Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
144  structures 18166  species 11  interactions 31269  sequences 29  architectures

Family: COX2 (PF00116)

Summary: Cytochrome C oxidase subunit II, periplasmic domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Cytochrome c oxidase subunit II". More...

Cytochrome c oxidase subunit II Edit Wikipedia article

Cytochrome c oxidase subunit II
Available structures
PDB Ortholog search: PDBe, RCSB
Identifiers
Symbols COX2; COII; MTCO2
External IDs OMIM516040 MGI102503 HomoloGene5017 ChEMBL: 6174 GeneCards: COX2 Gene
Orthologs
Species Human Mouse
Entrez 4513 17709
Ensembl ENSG00000198712 ENSMUSG00000064354
UniProt P00403 P00405
RefSeq (mRNA) n/a n/a
RefSeq (protein) YP_003024029 NP_904331
Location (UCSC) Chr MT:
0.01 – 0.01 Mb
Chr MT:
0.01 – 0.01 Mb
PubMed search [1] [2]
Cytochrome c oxidase subunit II, transmembrane domain
1qle opm.gif
Bacterial cytochrome c oxidase complex. Subunit II indicated by blue.
Identifiers
Symbol COX2_TM
Pfam PF02790
InterPro IPR011759
PROSITE PDOC00075
SCOP 1occ
SUPERFAMILY 1occ
TCDB 3.D.4
OPM superfamily 4
OPM protein 1v55
Cytochrome C oxidase subunit II, periplasmic domain
Identifiers
Symbol COX2
Pfam PF00116
InterPro IPR002429
PROSITE PDOC00075
SCOP 1occ
SUPERFAMILY 1occ
TCDB 3.D.4
OPM superfamily 4
OPM protein 1v55

Cytochrome c oxidase subunit 2, also known as cytochrome c oxidase polypeptide II, is a protein that in humans is encoded by the MT-CO2 gene.[1]

Cytochrome c oxidase subunit II, abbreviated COXII, COX2, COII, or MT-CO2, is the second subunit of cytochrome c oxidase.

Cytochrome c oxidase (EC 1.9.3.1)[2][3] is an oligomeric enzymatic complex which is a component of the respiratory chain and is involved in the transfer of electrons from cytochrome c to oxygen. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. The enzyme complex consists of 3-4 subunits (prokaryotes) to up to 13 polypeptides (mammals). In Leigh's disease, there may be an abnormality or deficiency of cytochrome oxidase.

Subunit 2 (COII) transfers the electrons from cytochrome c to the catalytic subunit 1. It contains two adjacent transmembrane regions in its N-terminus and the major part of the protein is exposed to the periplasmic or to the mitochondrial intermembrane space, respectively. COII provides the substrate-binding site and contains a copper centre called Cu(A) (see IPR001505), probably the primary acceptor in cytochrome c oxidase. An exception is the corresponding subunit of the cbb3-type oxidase which lacks the copper A redox-centre. Several bacterial COII have a C-terminal extension that contains a covalently bound haem c.

The N-terminal domain of cytochrome C oxidase contains two transmembrane alpha-helices.

References[edit]

  1. ^ "Entrez Gene: COX2 cytochrome c oxidase subunit II". 
  2. ^ Capaldi RA, Malatesta F, Darley-Usmar VM (July 1983). "Structure of cytochrome c oxidase". Biochim. Biophys. Acta 726 (2): 135–48. PMID 6307356. 
  3. ^ García-Horsman JA, Barquera B, Rumbley J, Ma J, Gennis RB (September 1994). "The superfamily of heme-copper respiratory oxidases". J. Bacteriol. 176 (18): 5587–600. PMC 196760. PMID 8083153. 

Further reading[edit]

References[edit]

  1. ^ "Entrez Gene: COX2 cytochrome c oxidase subunit II". 
  2. ^ Capaldi RA, Malatesta F, Darley-Usmar VM (July 1983). "Structure of cytochrome c oxidase". Biochim. Biophys. Acta 726 (2): 135–48. PMID 6307356. 
  3. ^ García-Horsman JA, Barquera B, Rumbley J, Ma J, Gennis RB (September 1994). "The superfamily of heme-copper respiratory oxidases". J. Bacteriol. 176 (18): 5587–600. PMC 196760. PMID 8083153. 

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Cytochrome C oxidase subunit II, periplasmic domain Provide feedback

No Pfam abstract.

Literature references

  1. Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, Yaono R, Yoshikawa S; , Science 1996;272:1136-1144.: The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A. PUBMED:8638158 EPMC:8638158


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002429

Cytochrome c oxidase (EC) [PUBMED:6307356, PUBMED:8083153] is an oligomeric enzymatic complex which is a component of the respiratory chain and is involved in the transfer of electrons from cytochrome c to oxygen. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. The number of polypeptides in the complex ranges from 3-4 (prokaryotes), up to 13(mammals).

Subunit 2 (CO II) transfers the electrons from cytochrome c to the catalytic subunit 1. It contains two adjacent transmembrane regions in its N terminus and the major part of the protein is exposed to the periplasmic or to the mitochondrial intermembrane space, respectively. CO II provides the substrate-binding site and contains a copper centre called Cu(A), probably the primary acceptor in cytochrome c oxidase. An exception is the corresponding subunit of the cbb3-type oxidase which lacks the copper A redox-centre. Several bacterial CO II have a C-terminal extension that contains a covalently bound haem c.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

Pfam Clan

This family is a member of clan CU_oxidase (CL0026), which has the following description:

Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain.

The clan contains the following 9 members:

Copper-bind COX2 Cu-oxidase Cu-oxidase_2 Cu-oxidase_3 Cu_bind_like Cupredoxin_1 Ephrin SoxE

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(32)
Full
(31269)
Representative proteomes NCBI
(28095)
Meta
(2586)
RP15
(349)
RP35
(789)
RP55
(1076)
RP75
(1320)
Jalview View  View  View  View  View  View  View  View 
HTML View    View  View  View  View     
PP/heatmap 1   View  View  View  View     
Pfam viewer View  View             

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(32)
Full
(31269)
Representative proteomes NCBI
(28095)
Meta
(2586)
RP15
(349)
RP35
(789)
RP55
(1076)
RP75
(1320)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(32)
Full
(31269)
Representative proteomes NCBI
(28095)
Meta
(2586)
RP15
(349)
RP35
(789)
RP55
(1076)
RP75
(1320)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Prosite
Previous IDs: none
Type: Domain
Author: Sonnhammer ELL, Griffiths-Jones SR
Number in seed: 32
Number in full: 31269
Average length of the domain: 106.00 aa
Average identity of full alignment: 48 %
Average coverage of the sequence by the domain: 47.64 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.0 22.0
Trusted cut-off 22.0 22.0
Noise cut-off 21.9 21.9
Model length: 120
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Interactions

There are 11 interactions for this family. More...

COX3 COX4_pro_2 COX6C COX2_TM Cytochrom_C COX4 COX1 CoxIIa COX2 COX6B COX_ARM

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the COX2 domain has been found. There are 144 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

Loading structure mapping...