1ZJZ | pdb_00001zjz

Structure of R-specific alcohol dehydrogenase (mutant G37D) from Lactobacillus brevis in complex with phenylethanol and NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 
    0.138 (Depositor), 0.130 (DCC) 
  • R-Value Work: 
    0.124 (Depositor), 0.130 (DCC) 
  • R-Value Observed: 
    0.124 (Depositor) 

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Ligand Structure Quality Assessment 

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Literature

Atomic Resolution Structures of R-specific Alcohol Dehydrogenase from Lactobacillus brevis Provide the Structural Bases of its Substrate and Cosubstrate Specificity

Schlieben, N.H.Niefind, K.Muller, J.Riebel, B.Hummel, W.Schomburg, D.

(2005) J Mol Biology 349: 801-813

  • DOI: https://doi.org/10.1016/j.jmb.2005.04.029
  • Primary Citation of Related Structures:  
    1ZJY, 1ZJZ, 1ZK0, 1ZK1, 1ZK2, 1ZK3, 1ZK4

  • PubMed Abstract: 

    The R-specific alcohol dehydrogenase (RADH) from Lactobacillus brevis is an NADP-dependent, homotetrameric member of the extended enzyme family of short-chain dehydrogenases/reductases (SDR) with a high biotechnological application potential. Its preferred in vitro substrates are prochiral ketones like acetophenone with almost invariably a small methyl group as one substituent and a bulky (often aromatic) moiety as the other. On the basis of an atomic-resolution structure of wild-type RADH in complex with NADP and acetophenone, we designed the mutant RADH-G37D, which should possess an improved cosubstrate specificity profile for biotechnological purposes, namely, a preference for NAD rather than NADP. Comparative kinetic measurements with wild-type and mutant RADH showed that this aim was achieved. To characterize the successful mutant structurally, we determined several, partly atomic-resolution, crystal structures of RADH-G37D both as an apo-enzyme and as ternary complex with NAD or NADH and phenylethanol. The increased affinity of RADH-G37D for NAD(H) depends on an interaction between the adenosine ribose moiety of NAD and the inserted aspartate side-chain. A structural comparison between RADH-G37D as apo-enzyme and as a part of a ternary complex revealed significant rearrangements of Ser141, Glu144, Tyr189 and Met205 in the vicinity of the active site. This plasticity contributes to generate a small hydrophobic pocket for the methyl group typical for RADH substrates, and a hydrophobic coat for the second, more variable and often aromatic, substituent. Around Ser141 we even found alternative conformations in the backbone. A structural adaptability in this region, which we describe here for the first time for an SDR enzyme, is probably functionally important, because it concerns Ser142, a member of the highly conserved catalytic tetrad typical for SDR enzymes. Moreover, it affects an extended proton relay system that has been identified recently as a critical element for the catalytic mechanism in SDR enzymes.


  • Organizational Affiliation

    Universität zu Köln, Institut für Biochemie, Zülpicher Strasse 47, D-50674 Köln, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
R-specific alcohol dehydrogenase251Levilactobacillus brevisMutation(s): 1 
EC: 1.1.1.2
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
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free:  0.138 (Depositor), 0.130 (DCC) 
  • R-Value Work:  0.124 (Depositor), 0.130 (DCC) 
  • R-Value Observed: 0.124 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.856α = 90
b = 79.847β = 90
c = 112.915γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NADClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-06-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-02-14
    Changes: Data collection