3TN7

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1016/j.biochi.2012.07.024

  • 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 hig ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Short-chain alcohol dehydrogenase
A, B
257Thermococcus sibiricus (strain MM 739 / DSM 12597)Mutation(s): 0 
Find proteins for C6A190 (Thermococcus sibiricus (strain MM 739 / DSM 12597))
Go to UniProtKB:  C6A190
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NJP
Query on NJP

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Download CCD File 
A, B
5-hydroxy-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
5-hydroxy-NADP
C21 H29 N7 O18 P3
PDVSLSLEJOIQNF-NNYOXOHSSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.146 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 146.180α = 90.00
b = 55.500β = 124.53
c = 82.770γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
XSCALEdata scaling
REFMACrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2012-12-19
    Type: Database references