1D4C

CRYSTAL STRUCTURE OF THE UNCOMPLEXED FORM OF THE FLAVOCYTOCHROME C FUMARATE REDUCTASE OF SHEWANELLA PUTREFACIENS STRAIN MR-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.210 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structure and mechanism of the flavocytochrome c fumarate reductase of Shewanella putrefaciens MR-1.

Leys, D.Tsapin, A.S.Nealson, K.H.Meyer, T.E.Cusanovich, M.A.Van Beeumen, J.J.

(1999) Nat Struct Biol 6: 1113-1117

  • DOI: https://doi.org/10.1038/70051
  • Primary Citation of Related Structures:  
    1D4C, 1D4D, 1D4E

  • PubMed Abstract: 

    Fumarate respiration is one of the most widespread types of anaerobic respiration. The soluble fumarate reductase of Shewanella putrefaciens MR-1 is a periplasmic tetraheme flavocytochrome c. The crystal structures of the enzyme were solved to 2.9 A for the uncomplexed form and to 2.8 A and 2.5 A for the fumarate and the succinate-bound protein, respectively. The structures reveal a flexible capping domain linked to the FAD-binding domain. A catalytic mechanism for fumarate reduction based on the structure of the complexed protein is proposed. The mechanism for the reverse reaction is a model for the homologous succinate dehydrogenase (complex II) of the respiratory chain. In flavocytochrome c fumarate reductase, all redox centers are in van der Waals contact with one another, thus providing an efficient conduit of electrons from the hemes via the FAD to fumarate.


  • Organizational Affiliation

    Laboratory of Protein Biochemistry and Protein Engineering, Department of Biochemistry, Physiology and Microbiology, K.L. Ledeganckstraat 35, 9000 Gent, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FLAVOCYTOCHROME C FUMARATE REDUCTASE
A, B, C, D
572Shewanella oneidensisMutation(s): 0 
EC: 1.3.99.1
UniProt
Find proteins for P83223 (Shewanella oneidensis (strain MR-1))
Explore P83223 
Go to UniProtKB:  P83223
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83223
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
AA [auth D],
I [auth A],
O [auth B],
U [auth C]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
HEC
Query on HEC

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
K [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
J [auth B],
P [auth C],
V [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.69α = 90
b = 216.36β = 90
c = 112.04γ = 90
Software Package:
Software NamePurpose
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-12-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation
  • Version 2.0: 2021-03-03
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary