1E7P | pdb_00001e7p

QUINOL:FUMARATE REDUCTASE FROM WOLINELLA SUCCINOGENES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.291 (Depositor) 
  • R-Value Work: 
    0.283 (Depositor) 
  • R-Value Observed: 
    0.283 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 1E7P

This is version 2.2 of the entry. See complete history

Literature

A Third Crystal Form of Wolinella Succinogenes Quinol:Fumarate Reductase Reveals Domain Closure at the Site of Fumarate Reduction

Lancaster, C.R.D.Gross, R.Simon, J.

(2001) Eur J Biochem 268: 1820

  • Primary Citation Related Structures: 
    1E7P

  • PubMed Abstract: 

    Quinol:fumarate reductase (QFR) is a membrane protein complex that couples the reduction of fumarate to succinate to the oxidation of quinol to quinone. Previously, the crystal structure of QFR from Wolinella succinogenes was determined based on two different crystal forms, and the site of fumarate binding in the flavoprotein subunit A of the enzyme was located between the FAD-binding domain and the capping domain [Lancaster, C.R.D., Kröger, A., Auer, M., & Michel, H. (1999) Nature 402, 377--385]. Here we describe the structure of W. succinogenes QFR based on a third crystal form and refined at 3.1 A resolution. Compared with the previous crystal forms, the capping domain is rotated in this structure by approximately 14 degrees relative to the FAD-binding domain. As a consequence, the topology of the dicarboxylate binding site is much more similar to those of membrane-bound and soluble fumarate reductase enzymes from other organisms than to that found in the previous crystal forms of W. succinogenes QFR. This and the effects of the replacement of Arg A301 by Glu or Lys by site-directed mutagenesis strongly support a common mechanism for fumarate reduction in this superfamily of enzymes.


  • Organizational Affiliation
    • Max-Planck-Institut für Biophysik, Abteilung Molekulare Membranbiologie, Frankfurt am Main, Germany. Roy.Lancaster@mpibp-frankfurt.mpg.de

Macromolecule Content 

  • Total Structure Weight: 533.04 kDa 
  • Atom Count: 37,072 
  • Modeled Residue Count: 4,592 
  • Deposited Residue Count: 4,604 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fumarate reductase flavoprotein subunit
A, D, G, J
656Wolinella succinogenesMutation(s): 0 
Gene Names: frdAWS0831
EC: 1.3.5.4 (PDB Primary Data), 1.3.5.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P17412 (Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / CCUG 13145 / JCM 31913 / LMG 7466 / NCTC 11488 / FDC 602W))
Explore P17412 
Go to UniProtKB:  P17412
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17412
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fumarate reductase iron-sulfur subunit
B, E, H, K
239Wolinella succinogenesMutation(s): 0 
Gene Names: frdBWS0830
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for P17596 (Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / CCUG 13145 / JCM 31913 / LMG 7466 / NCTC 11488 / FDC 602W))
Explore P17596 
Go to UniProtKB:  P17596
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17596
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Fumarate reductase cytochrome b subunit
C, F, I, L
256Wolinella succinogenesMutation(s): 1 
Gene Names: frdCWS0832
Membrane Entity: Yes 
UniProt
Find proteins for P17413 (Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / CCUG 13145 / JCM 31913 / LMG 7466 / NCTC 11488 / FDC 602W))
Explore P17413 
Go to UniProtKB:  P17413
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17413
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
EA [auth G],
M [auth A],
NA [auth J],
V [auth D]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
HEM

Query on HEM



Download:Ideal Coordinates CCD File
CA [auth F]
DA [auth F]
KA [auth I]
LA [auth I]
S [auth C]
CA [auth F],
DA [auth F],
KA [auth I],
LA [auth I],
S [auth C],
T [auth C],
UA [auth L],
VA [auth L]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
LMT

Query on LMT



Download:Ideal Coordinates CCD File
BA [auth F],
MA [auth I],
TA [auth L],
U [auth C]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
AA [auth E],
JA [auth H],
R [auth B],
SA [auth K]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S

Query on F3S



Download:Ideal Coordinates CCD File
IA [auth H],
Q [auth B],
RA [auth K],
Z [auth E]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
FES

Query on FES



Download:Ideal Coordinates CCD File
HA [auth H],
P [auth B],
QA [auth K],
Y [auth E]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
MLA

Query on MLA



Download:Ideal Coordinates CCD File
FA [auth G],
N [auth A],
OA [auth J],
W [auth D]
MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
GA [auth G],
O [auth A],
PA [auth J],
X [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.291 (Depositor) 
  • R-Value Work:  0.283 (Depositor) 
  • R-Value Observed: 0.283 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.074α = 90
b = 290.24β = 95.73
c = 153.614γ = 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: 2001-04-09
    Type: Initial release
  • Version 1.1: 2013-04-17
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2015-04-22
    Changes: Non-polymer description
  • Version 2.0: 2018-11-21
    Changes: Advisory, Atomic model, Data collection, Database references, Source and taxonomy, Structure summary
  • Version 2.1: 2023-12-13
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 2.2: 2024-10-23
    Changes: Structure summary