5DJQ

The structure of CBB3 cytochrome oxidase.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The structure of cbb3 cytochrome oxidase provides insights into proton pumping.

Buschmann, S.Warkentin, E.Xie, H.Langer, J.D.Ermler, U.Michel, H.

(2010) Science 329: 327-330

  • DOI: 10.1126/science.1187303
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The heme-copper oxidases (HCOs) accomplish the key event of aerobic respiration; they couple O2 reduction and transmembrane proton pumping. To gain new insights into the still enigmatic process, we structurally characterized a C-family HCO--essential ...

    The heme-copper oxidases (HCOs) accomplish the key event of aerobic respiration; they couple O2 reduction and transmembrane proton pumping. To gain new insights into the still enigmatic process, we structurally characterized a C-family HCO--essential for the pathogenicity of many bacteria--that differs from the two other HCO families, A and B, that have been structurally analyzed. The x-ray structure of the C-family cbb3 oxidase from Pseudomonas stutzeri at 3.2 angstrom resolution shows an electron supply system different from families A and B. Like family-B HCOs, C HCOs have only one pathway, which conducts protons via an alternative tyrosine-histidine cross-link. Structural differences around hemes b and b3 suggest a different redox-driven proton-pumping mechanism and provide clues to explain the higher activity of family-C HCOs at low oxygen concentrations.


    Related Citations: 
    • Identification and Characterization of the Novel Subunit CcoM in the cbb33Cytochrome c Oxidase from Pseudomonas stutzeri ZoBell.
      Kohlstaedt, M.,Buschmann, S.,Xie, H.,Resemann, A.,Warkentin, E.,Langer, J.D.,Michel, H.
      (2016) Mbio 7: e01921


    Organizational Affiliation

    Max-Planck-Institut für Biophysik, Max-von-Laue-Strasse 3, D-60438 Frankfurt/Main, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cbb3-type cytochrome c oxidase subunit CcoN1
A, D, G, K
474Pseudomonas stutzeriMutation(s): 0 
Gene Names: ccoN1
EC: 1.9.3.1
Find proteins for D9IA43 (Pseudomonas stutzeri)
Go to UniProtKB:  D9IA43
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cbb3-type cytochrome c oxidase subunit II
B, E, H, L
203Pseudomonas stutzeriMutation(s): 0 
Gene Names: ccoO1 (ccoO)
Find proteins for D9IA44 (Pseudomonas stutzeri)
Go to UniProtKB:  D9IA44
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cbb3-type cytochrome c oxidase subunit CcoP1
C, F, I, M
311Pseudomonas stutzeriMutation(s): 0 
Gene Names: ccoP1
Find proteins for D9IA45 (Pseudomonas stutzeri)
Go to UniProtKB:  D9IA45
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Putative uncharacterized protein
N, O, P, Q
36N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, D, G, K
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
FC6
Query on FC6

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Download CCD File 
C, F, I, M
HEXACYANOFERRATE(3-)
FERRI(III)HEXACYANIDE
C6 Fe N6
HCMVSLMENOCDCK-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, D, G, K
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PEO
Query on PEO

Download SDF File 
Download CCD File 
A, D, G, K
HYDROGEN PEROXIDE
H2 O2
MHAJPDPJQMAIIY-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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

Download SDF File 
Download CCD File 
A, D, G, K
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
HEC
Query on HEC

Download SDF File 
Download CCD File 
B, C, E, F, H, I, L, M
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 136.475α = 90.00
b = 279.933β = 90.00
c = 175.192γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
XDSdata reduction
SHARPphasing
XSCALEdata scaling
Omodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-07-27
    Type: Database references