Crystal structure of gox2253

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 

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Structural insights into substrate and coenzyme preference by SDR family protein Gox2253 from Gluconobater oxydans.

Yin, B.Cui, D.Zhang, L.Jiang, S.Machida, S.Yuan, Y.A.Wei, D.

(2014) Proteins 82: 2925-2935

  • DOI: https://doi.org/10.1002/prot.24603
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Gox2253 from Gluconobacter oxydans belongs to the short-chain dehydrogenases/reductases family, and catalyzes the reduction of heptanal, octanal, nonanal, and decanal with NADPH. To develop a robust working platform to engineer novel G. oxydans oxidoreductases with designed coenzyme preference, we adopted a structure based rational design strategy using computational predictions that considers the number of hydrogen bonds formed between enzyme and docked coenzyme. We report the crystal structure of Gox2253 at 2.6 Å resolution, ternary models of Gox2253 mutants in complex with NADH/short-chain aldehydes, and propose a structural mechanism of substrate selection. Molecular dynamics simulation shows that hydrogen bonds could form between 2'-hydroxyl group in the adenosine moiety of NADH and the side chain of Gox2253 mutant after arginine at position 42 is replaced with tyrosine or lysine. Consistent with the molecular dynamics prediction, Gox2253-R42Y/K mutants can use both NADH and NADPH as a coenzyme. Hence, the strategies here could provide a practical platform to engineer coenzyme selectivity for any given oxidoreductase and could serve as an additional consideration to engineer substrate-binding pockets.

  • Organizational Affiliation

    State Key Laboratory of Bioreactor Engineering, New World Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China; Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore, 117543, Singapore.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative oxidoreductase
A, B, C
342Gluconobacter oxydans 621HMutation(s): 0 
Gene Names: GOX2253
Find proteins for Q5FNR0 (Gluconobacter oxydans (strain 621H))
Explore Q5FNR0 
Go to UniProtKB:  Q5FNR0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5FNR0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.026α = 90
b = 159.253β = 90
c = 125.402γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-04
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references, Derived calculations