F420-dependent secondary alcohol dehydrogenase in complex with an F420-acetone adduct

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 

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Coenzyme binding in f(420)-dependent secondary alcohol dehydrogenase, a member of the bacterial luciferase family.

Aufhammer, S.W.Warkentin, E.Berk, H.Shima, S.Thauer, R.K.Ermler, U.

(2004) Structure 12: 361-370

  • DOI: https://doi.org/10.1016/j.str.2004.02.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    F(420)-dependent secondary alcohol dehydrogenase (Adf) from methanogenic archaea is a member of the growing bacterial luciferase family which are all TIM barrel enzymes, most of which with an unusual nonprolyl cis peptide bond. We report here on the crystal structure of Adf from Methanoculleus thermophilicus at 1.8 A resolution in complex with a F(420)-acetone adduct. The knowledge of the F(420) binding mode in Adf provides the molecular basis for modeling F(420) and FMN into the other enzymes of the family. A nonprolyl cis peptide bond was identified as an essential part of a bulge that serves as backstop at the Re-face of F(420) to keep it in a bent conformation. The acetone moiety of the F(420)-acetone adduct is positioned at the Si-face of F(420) deeply buried inside the protein. Isopropanol can be reliably modeled and a hydrogen transfer mechanism postulated. His39 and Glu108 can be identified as key players for binding of the acetone or isopropanol oxygens and for catalysis.

  • Organizational Affiliation

    Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
F420-dependent alcohol dehydrogenase330Methanoculleus thermophilusMutation(s): 0 
EC: 1.1.99
Find proteins for O93734 (Methanoculleus thermophilus)
Explore O93734 
Go to UniProtKB:  O93734
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO93734
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.824α = 90
b = 156.316β = 90
c = 60.199γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-30
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations