3D3F

Crystal Structure of Yvgn and cofactor NADPH from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1002/pro.178
  • Primary Citation of Related Structures:  

  • 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 aldo ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YvgN protein
A, B
275Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: yvgN
EC: 1.1.1.-
Find proteins for O32210 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O32210
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download SDF File 
Download CCD File 
A, B
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.236 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 80.517α = 90.00
b = 123.285β = 90.00
c = 57.226γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SAINTdata reduction
MOLREPphasing
PROTEUM PLUSdata collection
PROTEUMdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2014-01-29
    Type: Database references
  • Version 1.3: 2017-10-25
    Type: Refinement description