1B25

FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE FROM PYROCOCCUS FURIOSUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Formaldehyde ferredoxin oxidoreductase from Pyrococcus furiosus: the 1.85 A resolution crystal structure and its mechanistic implications.

Hu, Y.Faham, S.Roy, R.Adams, M.W.Rees, D.C.

(1999) J.Mol.Biol. 286: 899-914

  • DOI: 10.1006/jmbi.1998.2488
  • Primary Citation of Related Structures:  1B4N

  • PubMed Abstract: 
  • Crystal structures of formaldehyde ferredoxin oxidoreductase (FOR), a tungstopterin-containing protein from the hyperthermophilic archaeon Pyrococcus furiosus, have been determined in the native state and as a complex with the inhibitor glutarate at ...

    Crystal structures of formaldehyde ferredoxin oxidoreductase (FOR), a tungstopterin-containing protein from the hyperthermophilic archaeon Pyrococcus furiosus, have been determined in the native state and as a complex with the inhibitor glutarate at 1.85 A and 2. 4 A resolution, respectively. The native structure was solved by molecular replacement using the structure of the homologous P. furiosus aldehyde ferredoxin oxidoreductase (AOR) as the initial model. Residues are identified in FOR that may be involved in either the catalytic mechanism or in determining substrate specificity. The binding site on FOR for the physiological electron acceptor, P. furiosus ferredoxin (Fd), has been established from an FOR-Fd cocrystal structure. Based on the arrangement of redox centers in this structure, an electron transfer pathway is proposed that begins at the tungsten center, leads to the (4Fe:4S) cluster of FOR via one of the two pterins that coordinate the tungsten, and ends at the (4Fe:4S) cluster of ferredoxin. This pathway includes two residues that coordinate the (4Fe:4S) clusters, Cys287 of FOR and Asp14 of ferredoxin. Similarities in the active site structures between FOR and the unrelated molybdoenzyme aldehyde oxidoreductase from Desulfovibrio gigas suggest that both enzymes utilize a common mechanism for aldehyde oxidation.


    Related Citations: 
    • Purification and Molecular Characterization of the Tungsten-Containing Formaldehyde Ferredoxin Oxidoreductase from the Hyperthermophilic Archaeon Pyrococcus Furiosus: The Third of a Putative Five Member Tungstoenzyme Family
      Roy, R.,Mukund, S.,Schut, G.,Dunn, D.M.,Weiss, R.,Adams, M.W.W.
      (1999) J.Bacteriol. 181: 1171


    Organizational Affiliation

    Division of Chemistry and Chemical Engineering 147-75CH, California Institute of Technology, Pasadena, CA, 91125, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE)
A, B, C, D
619Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)N/A
Find proteins for Q8U1K3 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U1K3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B, C, D
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
PTT
Query on PTT

Download SDF File 
Download CCD File 
A, B, C, D
TUNGSTOPTERIN
C21 H25 Mg N10 O13 P2 S4 W
OMJGSXGVFAOTGU-BYZPVVMBSA-G
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 100.340α = 90.00
b = 170.850β = 90.00
c = 180.640γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
AMoREphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-03-24
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-12-07
    Type: Database references