H.J.Rozeboom,K.H.Kalk,J.A.Duine,B.W.Dijkstra

Key ref:

A.Oubrie et al. (1999). The 1.7 A crystal structure of the apo form of the soluble quinoprotein glucose dehydrogenase from Acinetobacter calcoaceticus reveals a novel internal conserved sequence repeat. J Mol Biol, 289, 319-333. PubMed id: 10366508 DOI: 10.1006/jmbi.1999.2766

Date:

22-Apr-99 Release date: 25-Feb-00

Protein chains

P13650  (DHGB_ACICA) -  Quinoprotein glucose dehydrogenase B

Seq: 478 a.a.

Struc: 434 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.5.2 - Quinoprotein glucose dehydrogenase.
• Reaction: D-glucose + ubiquinone = D-glucono-1,5-lactone + ubiquinol

D-glucose (Bound ligand (Het Group name = GOL) matches with 50.00% similarity) + ubiquinone = D-glucono-1,5-lactone + ubiquinol

• Cofactor: Calcium or magnesium; Pyrroloquinoline quinone

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

 Gene Ontology (GO) functional annotation 

• Biological process: oxidation-reduction process (2 terms)
• Biochemical function: catalytic activity (6 terms)

reference

DOI no: 10.1006/jmbi.1999.2766

J Mol Biol 289:319-333 (1999)

PubMed id: 10366508

The 1.7 A crystal structure of the apo form of the soluble quinoprotein glucose dehydrogenase from Acinetobacter calcoaceticus reveals a novel internal conserved sequence repeat.

A.Oubrie, H.J.Rozeboom, K.H.Kalk, J.A.Duine, B.W.Dijkstra.

ABSTRACT

The crystal structure of a dimeric apo form of the soluble quinoprotein glucose dehydrogenase (s-GDH) from Acinetobacter calcoaceticus has been solved by multiple isomorphous replacement followed by density modification, and was subsequently refined at 1. 72 A resolution to a final crystallographic R-factor of 16.5% and free R-factor of 20.8% [corrected]. The s-GDH monomer has a beta-propeller fold consisting of six four-stranded anti-parallel beta-sheets aligned around a pseudo 6-fold symmetry axis. The enzyme binds three calcium ions per monomer, two of which are located in the dimer interface. The third is bound in the putative active site, where it may bind and functionalize the pyrroloquinoline quinone (PQQ) cofactor. A data base search unexpectedly showed that four uncharacterized protein sequences are homologous to s-GDH with many residues in the putative active site absolutely conserved. This indicates that these homologs may have a similar structure and that they may catalyze similar PQQ-dependent reactions.A structure-based sequence alignment of the six four-stranded beta-sheets in s-GDH's beta-propeller fold shows an internally conserved sequence repeat that gives rise to two distinct conserved structural motifs. The first structural motif is found at the corner of the short beta-turn between the inner two beta-strands of the beta-sheets, where an Asp side-chain points back into the beta-sheet to form a hydrogen-bond with the OH/NH of a Tyr/Trp side-chain in the same beta-sheet. The second motif involves an Arg/Lys side-chain in the C beta-strand of one beta-sheet, which forms a bidentate salt-bridge with an Asp/Glu in the CD loop of the next beta-sheet. These intra and inter-beta-sheet hydrogen-bonds are likely to contribute to the stability of the s-GDH beta-propeller fold.

Selected figure(s)

Figure 5.
Figure 5. Stereo view of the Ca 2+ -sites of s-GDH in ball and stick representation: (a) Ca 2+ -binding in the putative active site; (b) and (c) in the dimerization inter- face. Carbon, nitrogen, oxygen, and calcium atoms are shown in white, blue, red, and yellow, respectively. Hydrogen-bonding interactions are marked with a broken line.

Figure 6.
Figure 6. Molecular surface drawing of one s-GDH monomer created using the program GRASP (Nicholls & Honig, 1993), showing the large negatively charged patch in the dimerization interface. Neutral, positively and negatively charged patches are shown in gray, blue, and red, respectively.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 289, 319-333) copyright 1999.

Figures were selected by the author.