1JVB

ALCOHOL DEHYDROGENASE FROM THE ARCHAEON SULFOLOBUS SOLFATARICUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the alcohol dehydrogenase from the hyperthermophilic archaeon Sulfolobus solfataricus at 1.85 A resolution.

Esposito, L.Sica, F.Raia, C.A.Giordano, A.Rossi, M.Mazzarella, L.Zagari, A.

(2002) J Mol Biol 318: 463-477

  • DOI: 10.1016/S0022-2836(02)00088-8
  • Primary Citation of Related Structures:  
    1JVB

  • PubMed Abstract: 
  • The crystal structure of a medium-chain NAD(H)-dependent alcohol dehydrogenase (ADH) from an archaeon has been solved by multiwavelength anomalous diffraction, using a selenomethionine-substituted enzyme. The protein (SsADH), extracted from the hyperthermophilic organism Sulfolobus solfataricus, is a homo-tetramer with a crystallographic 222 symmetry ...

    The crystal structure of a medium-chain NAD(H)-dependent alcohol dehydrogenase (ADH) from an archaeon has been solved by multiwavelength anomalous diffraction, using a selenomethionine-substituted enzyme. The protein (SsADH), extracted from the hyperthermophilic organism Sulfolobus solfataricus, is a homo-tetramer with a crystallographic 222 symmetry. Despite the low level of sequence identity, the overall fold of the monomer is similar to that of the other homologous ADHs of known structure. However, a significant difference is the orientation of the catalytic domain relative to the coenzyme-binding domain that results in a larger interdomain cleft. At the bottom of this cleft, the catalytic zinc ion is coordinated tetrahedrally and lacks the zinc-bound water molecule that is usually found in ADH apoform structures. The fourth coordination position is indeed occupied by a Glu residue, as found in bacterial tetrameric ADHs. Other differences are found in the architecture of the substrate pocket whose entrance is more restricted than in other ADHs. SsADH is the first tetrameric ADH X-ray structure containing a second zinc ion playing a structural role. This latter metal ion shows a peculiar coordination, with a glutamic acid residue replacing one of the four cysteine ligands that are highly conserved throughout the structural zinc-containing dimeric ADHs.


    Related Citations: 
    • NADP-dependent Bacterial Alcohol Dehydrogenases: Crystal Structure, Co-Factor-Binding and Co-Factor Specificity of the ADHS of Clostridium beijerinckii and Thermoanaerobacter brockii
      Korkhin, Y., Kalb, A.J., Peretz, M., Bogin, O., Burstein, Y., Frolow, F.
      (1998) J Mol Biol 278: 967
    • Three Dimensional Structure of Horse Liver Alcoholdehydrogenase at 2.4 Angstrom Resolution
      Eklund, H., Nordstrom, B., Zeppezauer, E., Soderlund, G., Ohlsson, I., Boiwe, T., Soderberg, B.O., Tapia, O., Branden, C.I., Akeson, A.
      (1976) J Mol Biol 102: 27
    • Crystal Structure of NADP(H)-Dependent Ketose Reductase from Besimia Argentifolii at 2.3 Angstrom Resolution
      Banfield, M.J., Salvucci, M.E., Baker, E.N., Smith, C.A.
      (2001) J Mol Biol 306: 239

    Organizational Affiliation

    Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 6, I-80134 Napoli, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(H)-DEPENDENT ALCOHOL DEHYDROGENASEA347Saccharolobus solfataricusMutation(s): 8 
Gene Names: adh
EC: 1.1.1.1
UniProt
Find proteins for P39462 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore P39462 
Go to UniProtKB:  P39462
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.191 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.316α = 90
b = 125.316β = 90
c = 115.59γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
DMmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-08-29
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance