2YIU

X-ray structure of the dimeric cytochrome BC1 complex from the soil bacterium paracoccus denitrificans at 2.7 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

X-Ray Structure of the Dimeric Cytochrome Bc(1) Complex from the Soil Bacterium Paracoccus Denitrificans at 2.7-A Resolution.

Kleinschroth, T.Castellani, M.Trinh, C.H.Morgner, N.Brutschy, B.Ludwig, B.Hunte, C.

(2011) Biochim.Biophys.Acta 1807: 1606

  • DOI: 10.1016/j.bbabio.2011.09.017

  • PubMed Abstract: 
  • The respiratory cytochrome bc(1) complex is a fundamental enzyme in biological energy conversion. It couples electron transfer from ubiquinol to cytochrome c with generation of proton motive force which fuels ATP synthesis. The complex from the α-pro ...

    The respiratory cytochrome bc(1) complex is a fundamental enzyme in biological energy conversion. It couples electron transfer from ubiquinol to cytochrome c with generation of proton motive force which fuels ATP synthesis. The complex from the α-proteobacterium Paracoccus denitrificans, a model for the medically relevant mitochondrial complexes, lacked structural characterization. We show by LILBID mass spectrometry that truncation of the organism-specific, acidic N-terminus of cytochrome c(1) changes the oligomerization state of the enzyme to a dimer. The fully functional complex was crystallized and the X-ray structure determined at 2.7-Å resolution. It has high structural homology to mitochondrial complexes and to the Rhodobacter sphaeroides complex especially for subunits cytochrome b and ISP. Species-specific binding of the inhibitor stigmatellin is noteworthy. Interestingly, cytochrome c(1) shows structural differences to the mitochondrial and even between the two Rhodobacteraceae complexes. The structural diversity in the cytochrome c(1) surface facing the ISP domain indicates low structural constraints on that surface for formation of a productive electron transfer complex. A similar position of the acidic N-terminal domains of cytochrome c(1) and yeast subunit QCR6p is suggested in support of a similar function. A model of the electron transfer complex with membrane-anchored cytochrome c(552), the natural substrate, shows that it can adopt the same orientation as the soluble substrate in the yeast complex. The full structural integrity of the P. denitrificans variant underpins previous mechanistic studies on intermonomer electron transfer and paves the way for using this model system to address open questions of structure/function relationships and inhibitor binding.


    Organizational Affiliation

    Institute for Biochemistry and Molecular Biology, ZMBZ, BIOSS Centre for Biological Signalling Studies, Stefan-Meier-Strasse 17, Albert-Ludwigs-University, 79104 Freiburg, Germany. thomas.kleinschroth@biochemie.uni-freiburg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME B
A, D
450Paracoccus denitrificansMutation(s): 0 
Gene Names: petB
Find proteins for P05418 (Paracoccus denitrificans)
Go to UniProtKB:  P05418
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C1, HEME PROTEIN
B, E
263Paracoccus denitrificansMutation(s): 0 
Gene Names: petC
Find proteins for P13627 (Paracoccus denitrificans)
Go to UniProtKB:  P13627
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT
C, F
190Paracoccus denitrificansMutation(s): 0 
Gene Names: petA
EC: 7.1.1.8
Find proteins for P05417 (Paracoccus denitrificans)
Go to UniProtKB:  P05417
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

Download SDF File 
Download CCD File 
C, F
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
HEC
Query on HEC

Download SDF File 
Download CCD File 
B, E
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
SMA
Query on SMA

Download SDF File 
Download CCD File 
A, D
STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SMAIC50: 130 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.238 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 85.300α = 90.00
b = 164.910β = 103.18
c = 100.610γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-26
    Type: Initial release
  • Version 1.1: 2011-11-23
    Type: Database references