Structure of Iron containing alcohol dehydrogenase from Thermococcus thioreducens in a monoclinic crystal form

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.146 

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The structure of an iron-containing alcohol dehydrogenase from a hyperthermophilic archaeon in two chemical states.

Larson, S.B.Jones, J.A.McPherson, A.

(2019) Acta Crystallogr F Struct Biol Commun 75: 217-226

  • DOI: https://doi.org/10.1107/S2053230X19001201
  • Primary Citation of Related Structures:  
    6C75, 6C76, 6C7L

  • PubMed Abstract: 

    An iron-containing alcohol dehydrogenase (FeADH) from the hyperthermophilic archaeon Thermococcus thioreducens was crystallized in unit cells belonging to space groups P2 1 , P2 1 2 1 2 1 and P4 3 2 1 2, and the crystal structures were solved at 2.4, 2.1 and 1.9 Å resolution, respectively, by molecular replacement using the FeADH from Thermotoga maritima (Schwarzenbacher et al., 2004) as a model. In the monoclinic and orthorhombic crystals the dehydrogenase (molecular mass 41.5 kDa) existed as a dimer containing a twofold noncrystallographic symmetry axis, which was crystallographic in the tetragonal crystals. In the monoclinic and orthorhombic asymmetric units one molecule contained iron and an NADP molecule, while the other did not. The tetragonal crystals lacked both iron and NADP. The structure is very similar to that of the FeADH from T. maritima (average r.m.s. difference for C α atoms of 1.8 Å for 341 aligned atoms). The iron, which is internally sequestered, is bound entirely by amino acids from one domain: three histidines and one aspartic acid. The coenzyme is in an extended conformation, a feature that is common to the large superfamily of NADH-dependent dehydrogenases that share a classical nucleotide-binding domain. A long broad tunnel passes entirely through the enzyme between the two domains, completely encapsulating the coenzyme.

  • Organizational Affiliation

    Department of Molecular Biology and Biochemistry, University of California, 530A Steinhaus Hall, Irvine, CA 92697-3900, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alcohol dehydrogenase
A, B
378Thermococcus thioreducensMutation(s): 0 
Gene Names: AMR53_06445SAMN05216170_0411
Find proteins for A0A0Q2QQL1 (Thermococcus thioreducens)
Explore A0A0Q2QQL1 
Go to UniProtKB:  A0A0Q2QQL1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0Q2QQL1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAP

Download Ideal Coordinates CCD File 
C21 H28 N7 O17 P3
Query on ATR

Download Ideal Coordinates CCD File 
C10 H16 N5 O13 P3
Query on FE

Download Ideal Coordinates CCD File 
C [auth A]FE (III) ION
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.146 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.125α = 90
b = 99.248β = 103.16
c = 67.487γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description