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PR01873

Identifier
CYTCOXIDASE4  [View Relations]  [View Alignment]  
Accession
PR01873
No. of Motifs
4
Creation Date
21-OCT-2004
Title
Cytochrome c oxidase subunit IV signature
Database References

PFAM; PF02936 COX4
INTERPRO; IPR004203
PDB; 1OCC
SCOP; 1OCC
CATH; 1OCC
Literature References
1. TSUKIHARA, T., AOYAMA, H., YAMASHITA, E., TOMIZAKI, T., YAMAGUCHI, H., 
SHINZAWA-ITOH, K., NAKASHIMA, R., YAONO, R. AND YOSHIKAWA, S.
The whole structure of the 13-subunit oxidized cytochrome c oxidase at 
2.8A.
SCIENCE 272 1136-1144 (1996).
 
2. TOMIZAKI, T., YAMASHITA, E., YAMAGUCHI, H., AOYAMA, H., TSUKIHARA, T., 
SHINZAWA-ITOH, K., NAKASHIMA, R., YAONO, R. AND YOSHIKAWA, S.
Structure analysis of bovine heart cytochrome c oxidase at 2.8A
resolution.
ACTA CRYSTALLOGR. D 55 31-45 (1999).

Documentation
Cytochrome c oxidase (COX) subunit IV is a mitochondrial inner
membrane protein that forms part of the 13-subunit COX complex,
the terminal oxidase in the mitochondrial electron transport chain.
The enzyme catalyses the reaction:
 
     4 ferrocytochrome c + O(2) = 4 ferricytochrome c + 2 H(2)O
 
This polypeptide belongs to a wider family of proteins that includes
the Dictyostelium discoideum COX VI and the Saccharomyces cerevisiae
protein YGX6.
 
The 3D structure of the whole bovine heart cytochrome c oxidase has
been determined to 2.8A resolution by means of X-ray crystallography 
[1,2]. The structure reveals 13 different subunits, five phosphatidyl 
ethanolamines, three phosphatidyl glycerols, two cholates, two haems A,
and a number of copper, magnesium and zinc ions [1]. A hydrogen-bonded
system, including a propionate of heme A, part of the peptide backbone,
and an imidazole ligand of CuA, may provide an electron transfer path-
way between CuA and heme A [1]. 
 
