PDBsum entry 1w2l

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Oxidoreductase PDB id
Protein chain
97 a.a. *
Waters ×131
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: CytochromE C domain of caa3 oxygen oxidoreductase
Structure: Cytochrome oxidase subunit ii. Chain: a. Fragment: cytochromE C domain, residues 218-316. Engineered: yes
Source: Rhodothermus marinus. Organism_taxid: 29549. Expressed in: escherichia coli. Expression_system_taxid: 511693.
1.30Å     R-factor:   0.142     R-free:   0.169
Authors: V.Srinivasan,C.Rajendran,F.L.Sousa,A.M.P.Melo,L.M.Saraiva, M.M.Pereira,M.Santana,M.Teixeira,H.Michel
Key ref:
V.Srinivasan et al. (2005). Structure at 1.3 A resolution of Rhodothermus marinus caa(3) cytochrome c domain. J Mol Biol, 345, 1047-1057. PubMed id: 15644203 DOI: 10.1016/j.jmb.2004.10.069
06-Jul-04     Release date:   19-Jan-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9F3S9  (Q9F3S9_RHOMR) -  Cytochrome c oxidase subunit 2
316 a.a.
97 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Cytochrome-c oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O
4 × ferrocytochrome c
Bound ligand (Het Group name = HEM)
matches with 63.00% similarity
+ O(2)
+ 4 × H(+)
= 4 × ferricytochrome c
+ 2 × H(2)O
      Cofactor: Cu cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     electron carrier activity     2 terms  


DOI no: 10.1016/j.jmb.2004.10.069 J Mol Biol 345:1047-1057 (2005)
PubMed id: 15644203  
Structure at 1.3 A resolution of Rhodothermus marinus caa(3) cytochrome c domain.
V.Srinivasan, C.Rajendran, F.L.Sousa, A.M.Melo, L.M.Saraiva, M.M.Pereira, M.Santana, M.Teixeira, H.Michel.
The cytochrome c domain of subunit II from the Rhodothermus marinus caa(3) HiPIP:oxygen oxidoreductase, a member of the superfamily of heme-copper-containing terminal oxidases, was produced in Escherichia coli and characterised. The recombinant protein, which shows the same optical absorption and redox properties as the corresponding domain in the holo enzyme, was crystallized and its structure was determined to a resolution of 1.3 A by the multiwavelength anomalous dispersion (MAD) technique using the anomalous dispersion of the heme iron atom. The model was refined to final R(cryst) and R(free) values of 13.9% and 16.7%, respectively. The structure reveals the insertion of two short antiparallel beta-strands forming a small beta-sheet, an interesting variation of the classical all alpha-helical cytochrome c fold. This modification appears to be common to all known caa(3)-type terminal oxidases, as judged by comparative modelling and by analyses of the available amino acid sequences for these enzymes. This is the first high-resolution crystal structure reported for a cytochrome c domain of a caa(3)-type terminal oxidase. The R.marinus caa(3) uses HiPIP as the redox partner. The calculation of the electrostatic potential at the molecular surface of this extra C-terminal domain provides insights into the binding to its redox partner on one side and its interaction with the remaining subunit II on the other side.
  Selected figure(s)  
Figure 4.
Figure 4. Electrostatic potential map at the molecular surface of the cytochrome c domain from R. marinus caa[3] HiPIP:oxygen oxidoreductase. Red zones correspond to negative potentials and blue to positive potential values. The range spans -10 to +10 k[B]T (k[B], Boltzmann constant and T, temperature). (a) The molecule is viewed from the side proximal to the heme. (b) Viewed distal to the heme. (c) The same potential map at the molecular surface of the subunit II, the CuA of R. marinus caa[3] HiPIP:oxygen oxidoreductase. The Figure was prepared using the program GRASP.18
Figure 5.
Figure 5. Superposition of the C^a-backbone trace of the crystal structure with (a) cytochrome c[551] from P. aeruginosa, (b) cytochrome c isozyme 1 from S. cerevisiae. The structures were aligned by the least-squares algorithm implemented in O.23 The crystal structure is shown in blue and the aligned cytochromes in orange. The heme group is illustrated in green.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 345, 1047-1057) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22763450 J.A.Lyons, D.Aragão, O.Slattery, A.V.Pisliakov, T.Soulimane, and M.Caffrey (2012).
Structural insights into electron transfer in caa3-type cytochrome oxidase.
  Nature, 487, 514-518.
PDB code: 2yev
18676644 A.F.Veríssimo, F.L.Sousa, A.M.Baptista, M.Teixeira, and M.M.Pereira (2008).
Thermodynamic redox behavior of the heme centers in A-type heme-copper oxygen reductases: comparison between the two subfamilies.
  Biophys J, 95, 4448-4455.  
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