6AWF

Escherichia coli quinol:fumarate reductase crystallized without dicarboxylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.285 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

New crystal forms of the integral membrane Escherichia coli quinol:fumarate reductase suggest that ligands control domain movement.

Starbird, C.A.Tomasiak, T.M.Singh, P.K.Yankovskaya, V.Maklashina, E.Eisenbach, M.Cecchini, G.Iverson, T.M.

(2018) J. Struct. Biol. 202: 100-104

  • DOI: 10.1016/j.jsb.2017.11.004

  • PubMed Abstract: 
  • Quinol:fumarate reductase (QFR) is an integral membrane protein and a member of the respiratory Complex II superfamily. Although the structure of Escherichia coli QFR was first reported almost twenty years ago, many open questions of catalysis remain ...

    Quinol:fumarate reductase (QFR) is an integral membrane protein and a member of the respiratory Complex II superfamily. Although the structure of Escherichia coli QFR was first reported almost twenty years ago, many open questions of catalysis remain. Here we report two new crystal forms of QFR, one grown from the lipidic cubic phase and one grown from dodecyl maltoside micelles. QFR crystals grown from the lipid cubic phase processed as P1, merged to 7.5 Å resolution, and exhibited crystal packing similar to previous crystal forms. Crystals grown from dodecyl maltoside micelles processed as P21, merged to 3.35 Å resolution, and displayed a unique crystal packing. This latter crystal form provides the first view of the E. coli QFR active site without a dicarboxylate ligand. Instead, an unidentified anion binds at a shifted position. In one of the molecules in the asymmetric unit, this is accompanied by rotation of the capping domain of the catalytic subunit. In the other molecule, this is associated with loss of interpretable electron density for this same capping domain. Analysis of the structure suggests that the ligand adjusts the position of the capping domain.


    Organizational Affiliation

    Graduate Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN 37232, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fumarate reductase flavoprotein subunit
A, E
602Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: frdA
EC: 1.3.5.4
Find proteins for P00363 (Escherichia coli (strain K12))
Go to UniProtKB:  P00363
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fumarate reductase iron-sulfur subunit
B, F
243Escherichia coli O157:H7Mutation(s): 0 
Gene Names: frdB
EC: 1.3.5.1
Find proteins for P0AC49 (Escherichia coli O157:H7)
Go to UniProtKB:  P0AC49
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fumarate reductase subunit C
C, G
130Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: frdC
Find proteins for B7MKV9 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MKV9
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Fumarate reductase subunit D
D, H
119Escherichia coli O45:K1 (strain S88 / ExPEC)Mutation(s): 0 
Gene Names: frdD
Find proteins for B7MKV8 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Go to UniProtKB:  B7MKV8
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
B, F
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
A, E
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
F3S
Query on F3S

Download SDF File 
Download CCD File 
B, F
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FAD
Query on FAD

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Download CCD File 
A, E
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
FES
Query on FES

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Download CCD File 
B, F
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.285 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 113.318α = 90.00
b = 117.986β = 98.80
c = 125.291γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-09-05 
  • Released Date: 2017-12-06 
  • Deposition Author(s): Iverson, T.M.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM061606
Department of Veterans AffairsUnited StatesBX001077

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2018-03-14
    Type: Database references