1RHC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 10.1016/j.str.2004.02.010
  • Primary Citation of Related Structures:  
    1RHC

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
F420-dependent alcohol dehydrogenaseA330Methanoculleus thermophilusMutation(s): 0 
Gene Names: adf
EC: 1.1.99
Find proteins for O93734 (Methanoculleus thermophilus)
Explore O93734 
Go to UniProtKB:  O93734
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F42
Query on F42

Download Ideal Coordinates CCD File 
E [auth A]COENZYME F420
C29 H36 N5 O18 P
GEHSZWRGPHDXJO-NALJQGANSA-N
 Ligand Interaction
ACN
Query on ACN

Download Ideal Coordinates CCD File 
F [auth A]ACETONE
C3 H6 O
CSCPPACGZOOCGX-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
D [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing

Structure Validation

View Full Validation Report



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