Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 63357.36 
• Atom Count: 4198 
• Residue Count: 572 
• Unique protein chains: 1

1D4D

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

• DOI: 10.2210/pdb1D4D/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Shewanella oneidensis (strain MR-1)


• 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: 2.5 Å
• R-Value Free: 0.305 
• R-Value Work: 0.239 

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.Mol.Biol. 6: 1113-1117

• PubMed: 10581551 
• DOI: 10.1038/70051
• Primary Citation of Related Structures:  
  1D4E, 1D4C


• 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
FLAVOCYTOCHROME C FUMARATE REDUCTASE	A	572	Shewanella oneidensis (strain MR-1)	Mutation(s): 0  EC: 1.3.5.4
Find proteins for P83223 (Shewanella oneidensis (strain MR-1)) Go to UniProtKB:  P83223

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SIN	A	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
FAD	A	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
HEM	A	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.305 
• R-Value Work: 0.239 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 72.863	α = 90.00
b = 72.863	β = 90.00
c = 216.469	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-10-03 
• 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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2018-01-31
  Type: Experimental preparation