1M57

Structure of cytochrome c oxidase from Rhodobacter sphaeroides (EQ(I-286) mutant))


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.293 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The X-ray crystal structures of wild-type and EQ(I-286) mutant cytochrome c oxidases from Rhodobacter sphaeroides.

Svensson-Ek, M.Abramson, J.Larsson, G.Tornroth, S.Brzezinski, P.Iwata, S.

(2002) J.Mol.Biol. 321: 329-339

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structure of cytochrome c oxidase from Rhodobacter sphaeroides has been solved at 2.3/2.8A (anisotropic resolution). This high-resolution structure revealed atomic details of a bacterial terminal oxidase including water molecule positions and a p ...

    The structure of cytochrome c oxidase from Rhodobacter sphaeroides has been solved at 2.3/2.8A (anisotropic resolution). This high-resolution structure revealed atomic details of a bacterial terminal oxidase including water molecule positions and a potential oxygen pathway, which has not been reported in other oxidase structures. A comparative study of the wild-type and the EQ(I-286) mutant enzyme revealed structural rearrangements around E(I-286) that could be crucial for proton transfer in this enzyme. In the structure of the mutant enzyme, EQ(I-286), which cannot transfer protons during oxygen reduction, the side-chain of Q(I-286) does not have the hydrogen bond to the carbonyl oxygen of M(I-107) that is seen in the wild-type structure. Furthermore, the Q(I-286) mutant has a different arrangement of water molecules and residues in the vicinity of the Q side-chain. These differences between the structures could reflect conformational changes that take place upon deprotonation of E(I-286) during turnover of the wild-type enzyme, which could be part of the proton-pumping machinery of the enzyme.


    Organizational Affiliation

    Department of Biochemistry, Biomedical Center, Uppsala University, Box 576, Uppsala, Sweden. margareta.e.ek@astrazeneca.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
A, G
566Rhodobacter sphaeroidesMutation(s): 1 
Gene Names: ctaD
EC: 1.9.3.1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase wild-type
Find proteins for P33517 (Rhodobacter sphaeroides)
Go to UniProtKB:  P33517
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
B, H
264Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: ctaC (coxII, ctaB)
EC: 1.9.3.1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase wild-type
Find proteins for Q03736 (Rhodobacter sphaeroides)
Go to UniProtKB:  Q03736
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
C, I
266Rhodobacter sphaeroidesMutation(s): 0 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase wild-type
Find proteins for P84153 (Rhodobacter sphaeroides)
Go to UniProtKB:  P84153
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C OXIDASE
D, J
51Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: coxIV
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)
Protein: 
Cytochrome C Oxidase wild-type
Find proteins for Q8KRK5 (Rhodobacter sphaeroides)
Go to UniProtKB:  Q8KRK5
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA

Download SDF File 
Download CCD File 
A, G
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
 Ligand Interaction
PEH
Query on PEH

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Download CCD File 
A, C, D, G, I, J
DI-STEAROYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
 Ligand Interaction
CA
Query on CA

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

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Download CCD File 
A, G
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

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Download CCD File 
A, B, G, H
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.293 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 340.720α = 90.00
b = 340.720β = 90.00
c = 89.760γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-08-28
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance