1QLB

respiratory complex II-like fumarate reductase from Wolinella succinogenes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of Fumarate Reductase from Wolinella Succinogenes at 2.2 Angstroms Resolution

Lancaster, C.R.D.Kroeger, A.Auer, M.Michel, H.

(1999) Nature 402: 377

  • DOI: 10.1038/46483
  • Primary Citation of Related Structures:  
    1QLB

  • PubMed Abstract: 
  • Fumarate reductase couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, in a reaction opposite to that catalysed by the related complex II of the respiratory chain (succinate dehydrogenase). Here we describe the crystal structure at 2 ...

    Fumarate reductase couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, in a reaction opposite to that catalysed by the related complex II of the respiratory chain (succinate dehydrogenase). Here we describe the crystal structure at 2.2 A resolution of the three protein subunits containing fumarate reductase from the anaerobic bacterium Wolinella succinogenes. Subunit A contains the site of fumarate reduction and a covalently bound flavin adenine dinucleotide prosthetic group. Subunit B contains three iron-sulphur centres. The menaquinol-oxidizing subunit C consists of five membrane-spanning, primarily helical segments and binds two haem b molecules. On the basis of the structure, we propose a pathway of electron transfer from the dihaem cytochrome b to the site of fumarate reduction and a mechanism of fumarate reduction. The relative orientations of the soluble and membrane-embedded subunits of succinate:quinone oxidoreductases appear to be unique.


    Organizational Affiliation

    Max-Planck-Institut für Biophysik, Frankfurt am Main, Germany. lancaster@mpibp-frankfurt.mpg.de



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FUMARATE REDUCTASE FLAVOPROTEIN SUBUNITA, D656Wolinella succinogenesMutation(s): 0 
EC: 1.3.99.1 (PDB Primary Data), 1.3.5.4 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P17412 (Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W))
Explore P17412 
Go to UniProtKB:  P17412
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FUMARATE REDUCTASE IRON-SULFUR PROTEINB, E239Wolinella succinogenesMutation(s): 0 
EC: 1.3.99.1 (PDB Primary Data), 1.3.5.4 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P17596 (Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W))
Explore P17596 
Go to UniProtKB:  P17596
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
FUMARATE REDUCTASE CYTOCHROME B SUBUNITC, F256Wolinella succinogenesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P17413 (Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W))
Explore P17413 
Go to UniProtKB:  P17413
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
G [auth A], P [auth D]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
HEM
Query on HEM

Download Ideal Coordinates CCD File 
M [auth C], N [auth C], V [auth F], W [auth F]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
LMT
Query on LMT

Download Ideal Coordinates CCD File 
O [auth C], X [auth F]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
L [auth B], U [auth E]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download Ideal Coordinates CCD File 
K [auth B], T [auth E]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
J [auth B], S [auth E]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
FUM
Query on FUM

Download Ideal Coordinates CCD File 
H [auth A], Q [auth D]FUMARIC ACID
C4 H4 O4
VZCYOOQTPOCHFL-OWOJBTEDSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
I [auth A], R [auth D]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.4α = 90
b = 85.05β = 96.46
c = 188.85γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-11-29
    Type: Initial release
  • Version 1.1: 2012-07-18
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance