6H1M

Neutron structure of Lactobacillus brevis alcohol dehydrogenase


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


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Literature

Neutron and X-ray crystal structures of Lactobacillus brevis alcohol dehydrogenase reveal new insights into hydrogen-bonding pathways.

Hermann, J.Nowotny, P.Schrader, T.E.Biggel, P.Hekmat, D.Weuster-Botz, D.

(2018) Acta Crystallogr F Struct Biol Commun 74: 754-764

  • DOI: 10.1107/S2053230X18015273
  • Primary Citation of Related Structures:  
    6H07, 6H1M

  • 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 ...

    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 3 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 min 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 2+ ) or manganese (Mn 2+ ) 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 min of 1.48 Å. The high-resolution X-ray structure suggested partial occupancy of Mn 2+ and Mg 2+ at the ion-binding site. This is supported by the different binding affinity of Mn 2+ and Mg 2+ to the tetrameric structure calculated via free-energy molecular-dynamics simulations.


    Organizational Affiliation

    Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstrasse 15, 85748 Garching, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
R-specific alcohol dehydrogenaseA251Levilactobacillus brevisMutation(s): 0 
Gene Names: radh
UniProt
Find proteins for Q84EX5 (Levilactobacillus brevis)
Explore Q84EX5 
Go to UniProtKB:  Q84EX5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84EX5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.508α = 90
b = 84.572β = 90
c = 115.419γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
Cootmodel building
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySPP 1934

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-12
    Type: Initial release