6H07

X-ray structure of Lactobacillus brevis alcohol dehydrogenase

Summary for 6H07

• Entry DOI: 10.2210/pdb6h07/pdb
• Related: 6h1m
• Descriptor: R-specific alcohol dehydrogenase, MAGNESIUM ION, MANGANESE (II) ION, ... (4 entities in total)
• Functional Keywords: short chain reductases/dehydrogenases, magnesium dependence, r-specific alcohol dehydrogenase, oxidoreductase
• Biological source: Lactobacillus brevis
• Total number of polymer chains: 2
• Total formula weight: 53391.37

Authors

Hermann, J.,Nowotny, P.,Biggel, P.,Schneider, S.,Hekmat, D.,Weuster-Botz, D. (deposition date: 2018-07-06, release date: 2018-12-12, Last modification date: 2024-01-17)

Primary citation

Hermann, J.,Nowotny, P.,Schrader, T.E.,Biggel, P.,Hekmat, D.,Weuster-Botz, D.
Neutron and X-ray crystal structures of Lactobacillus brevis alcohol dehydrogenase reveal new insights into hydrogen-bonding pathways.
Acta Crystallogr F Struct Biol Commun, 74:754-764, 2018

PubMed Abstract: Lactobacillus brevis alcohol dehydrogenase (LbADH) is a well studied homotetrameric enzyme which catalyzes the enantioselective reduction of prochiral ketones to the corresponding secondary alcohols. LbADH is stable and enzymatically active at elevated temperatures and accepts a broad range of substrates, making it a valuable tool in industrial biocatalysis. Here, the expression, purification and crystallization of LbADH to generate large, single crystals with a volume of up to 1 mm suitable for neutron diffraction studies are described. Neutron diffraction data were collected from an H/D-exchanged LbADH crystal using the BIODIFF instrument at the Heinz Maier-Leibnitz Zentrum (MLZ), Garching, Germany to a resolution d of 2.15 Å in 16 days. This allowed the first neutron crystal structure of LbADH to be determined. The neutron structure revealed new details of the hydrogen-bonding network originating from the ion-binding site of LbADH and provided new insights into the reasons why divalent magnesium (Mg) or manganese (Mn) ions are necessary for its activity. X-ray diffraction data were obtained from the same crystal at the European Synchrotron Radiation Facility (ESRF), Grenoble, France to a resolution d of 1.48 Å. The high-resolution X-ray structure suggested partial occupancy of Mn and Mg at the ion-binding site. This is supported by the different binding affinity of Mn and Mg to the tetrameric structure calculated via free-energy molecular-dynamics simulations.

PubMed: 30511668
DOI: 10.1107/S2053230X18015273

Experimental method

X-RAY DIFFRACTION (1.482 Å)