Structure of the glycerol dehydrogenase AKR11B4 from Gluconobacter oxydans

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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The Three-Dimensional Structure of AKR11B4, a Glycerol Dehydrogenase from Gluconobacter oxydans, Reveals a Tryptophan Residue as an Accelerator of Reaction Turnover.

Richter, N.Breicha, K.Hummel, W.Niefind, K.

(2010) J Mol Biol 404: 353-362

  • DOI: https://doi.org/10.1016/j.jmb.2010.09.049
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The NADP-dependent glycerol dehydrogenase (EC from Gluconobacter oxydans is a member of family 11 of the aldo-keto reductase (AKR) enzyme superfamily; according to the systematic nomenclature within the AKR superfamily, the term AKR11B4 has been assigned to the enzyme. AKR11B4 is a biotechnologically attractive enzyme because of its broad substrate spectrum, combined with its distinctive regioselectivity and stereoselectivity. These features can be partially rationalized based on a 2-Å crystal structure of apo-AKR11B4, which we describe and interpret here against the functional complex structures of other members of family 11 of the AKR superfamily. The structure of AKR11B4 shows the AKR-typical (β/α)(8) TIM-barrel fold, with three loops and the C-terminal tail determining the particular enzymatic properties. In comparison to AKR11B1 (its closest AKR relative), AKR11B4 has a relatively broad binding cleft for the cosubstrate NADP/NADPH. In the crystalline environment, it is completely blocked by the C-terminal segment of a neighboring protomer. The structure reveals a conspicuous tryptophan residue (Trp23) that has to adopt an unconventional and strained side-chain conformation to permit cosubstrate binding. We predict and confirm by site-directed mutagenesis that Trp23 is an accelerator of (co)substrate turnover. Furthermore, we show that, simultaneously, this tryptophan residue is a critical determinant for substrate binding by the enzyme, while enantioselectivity is probably governed by a methionine residue within the C-terminal tail. We present structural reasons for these notions based on ternary complex models of AKR11B4, NADP, and either octanal, d-glyceraldehyde, or l-glyceraldehyde.

  • Organizational Affiliation

    Evocatal GmbH, Merowingerplatz 1A, D-40225 Düsseldorf, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative oxidoreductase348Gluconobacter oxydansMutation(s): 0 
Gene Names: GOX1615
EC: 1.1.1
Find proteins for Q5FQJ0 (Gluconobacter oxydans (strain 621H))
Explore Q5FQJ0 
Go to UniProtKB:  Q5FQJ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5FQJ0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.25α = 90
b = 62.39β = 90.47
c = 59.82γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references