1D4C | pdb_00001d4c

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

• PDB DOI: https://doi.org/10.2210/pdb1D4C/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Shewanella oneidensis
• Mutation(s): No 


• Deposited: 1999-10-03 Released: 1999-12-01 
• Deposition Author(s): Leys, D., Tsapin, A.S., Meyer, T.E., Cusanovich, M.A., Van Beeumen, J.J.

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Experimental Data Snapshot

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

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

• PubMed: 10581551 
• 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 253.23 kDa 
• Atom Count: 17,470 
• Modeled Residue Count: 2,274 
• Deposited Residue Count: 2,288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FLAVOCYTOCHROME C FUMARATE REDUCTASE	A, B, C, D	572	Shewanella oneidensis	Mutation(s): 0  EC: 1.3.99.1 (PDB Primary Data), 1.3.2.4 (UniProt)
UniProt
Find proteins for P83223 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore P83223  Go to UniProtKB:  P83223

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	AA [auth D], I [auth A], O [auth B], U [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
HEC	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	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 (Depositor) 
• R-Value Work:  0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.69	α = 90
b = 216.36	β = 90
c = 112.04	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-12-01 
Deposition Author(s): Leys, D., Tsapin, A.S., Meyer, T.E., Cusanovich, M.A., Van Beeumen, J.J.

Revision History  

• 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
• Version 2.1: 2024-10-30
  Changes: Data collection, Database references, Structure summary