{PDOC00075}
{PS00078; COX2}
{PS50999; COX2_TM}
{PS50857; COX2_CUA}
{BEGIN}
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* Cytochrome c oxidase subunit II signature and profiles *
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Cytochrome  c  oxidase  (EC  1.9.3.1) [1,2] 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).

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  center  called  Cu(A), located in the
extramembrane  domain  (see  <PDB:1OCZ;  B>), 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-center. Several bacterial CO
II have a C-terminal extension that contains a covalently bound heme c.

It has been shown [3,4] that nitrous oxide reductase (EC 1.7.99.6) (gene nosZ)
of Pseudomonas has sequence similarity in its C-terminus to CO II. This enzyme
is part of the bacterial respiratory system which is activated under anaerobic
conditions in  the presence of nitrate or nitrous oxide. NosZ is a periplasmic
homodimer that  contains  a  dinuclear copper center, probably located in a 3-
dimensional fold  similar  to the cupredoxin-like fold that has been suggested
for the copper-binding site of CO II [3].

The  dinuclear  purple copper center is formed by 2 histidines and 2 cysteines
[5].  We used this region as a signature pattern. The conserved valine and the
conserved methionine are said to be involved in stabilizing the copper-binding
fold  by  interacting  with  each  other.  We also developed two profiles, one
directed against the transmembrane region and one against the copper center.

-Consensus pattern: V-x-H-x(33,40)-C-x(3)-C-x(3)-H-x(2)-M
           [The 2 C's and the 2 H's are copper ligands]
-Sequences known to belong to this class detected by the pattern: ALL,  except
 for Paramecium  primaurelia  as well as in some plants where the pattern ends
 with Thr; an RNA editing event at this position could change this Thr to Met.
-Other sequence(s) detected in Swiss-Prot: NONE.

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

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

-Note: Cytochrome cbb(3) subunit 2 does not belong to this family.

-Last update: June 2004 / Text revised; profiles added.

[ 1] Capaldi R.A., Malatesta F., Darley-Usmar V.M.
     "Structure of cytochrome c oxidase."
     Biochim. Biophys. Acta 726:135-148(1983).
     PubMed=6307356
[ 2] Garcia-Horsman J.A., Barquera B., Rumbley J., Ma J., Gennis R.B.
     J. Bacteriol. 176:5587-5600(1994).
[ 3] van der Oost J., Lappalainen P., Musacchio A., Warne A., Lemieux L.,
     Rumbley J., Gennis R.B., Aasa R., Pascher T., Malmstrom B.G., Saraste M.
     EMBO J. 11:3209-3217(1992).
[ 4] Zumft W.G., Dreusch A., Lochelt S., Cuypers H., Friedrich B.,
     Schneider B.
     "Derived amino acid sequences of the nosZ gene (respiratory N2O
     reductase) from Alcaligenes eutrophus, Pseudomonas aeruginosa and
     Pseudomonas stutzeri reveal potential copper-binding residues.
     Implications for the CuA site of N2O reductase and cytochrome-c
     oxidase."
     Eur. J. Biochem. 208:31-40(1992).
     PubMed=1324835
[ 5] Saraste M.
     Unpublished observations (1994).

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{END}