Crystal Structure of Yvgn and cofactor NADPH from Bacillus subtilis

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.240 

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Structural and biochemical analyses of YvgN and YtbE from Bacillus subtilis

Lei, J.Zhou, Y.F.Li, L.F.Su, X.-D.

(2009) Protein Sci 18: 1792-1800

  • DOI: https://doi.org/10.1002/pro.178
  • Primary Citation of Related Structures:  
    3B3D, 3D3F, 3F7J

  • PubMed Abstract: 

    Bacillus subtilis is one of the most studied gram-positive bacteria. In this work, YvgN and YtbE from B. subtilis, assigned as AKR5G1 and AKR5G2 of aldo-keto reductase (AKR) superfamily. AKR catalyzes the NADPH-dependent reduction of aldehyde or aldose substrates to alcohols. YvgN and YtbE were studied by crystallographic and enzymatic analyses. The apo structures of these proteins were determined by molecular replacement, and the structure of holoenzyme YvgN with NADPH was also solved, revealing the conformational changes upon cofactor binding. Our biochemical data suggest both YvgN and YtbE have preferential specificity for derivatives of benzaldehyde, such as nitryl or halogen group substitution at the 2 or 4 positions. These proteins also showed broad catalytic activity on many standard substrates of AKR, such as glyoxal, dihydroxyacetone, and DL-glyceraldehyde, suggesting a possible role in bacterial detoxification.

  • Organizational Affiliation

    National laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
YvgN protein
A, B
275Bacillus subtilisMutation(s): 0 
Gene Names: yvgN
EC: 1.1.1 (UniProt), (UniProt)
Find proteins for O32210 (Bacillus subtilis (strain 168))
Explore O32210 
Go to UniProtKB:  O32210
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO32210
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NDP

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C21 H30 N7 O17 P3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.517α = 90
b = 123.285β = 90
c = 57.226γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
SAINTdata reduction
PROTEUMdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2014-01-29
    Changes: Database references
  • Version 1.3: 2017-10-25
    Changes: Refinement description
  • Version 1.4: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description