SUPERFAMILY 1.75 HMM library and genome assignments server


Cytochrome c oxidase subunit III-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Membrane and cell surface proteins and peptides [ 56835] (58)
Fold:   Cytochrome c oxidase subunit III-like [ 81453]
Superfamily:   Cytochrome c oxidase subunit III-like [ 81452]
Families:   Cytochrome c oxidase subunit III-like [ 81451] (3)


Superfamily statistics
Genomes (1,331) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 2,335 16,627 6
Proteins 2,302 16,535 6


Functional annotation
General category Metabolism
Detailed category Energy

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)single-organism metabolic process0.098480.03946Least InformativeInherited
Biological Process (BP)oxidation-reduction process7.153e-077.285e-07Moderately InformativeDirect
Biological Process (BP)energy derivation by oxidation of organic compounds8.658e-099.37e-09InformativeDirect
Biological Process (BP)respiratory electron transport chain1.385e-111.685e-11Highly InformativeDirect
Molecular Function (MF)transporter activity1.008e-051.882e-05Moderately InformativeDirect
Molecular Function (MF)oxidoreductase activity4.496e-061.462e-06Moderately InformativeDirect
Molecular Function (MF)inorganic cation transmembrane transporter activity2.058e-095.105e-08InformativeDirect
Molecular Function (MF)heme-copper terminal oxidase activity1.97e-093.948e-11Highly InformativeDirect
Molecular Function (MF)hydrogen ion transmembrane transporter activity6.742e-121.503e-12Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.0031380.03409Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.003220.006452Least InformativeInherited

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) single-organism metabolic process 0.03946 Least Informative Inherited
Biological Process (BP) oxidation-reduction process 7.285e-07 Moderately Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 9.37e-09 Informative Direct
Biological Process (BP) respiratory electron transport chain 1.685e-11 Highly Informative Direct
Molecular Function (MF) transporter activity 1.882e-05 Moderately Informative Direct
Molecular Function (MF) oxidoreductase activity 1.462e-06 Moderately Informative Direct
Molecular Function (MF) inorganic cation transmembrane transporter activity 5.105e-08 Informative Direct
Molecular Function (MF) heme-copper terminal oxidase activity 3.948e-11 Highly Informative Direct
Molecular Function (MF) hydrogen ion transmembrane transporter activity 1.503e-12 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.03409 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.006452 Least Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Acting on a heme group of donors0Highly InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Acting on a heme group of donors0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Cellular componentMembrane0Least InformativeDirect
Cellular componentMitochondrion0Moderately InformativeDirect
Cellular componentMitochondrion inner membrane0InformativeDirect
DomainTransmembrane0Least InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR000298 SSF81452 Protein matches
Abstract

Cytochrome c oxidase is the terminal enzyme of the respiratory chain of mitochondria and many aerobic bacteria. It catalyzes the transfer of electrons from reduced cytochrome c to molecular oxygen:

4 cytochrome c+2 + 4 H+ + O2 --> 4 cytochrome c+3 + 2 H2O

This reaction is coupled to the pumping of four additional protons across the mitochondrial or bacterial membrane [PubMed10563795, PubMed16598262].

Cytochrome c oxidase is an oligomeric enzymatic complex that is located in the mitochondrial inner membrane of eukaryotes and in the plasma membrane of aerobic prokaryotes. The core structure of prokaryotic and eukaryotic cytochrome c oxidase contains three common subunits, I, II and III. In prokaryotes, subunits I and III can be fused and a fourth subunit is sometimes found, whereas in eukaryotes there are a variable number of additional small polypeptidic subunits [PubMed8383670]. The functional role of subunit III is not yet understood.

As the bacterial respiratory systems are branched, they have a number of distinct terminal oxidases, rather than the single cytochrome c oxidase present in the eukaryotic mitochondrial systems. Although the cytochrome o oxidases do not catalyze the cytochrome c but the quinol (ubiquinol) oxidation they belong to the same haem-copper oxidase superfamily as cytochrome c oxidases. Members of this family share sequence similarities in all three core subunits: subunit I is the most conserved subunit, whereas subunit II is the least conserved [PubMed1316894, PubMed2162835, PubMed8083153].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 4 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Cytochrome c oxidase subunit III-like domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 4 hidden Markov models representing the Cytochrome c oxidase subunit III-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]