2VWQ

Haloferax mediterranei glucose dehydrogenase in complex with NADP and Zn.

Summary for 2VWQ

• Entry DOI: 10.2210/pdb2vwq/pdb
• Related: 2B5V 2B5W 2VWG 2VWH 2VWP
• Descriptor: GLUCOSE DEHYDROGENASE, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, ZINC ION, ... (4 entities in total)
• Functional Keywords: oxidoreductase, glucose dehydrogenase, zinc dependent medium chain alcohol dehydrogenase family, alcohol dehydrogenase
• Biological source: HALOFERAX MEDITERRANEI
• Total number of polymer chains: 1
• Total formula weight: 40091.54

Authors

Baker, P.J.,Britton, K.L.,Fisher, M.,Esclapez, J.,Pire, C.,Bonete, M.J.,Ferrer, J.,Rice, D.W. (deposition date: 2008-06-26, release date: 2009-01-13, Last modification date: 2023-12-13)

Primary citation

Baker, P.J.,Britton, K.L.,Fisher, M.,Esclapez, J.,Pire, C.,Bonete, M.J.,Ferrer, J.,Rice, D.W.
Active site dynamics in the zinc-dependent medium chain alcohol dehydrogenase superfamily.
Proc. Natl. Acad. Sci. U.S.A., 106:779-784, 2009

PubMed Abstract: Despite being the subject of intensive investigations, many aspects of the mechanism of the zinc-dependent medium chain alcohol dehydrogenase (MDR) superfamily remain contentious. We have determined the high-resolution structures of a series of binary and ternary complexes of glucose dehydrogenase, an MDR enzyme from Haloferax mediterranei. In stark contrast to the textbook MDR mechanism in which the zinc ion is proposed to remain stationary and attached to a common set of protein ligands, analysis of these structures reveals that in each complex, there are dramatic differences in the nature of the zinc ligation. These changes arise as a direct consequence of linked movements of the zinc ion, a zinc-bound bound water molecule, and the substrate during progression through the reaction. These results provide evidence for the molecular basis of proton traffic during catalysis, a structural explanation for pentacoordinate zinc ion intermediates, a unifying view for the observed patterns of metal ligation in the MDR family, and highlight the importance of dynamic fluctuations at the metal center in changing the electrostatic potential in the active site, thereby influencing the proton traffic and hydride transfer events.

PubMed: 19131516
DOI: 10.1073/pnas.0807529106

Experimental method

X-RAY DIFFRACTION (2.1 Å)