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Cytochrome c oxidase (EC 1.9.3.1) [1] is an oligomeric enzymatic complex which is a component of the respiratory chain complex 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. In addition to the three large subunits that form the catalytic center of the enzyme complex there are, in eukaryotes, a variable number of small polypeptidic subunits. One of these subunits which is known as Vb in mammals, V in slime mold and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three to four conserved cysteines that coordinate the zinc ion [2,3]. Two of these cysteines are clustered in the C-terminal section of the subunit; we have used this region as a signature pattern. We also developed a profile that covers the whole subunit Vb zinc binding region.

January 2008 / Text revised; profile added.

PROSITE methods (with tools and information) covered by this documentation:

COX5B_2, PS51359; Cytochrome c oxidase subunit Vb, zinc binding domain profile  (MATRIX)

Sequences known to belong to this class detected by the profile: ALL Other sequence(s) detected in Swiss-Prot: NONE.

• Domain architecture view of Swiss-Prot proteins matching PS51359 • Retrieve an alignment of Swiss-Prot true positive hits:   Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format • Retrieve the sequence logo from the alignment • Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS51359 • Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS51359 • Scan Swiss-Prot/TrEMBL entries against PS51359 • view ligand binding statistics

Matching PDB structures: 1OCC 1OCO 1OCR 1OCZ ... [ALL]

COX5B_1, PS00848; Cytochrome c oxidase subunit Vb, zinc binding region signature  (PATTERN)

Consensus pattern: [LIVM](2)-[FYW]-x(10)-C-x(2)-C-G-x(2)-[FY]-K-L The 2 C's may bind zinc Sequences known to belong to this class detected by the pattern: ALL Other sequence(s) detected in Swiss-Prot: NONE.

• Retrieve an alignment of Swiss-Prot true positive hits:   Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format • Retrieve the sequence logo from the alignment • Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS00848 • Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS00848 • Scan Swiss-Prot/TrEMBL entries against PS00848 • view ligand binding statistics

Matching PDB structures: 1OCC 1OCO 1OCR 1OCZ ... [ALL]

1	Authors	Capaldi R.A., Malatesta F., Darley-Usmar V.M.
	Title	Structure of cytochrome c oxidase.
	Source	Biochim. Biophys. Acta 726:135-148(1983).
	PubMed ID	6307356

2	Authors	Rizzuto R., Sandona D., Brini M., Capaldi R.A., Bisson R.
	Title	The most conserved nuclear-encoded polypeptide of cytochrome c oxidase is the putative zinc-binding subunit: primary structure of subunit V from the slime mold Dictyostelium discoideum.
	Source	Biochim. Biophys. Acta 1129:100-104(1991).
	PubMed ID	1661610

3	Authors	Tsukihara T., Aoyama H., Yamashita E., Tomizaki T., Yamaguchi H., Shinzawa-Itoh K., Nakashima R., Yaono R., Yoshikawa S.
	Title	The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A.
	Source	Science 272:1136-1144(1996).
	PubMed ID	8638158

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