1M56

Structure of cytochrome c oxidase from Rhodobactor sphaeroides (Wild Type)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 

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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

  • DOI: 10.1016/s0022-2836(02)00619-8
  • Primary Citation of Related Structures:  
    1M57, 1M56

  • 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASEA, G566Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: ctaD
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane protein
Mpstruc		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)
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Go to UniProtKB:  P33517
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASEB, H264Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: ctaC, coxII, ctaB
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane protein
Mpstruc		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)
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Go to UniProtKB:  Q03736
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASEC, I266Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: EBL86_02290
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane protein
Mpstruc		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)
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C OXIDASED, J51Rhodobacter sphaeroidesMutation(s): 0 
Gene Names: coxIV
EC: 1.9.3.1
Membrane protein
Mpstruc		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)
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Go to UniProtKB:  Q8KRK5
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEA
Query on HEA
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A, G
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L		 Ligand Interaction
PEH
Query on PEH
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A, C, D, G, I, J
DI-STEAROYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N		 Ligand Interaction
CU
Query on CU
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A, B, G, H
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
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A, G
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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A, G
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 340.36α = 90
b = 340.36β = 90
c = 89.668γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

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