5KKZ

Rhodobacter sphaeroides bc1 with famoxadone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Hydrogen Bonding to the Substrate Is Not Required for Rieske Iron-Sulfur Protein Docking to the Quinol Oxidation Site of Complex III.

Esser, L.Zhou, F.Zhou, Y.Xiao, Y.Tang, W.K.Yu, C.A.Qin, Z.Xia, D.

(2016) J.Biol.Chem. 291: 25019-25031

  • DOI: 10.1074/jbc.M116.744391
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Complex III or the cytochrome (cyt) bc1 complex constitutes an integral part of the respiratory chain of most aerobic organisms and of the photosynthetic apparatus of anoxygenic purple bacteria. The function of cyt bc1 is to couple the reaction of el ...

    Complex III or the cytochrome (cyt) bc1 complex constitutes an integral part of the respiratory chain of most aerobic organisms and of the photosynthetic apparatus of anoxygenic purple bacteria. The function of cyt bc1 is to couple the reaction of electron transfer from ubiquinol to cytochrome c to proton pumping across the membrane. Mechanistically, the electron transfer reaction requires docking of its Rieske iron-sulfur protein (ISP) subunit to the quinol oxidation site (QP) of the complex. Formation of an H-bond between the ISP and the bound substrate was proposed to mediate the docking. Here we show that the binding of oxazolidinedione-type inhibitors famoxadone, jg144, and fenamidone induces docking of the ISP to the QP site in the absence of the H-bond formation both in mitochondrial and bacterial cyt bc1 complexes, demonstrating that ISP docking is independent of the proposed direct ISP-inhibitor interaction. The binding of oxazolidinedione-type inhibitors to cyt bc1 of different species reveals a toxophore that appears to interact optimally with residues in the QP site. The effect of modifications or additions to the toxophore on the binding to cyt bc1 from different species could not be predicted from structure-based sequence alignments, as demonstrated by the altered binding mode of famoxadone to bacterial cyt bc1.


    Organizational Affiliation

    From the Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b
A, E, K, O
445Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: petB (fbcB)
Find proteins for Q02761 (Rhodobacter sphaeroides)
Go to UniProtKB:  Q02761
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c1
B, F, L, P
272Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: petC (fbcC)
Find proteins for Q02760 (Rhodobacter sphaeroides)
Go to UniProtKB:  Q02760
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquinol-cytochrome c reductase iron-sulfur subunit
C, G, M, Q
187Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: petA (fbcF)
EC: 7.1.1.8
Find proteins for Q02762 (Rhodobacter sphaeroides)
Go to UniProtKB:  Q02762
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LOP
Query on LOP

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A, E, K, O
(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
LAURYL OLEYL PHOSPHATIDYL ETHANOLAMINE
C35 H68 N O8 P
FUUNMZKPCMPCHT-ILGKRYBBSA-N
 Ligand Interaction
ASC
Query on ASC

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Download CCD File 
A, E, K, O
ASCORBIC ACID
C6 H8 O6
CIWBSHSKHKDKBQ-JLAZNSOCSA-N
 Ligand Interaction
FMX
Query on FMX

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A, E, K, O
FAMOXADONE
5-METHYL-5-(4-PHENOXYPHENYL)-3-(PHENYLAMINO)-2,4-OXAZOLIDINEDIONE
C22 H18 N2 O4
PCCSBWNGDMYFCW-QFIPXVFZSA-N
 Ligand Interaction
FES
Query on FES

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C, G, M, Q
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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A, E, K, O
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
HEC
Query on HEC

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B, F, L, P
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
BOG
Query on BOG

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Download CCD File 
B, F, K, P
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
SR
Query on SR

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Download CCD File 
A, B, F, K, L, P
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.215 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 120.773α = 63.92
b = 128.277β = 88.63
c = 128.283γ = 63.38
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2016-10-19
    Type: Derived calculations
  • Version 1.2: 2016-11-02
    Type: Database references
  • Version 1.3: 2016-12-07
    Type: Database references