CYTCOXIDASE4 is a 4-element fingerprint that provides a signature for
cytochrome c oxidase subunit IV. The fingerprint was derived from an
initial alignment of 9 sequences: the motifs were drawn from conserved
regions spanning virtually the full alignment length, focusing on those
areas that characterise type IV isoforms but distinguish them from
closely-related members of the cytochrome c oxidase IV family. Three
iterations on SPTR44_27f were required to reach convergence, at which
point a true set comprising 25 sequences was identified.
Summary Information
25 codes involving  4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
425252525
30000
20000
1234
True Positives
CX41_BOVIN    CX41_HUMAN    CX41_MOUSE    CX41_RABIT    
CX41_RAT CX41_THUOB CX42_HUMAN CX42_MOUSE
CX42_RAT CX42_THUOB Q27123 Q66L34
Q6DJG5 Q6GN62 Q6P666 Q6PBL1
Q6PH92 Q6TNV0 Q71SZ7 Q7YZE4
Q7YZF0 Q7YZF1 Q8T4H8 Q9U329
Q9VIQ8
Sequence Titles
CX41_BOVIN  Cytochrome c oxidase subunit IV isoform 1, mitochondrial precursor (EC 1.9.3.1) (COX IV-1) (Cytochrome c oxidase polypeptide IV) - Bos taurus (Bovine). 
CX41_HUMAN Cytochrome c oxidase subunit IV isoform 1, mitochondrial precursor (EC 1.9.3.1) (COX IV-1) (Cytochrome c oxidase polypeptide IV) - Homo sapiens (Human).
CX41_MOUSE Cytochrome c oxidase subunit IV isoform 1, mitochondrial precursor (EC 1.9.3.1) (COX IV-1) (Cytochrome c oxidase polypeptide IV) - Mus musculus (Mouse).
CX41_RABIT Cytochrome c oxidase subunit IV isoform 1, mitochondrial precursor (EC 1.9.3.1) (COX IV-1) (Cytochrome c oxidase polypeptide IV) - Oryctolagus cuniculus (Rabbit).
CX41_RAT Cytochrome c oxidase subunit IV isoform 1, mitochondrial precursor (EC 1.9.3.1) (COX IV-1) (Cytochrome c oxidase polypeptide IV) - Rattus norvegicus (Rat).
CX41_THUOB Cytochrome c oxidase subunit IV isoform 1, mitochondrial precursor (EC 1.9.3.1) (COX IV-1) - Thunnus obesus (Bigeye tuna).
CX42_HUMAN Cytochrome c oxidase subunit IV isoform 2, mitochondrial precursor (EC 1.9.3.1) (COX IV-2) - Homo sapiens (Human).
CX42_MOUSE Cytochrome c oxidase subunit IV isoform 2, mitochondrial precursor (EC 1.9.3.1) (COX IV-2) - Mus musculus (Mouse).
CX42_RAT Cytochrome c oxidase subunit IV isoform 2, mitochondrial precursor (EC 1.9.3.1) (COX IV-2) - Rattus norvegicus (Rat).
CX42_THUOB Cytochrome c oxidase subunit IV isoform 2, mitochondrial precursor (EC 1.9.3.1) (COX IV-2) - Thunnus obesus (Bigeye tuna).
Q27123 Cytochrome c oxidase subunit IV - Urechis caupo (Innkeeper worm) (Spoonworm).
Q66L34 Hypothetical protein - Xenopus laevis (African clawed frog).
Q6DJG5 MGC84307 protein - Xenopus laevis (African clawed frog).
Q6GN62 MGC83001 protein - Xenopus laevis (African clawed frog).
Q6P666 Hypothetical protein - Homo sapiens (Human).
Q6PBL1 Hypothetical protein zgc:73355 - Brachydanio rerio (Zebrafish) (Danio rerio).
Q6PH92 MGC68573 protein - Xenopus laevis (African clawed frog).
Q6TNV0 Cytochrome c oxidase subunit IV isoform 1 - Brachydanio rerio (Zebrafish) (Danio rerio).
Q71SZ7 Cytochrome c oxidase subunit IV - Meleagris gallopavo (Common turkey).
Q7YZE4 Cytochrome c oxidase polypeptide IV - Drosophila mauritiana (Fruit fly).
Q7YZF0 Cytochrome c oxidase polypeptide IV - Drosophila simulans (Fruit fly).
Q7YZF1 Cytochrome c oxidase polypeptide IV - Drosophila simulans (Fruit fly).
Q8T4H8 AT07685p (CG10396-PA) - Drosophila melanogaster (Fruit fly).
Q9U329 Hypothetical protein W09C5.8 - Caenorhabditis elegans.
Q9VIQ8 CG10664-PA (Cg10664-pb) (GM14452p) - Drosophila melanogaster (Fruit fly).
Scan History
SPTR44_27f 3  100  NSINGLE    
Initial Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
ADRRDYPLPDVAHV CX41_MOUSE 39 39 -
VDRRDYPLPDVAHV CX41_RABIT 39 39 -
VDRRDYPLPDVAHV CX41_BOVIN 39 39 -
FDRRENPLPDICYV CX41_THUOB 39 39 -
ADRVDYPLPAVRFR Q9VIQ8 53 53 -
WDRLDTPLPDRPYK CX42_THUOB 47 47 -
YAQRYYPMPEEPFC CX42_HUMAN 41 41 -
IDLPEFPAPAVRYG Q27123 58 58 -

Motif 2 width=19
Element Seqn Id St Int Rpt
RIQFNESFAEMNRGTNEWK CX41_MOUSE 83 30 -
RIQFNESFAEMNRGTNEWK CX41_RABIT 83 30 -
RLKFKESFAEMNRSTNEWK CX41_BOVIN 83 30 -
RISFKQSFAEMNKGSSEWK CX41_THUOB 83 30 -
RASFCQTIAEVQAGSGEWK Q9VIQ8 96 29 -
RLMFCQTYSEMKQPSSEWK CX42_THUOB 91 30 -
RLQFNETFAEMNRRSNEWK CX42_HUMAN 85 30 -
RASFRETYSEMKAPNGEWK Q27123 101 29 -

