3MK7

The structure of CBB3 cytochrome oxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    5DJQ, 3MK7

  • 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 for the pathogenicity of many bacteria--that differs from the two other HCO families, A and B, that have been structurally analyzed ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase, cbb3-type, subunit NA, D, G, J [auth K]474Pseudomonas stutzeriMutation(s): 0 
Gene Names: ccoN1
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for D9IA43 (Pseudomonas stutzeri)
Explore D9IA43 
Go to UniProtKB:  D9IA43
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase, cbb3-type, subunit OB, E, H, K [auth L]203Pseudomonas stutzeriMutation(s): 0 
Gene Names: ccoO1ccoOCXK99_03610
Membrane Entity: Yes 
UniProt
Find proteins for D9IA44 (Pseudomonas stutzeri)
Explore D9IA44 
Go to UniProtKB:  D9IA44
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase, cbb3-type, subunit PC, F, I, L [auth M]311Pseudomonas stutzeriMutation(s): 0 
Gene Names: ccoP1
Membrane Entity: Yes 
UniProt
Find proteins for D9IA45 (Pseudomonas stutzeri)
Explore D9IA45 
Go to UniProtKB:  D9IA45
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30-mer peptideM [auth U], N [auth X], O [auth Y], P [auth Z]30Pseudomonas stutzeriMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC (Subject of Investigation/LOI)
Query on HEC

Download Ideal Coordinates CCD File 
EB [auth L] , GB [auth M] , HB [auth M] , IA [auth E] , JA [auth F] , KA [auth F] , TA [auth H] , VA [auth I] , 
EB [auth L],  GB [auth M],  HB [auth M],  IA [auth E],  JA [auth F],  KA [auth F],  TA [auth H],  VA [auth I],  WA [auth I],  X [auth B],  Y [auth C],  Z [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
BA [auth D], CA [auth D], MA [auth G], NA [auth G], Q [auth A], R [auth A], XA [auth K], YA [auth K]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
FC6 (Subject of Investigation/LOI)
Query on FC6

Download Ideal Coordinates CCD File 
AA [auth C], FB [auth M], LA [auth F], UA [auth I]HEXACYANOFERRATE(3-)
C6 Fe N6
HCMVSLMENOCDCK-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
CB [auth K], FA [auth D], SA [auth G], V [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CU
Query on CU

Download Ideal Coordinates CCD File 
DA [auth D], OA [auth G], S [auth A], ZA [auth K]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
AB [auth K], BB [auth K], EA [auth D], HA [auth E], PA [auth G], QA [auth G], T [auth A], W [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PEO
Query on PEO

Download Ideal Coordinates CCD File 
DB [auth K], GA [auth D], RA [auth G], U [auth A]HYDROGEN PEROXIDE
H2 O2
MHAJPDPJQMAIIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.475α = 90
b = 279.933β = 90
c = 175.192γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHELXDphasing
SHARPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance