3AWD

Crystal structure of gox2181


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Biochemical and structural analysis of Gox2181, a new member of the SDR superfamily from Gluconobacter oxydans.

Liu, X.Yuan, Z.Adam Yuan, Y.Lin, J.Wei, D.

(2011) Biochem.Biophys.Res.Commun. 415: 410-415

  • DOI: 10.1016/j.bbrc.2011.10.083

  • PubMed Abstract: 
  • Gluconobacter oxydans enable to oxidize sugars and polyols incompletely to corresponding materials with potential industrial applications, containing around 75 putative dehydrogenases. One of these putative dehydrogenases, Gox2181, was cloned and exp ...

    Gluconobacter oxydans enable to oxidize sugars and polyols incompletely to corresponding materials with potential industrial applications, containing around 75 putative dehydrogenases. One of these putative dehydrogenases, Gox2181, was cloned and expressed in Escherichia coli BL21 (DE3), and its X-ray crystal structure was determined to a resolution of 1.8 Å. Gox2181 formed a homo-tetramer in the crystal that was coincident with the apparent molecular mass determined in the solution. Gox2181 displayed α/β-folding patterns, the conserved catalytic tetrad of Asn119-Ser147-Tyr162-Lys166, and the NAD-binding pocket, which aligned well with the 'classical' type of short-chain dehydrogenase/reductase (SDR) enzymes. Gox2181 was denoted SDR51C based on the SDR nomenclature system. The purified recombinant Gox2181 was demonstrated to be NAD(H)-dependent and active towards a wide range of substrates, including sugar alcohols, secondary alcohols, ketones, and ketoses. Among the substrates tested, Gox2181 displayed preference for secondary hydroxyl or carbonyl groups, showing low K(m) values with d-arabitol and butanedione.


    Organizational Affiliation

    State Key Laboratory of Bioreactor Engineering, NewWorld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative polyol dehydrogenase
A, B, C, D
260Gluconobacter oxydans (strain 621H)Mutation(s): 0 
Find proteins for Q5FNX9 (Gluconobacter oxydans (strain 621H))
Go to UniProtKB:  Q5FNX9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

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Download CCD File 
B, C
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.273α = 90.00
b = 121.416β = 90.00
c = 136.546γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
PHASESphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-01
    Type: Initial release