3AI3

The crystal structure of L-Sorbose reductase from Gluconobacter frateurii complexed with NADPH and L-sorbose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Crystal Structure of l-Sorbose Reductase from Gluconobacter frateurii Complexed with NADPH and l-Sorbose

Kubota, K.Nagata, K.Okai, M.Miyazono, K.Soemphol, W.Ohtsuka, J.Yamamura, A.Saichana, N.Toyama, H.Matsushita, K.Tanokura, M.

(2011) J.Mol.Biol. 407: 543-555

  • DOI: 10.1016/j.jmb.2011.01.008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • l-Sorbose reductase from Gluconobacter frateurii (SR) is an NADPH-dependent oxidoreductase. SR preferentially catalyzes the reversible reaction between d-sorbitol and l-sorbose with high substrate specificity. To elucidate the structural basis of the ...

    l-Sorbose reductase from Gluconobacter frateurii (SR) is an NADPH-dependent oxidoreductase. SR preferentially catalyzes the reversible reaction between d-sorbitol and l-sorbose with high substrate specificity. To elucidate the structural basis of the catalytic mechanism and the substrate specificity of SR, we have determined the structures of apo-SR, SR in complex with NADPH, and the inactive mutant (His116Leu) of SR in complex with NADPH and l-sorbose at 2.83 Å, 1.90 Å, and 1.80 Å resolutions, respectively. Our results show that SR belongs to the short-chain dehydrogenase/reductase (SDR) family and forms a tetrameric structure. Although His116 is not conserved among SDR family enzymes, the structures of SR have revealed that His116 is important for the stabilization of the proton relay system and for active-site conformation as a fourth catalytic residue. In the ternary complex structure, l-sorbose is recognized by 11 hydrogen bonds. Site-directed mutagenesis of residues around the l-sorbose-binding site has shown that the loss of almost full enzymatic activity was caused by not only the substitution of putative catalytic residues but also the substitution of the residue used for the recognition of the C4 hydroxyl groups of l-sorbose (Glu154) and of the residues used for the construction of the substrate-binding pocket (Cys146 and Gly188). The recognition of the C4 hydroxyl group of l-sorbose would be indispensable for the substrate specificity of SR, which recognizes only l-sorbose and d-sorbitol but not other sugars. Our results indicated that these residues were crucial for the substrate recognition and specificity of SR.


    Organizational Affiliation

    Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADPH-sorbose reductase
A, C, E, G
263Gluconobacter frateuriiMutation(s): 1 
Gene Names: sboA
Find proteins for A4PB64 (Gluconobacter frateurii)
Go to UniProtKB:  A4PB64
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SOE
Query on SOE

Download SDF File 
Download CCD File 
E, G
alpha-L-sorbopyranose
L-sorbose in pyranose form
C6 H12 O6
LKDRXBCSQODPBY-BGPJRJDNSA-N
 Ligand Interaction
SOL
Query on SOL

Download SDF File 
Download CCD File 
A, C, E, G
L-sorbose
C6 H12 O6
BJHIKXHVCXFQLS-OTWZMJIISA-N
 Ligand Interaction
NDP
Query on NDP

Download SDF File 
Download CCD File 
A, C, E, G
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: 1.8 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 61.040α = 90.00
b = 124.410β = 90.00
c = 124.540γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
XDSdata reduction
REFMACrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-11-20
    Type: Non-polymer description