Crystal structure of short-chain alcohol dehydrogenase from hyperthermophilic archaeon Thermococcus sibiricus complexed with 5-hydroxy-NADP

Experimental Data Snapshot

  • Resolution: 1.68 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 

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Structural insight into the molecular basis of polyextremophilicity of short-chain alcohol dehydrogenase from the hyperthermophilic archaeon Thermococcus sibiricus.

Bezsudnova, E.Y.Boyko, K.M.Polyakov, K.M.Dorovatovskiy, P.V.Stekhanova, T.N.Gumerov, V.M.Ravin, N.V.Skryabin, K.G.Kovalchuk, M.V.Popov, V.O.

(2012) Biochimie 94: 2628-2638

  • DOI: https://doi.org/10.1016/j.biochi.2012.07.024
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Biochemical analysis of enantioselective short-chain alcohol dehydrogenase from the hyperthermophilic archaeon Thermococcus sibiricus (TsAdh319) revealed unique polyextremophilic properties of the enzyme - half-life of 1 h at 100 °C, tolerance to high salt (up to 4 M) and organic solvents (50% v/v) concentrations. To elucidate the molecular basis of TsAdh319 polyextremophilicity, we determined the crystal structure of the enzyme in a binary complex with 5-hydroxy-NADP at 1.68 Å resolution. TsAdh319 has a tetrameric structure both in the crystals and in solution with an intersubunit disulfide bond. The substrate-binding pocket is hydrophobic, spacious and open that is consistent with the observed promiscuity in substrate specificity of TsAdh319. The present study revealed an extraordinary number of charged residues on the surface of TsAdh319, 70% of which were involved in ion pair interactions. Further we compared the structure of TsAdh319 with the structures of other homologous short-chain dehydrogenases/reductases (SDRs) from thermophilic and mesophilic organisms. We found that TsAdh319 has the highest arginine and aspartate + glutamate contents compared to the counterparts. The frequency of occurrence of salt bridges on the surface of TsAdh319 is the highest among the SDRs under consideration. No differences in the proline, tryptophan, and phenylalanine contents are observed; the compactness of the protein core of TsAdh319, the monomer and tetramer organization do not differ from that of the counterparts. We suggest that the unique thermostability of TsAdh319 is associated with the rigidity and simultaneous "resilience" of the structure provided by a compact hydrophobic core and a large number of surface ion pairs. An extensive salt bridge network also might maintain the structural integrity of TsAdh319 in high salinity.

  • Organizational Affiliation

    A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky Pr. 33, Moscow 119071, Russia. eubez@yandex.ru

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Short-chain alcohol dehydrogenase
A, B
257Thermococcus sibiricus MM 739Mutation(s): 0 
Gene Names: TSIB_0319
Find proteins for C6A190 (Thermococcus sibiricus (strain DSM 12597 / MM 739))
Explore C6A190 
Go to UniProtKB:  C6A190
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6A190
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.68 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.18α = 90
b = 55.5β = 124.53
c = 82.77γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2012-12-19
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description