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PDBsum entry 1k2w

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protein Protein-protein interface(s) links
Oxidoreductase PDB id
1k2w
Jmol
Contents
Protein chains
256 a.a. *
Waters ×170
* Residue conservation analysis
PDB id:
1k2w
Name: Oxidoreductase
Title: Crystal structure of sorbitol dehydrogenase from r. Sphaeroides
Structure: Sorbitol dehydrogenase. Chain: a, b. Synonym: l-iditol 2-dehydrogenase, polyol dehydrogenase. Engineered: yes
Source: Rhodobacter sphaeroides. Organism_taxid: 1063. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
2.40Å     R-factor:   0.188     R-free:   0.238
Authors: A.Philippsen,T.Schirmer,J.Stetefeld
Key ref:
A.Philippsen et al. (2005). Structure of zinc-independent sorbitol dehydrogenase from Rhodobacter sphaeroides at 2.4 A resolution. Acta Crystallogr D Biol Crystallogr, 61, 374-379. PubMed id: 15805591 DOI: 10.1107/S0907444904034390
Date:
29-Sep-01     Release date:   11-Nov-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q59787  (DHSO_RHOSH) -  Sorbitol dehydrogenase
Seq:
Struc:
256 a.a.
256 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.1.1.14  - L-iditol 2-dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-iditol + NAD+ = L-sorbose + NADH
L-iditol
+ NAD(+)
= L-sorbose
+ NADH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     oxidoreductase activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1107/S0907444904034390 Acta Crystallogr D Biol Crystallogr 61:374-379 (2005)
PubMed id: 15805591  
 
 
Structure of zinc-independent sorbitol dehydrogenase from Rhodobacter sphaeroides at 2.4 A resolution.
A.Philippsen, T.Schirmer, M.A.Stein, F.Giffhorn, J.Stetefeld.
 
  ABSTRACT  
 
Recombinant sorbitol dehydrogenase (SDH) from Rhodobacter sphaeroides has been crystallized in the absence of the cofactor NAD(H) and its structure determined to 2.4 A resolution using molecular replacement (refined R and R free factors of 18.8 and 23.8%, respectively). As expected from the sequence and shown by the conserved fold, SDH can be assigned to the short-chain dehydrogenase/reductase protein family. The cofactor NAD and the substrate sorbitol have been modelled into the structure and the active-site architecture, which displays the highly conserved catalytic tetrad of Asn-Ser-Tyr-Lys residues, is discussed in relation to the enzyme mechanism. This is the first structure of a bacterial SDH belonging to the SDR family.
 
  Selected figure(s)  
 
Figure 4.
Figure 4 Active site of R. sphaeroides SDH with modelled NAD and sorbitol. (a) Stereo representation of NAD-binding residues in the molecular-replacement model [75]1geg (yellow) fitted to the corresponding residues in R. sphaeroides SDH (white). The almost perfect overlap of the NAD-binding residues is the basis for the modelling of the cofactor NAD into the active site of R. sphaeroides SDH. (b) Stereo representation of the active site of R. sphaeroides SDH based on the apo form of the enzyme with modelled and energy-minimized NAD (green) and sorbitol (yellow). The thick purple bonds indicate the main interaction of the C2 carbon and hydroxyl group of the sugar sandwiched between the nicotinamide ring and Tyr152. The intricate hydrogen-bonding network is indicated by thin purple lines; the region of the electron sink is denoted by an asterisk.
Figure 5.
Figure 5 NAD-binding pocket and substrate-access tunnel. (a) Binding pocket for NAD formed by R. sphaeroides SDH. (b) Side view of the surface of R. sphaeroides SDH with bound NAD. The surface is cut to reveal the NAD-binding site (yellow) and substrate-binding site (blue), as well as the active-site access direction (arrow).
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 374-379) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21543846 H.Yennawar, M.Møller, R.Gillilan, and N.Yennawar (2011).
X-ray crystal structure and small-angle X-ray scattering of sheep liver sorbitol dehydrogenase.
  Acta Crystallogr D Biol Crystallogr, 67, 440-446.  
19443443 S.Mukherjee, and Y.Zhang (2009).
MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming.
  Nucleic Acids Res, 37, e83.  
18063719 J.Jose, and T.F.Meyer (2007).
The autodisplay story, from discovery to biotechnical and biomedical applications.
  Microbiol Mol Biol Rev, 71, 600-619.  
16369779 J.Jose (2006).
Autodisplay: efficient bacterial surface display of recombinant proteins.
  Appl Microbiol Biotechnol, 69, 607-614.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.