Motif 3 width=14
Element Seqn Id St Int Rpt
YVYGPIPHTFDRDW CX41_MOUSE 124 22 -
YVYGPIPHTFDKEW CX41_RABIT 124 22 -
YVYGPIPHTFEEEW CX41_BOVIN 124 22 -
YVYGAVPHTFDPEY CX41_THUOB 124 22 -
FVYDELPVTFDEEH Q9VIQ8 137 22 -
YVYPPRPRTFDDEW CX42_THUOB 132 22 -
YVFPPKPITLTDER CX42_HUMAN 126 22 -
NVYPPLPHTINEEY Q27123 142 22 -

Motif 4 width=17
Element Seqn Id St Int Rpt
PIQGFSAKWDYDKNEWK CX41_MOUSE 152 14 -
PIQGFSAKWDYNKNEWR CX41_RABIT 152 14 -
PIQGFSAKWDYDKNEWK CX41_BOVIN 152 14 -
PVEGFSAHWDYENKQWK CX41_THUOB 152 14 -
PVTGLTSKWDYENKKWK Q9VIQ8 165 14 -
PIEGFSAKWDYEKGQWK CX42_THUOB 160 14 -
PVQGLASHWDYEKKQWK CX42_HUMAN 154 14 -
PITGVASKYDYENNRWK Q27123 170 14 -
Final Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
ADRRDYPLPDVAHV CX41_MOUSE 39 39 -
VDRRDYPLPDVAHV CX41_RAT 39 39 -
VDRRDYPLPDVAHV CX41_RABIT 39 39 -
VDRRDYPLPDVAHV CX41_BOVIN 39 39 -
MDRRDHPLPEVAHV CX41_HUMAN 39 39 -
MDRRDHPLPEVAHV Q6P666 39 39 -
IDRRDVPLPDIAFV Q66L34 39 39 -
VDRRDVPLPEAAFV Q71SZ7 41 41 -
VDRRDVPLPDIAFV Q6GN62 39 39 -
FDRRESPLPEIKFV Q6TNV0 39 39 -
SDRLDTPLPDRPYK Q6PBL1 48 48 -
FDRRENPLPDICYV CX41_THUOB 39 39 -
ADRVDYPLPAVRFR Q7YZE4 53 53 -
ADRVDYPLPAVRFR Q7YZF0 53 53 -
ADRVDYPLPAVRFR Q7YZF1 53 53 -
ADRVDYPLPAVRFR Q9VIQ8 53 53 -
YDHRVFPLPDIPFQ Q6PH92 44 44 -
YDHRAFPLPDIPFQ Q6DJG5 44 44 -
WDRLDTPLPDRPYK CX42_THUOB 47 47 -
YAQRYYPMPEEPFC CX42_HUMAN 41 41 -
YAQRSYPMPDEPFC CX42_MOUSE 42 42 -
YAQRSYPMPDEPYC CX42_RAT 42 42 -
IDLPEFPAPAVRYG Q27123 58 58 -
FDSPDCPFPAIRYR Q8T4H8 48 48 -
QDRLDYWYPAIRFR Q9U329 47 47 -

Motif 2 width=19
Element Seqn Id St Int Rpt
RIQFNESFAEMNRGTNEWK CX41_MOUSE 83 30 -
RIQFNESFAEMNKGTNEWK CX41_RAT 83 30 -
RIQFNESFAEMNRGTNEWK CX41_RABIT 83 30 -
RLKFKESFAEMNRSTNEWK CX41_BOVIN 83 30 -
RIKFKESFAEMNRGSNEWK CX41_HUMAN 83 30 -
RIKFKESFAEMNRGSNEWK Q6P666 83 30 -
RIKFHESYTEMNQGSSEWK Q66L34 83 30 -
RIKFNESYAEMNKGTNEWK Q71SZ7 85 30 -
RIKFHESYTEMNQGSSEWK Q6GN62 83 30 -
RISFKESFAEMNQGSGEWK Q6TNV0 83 30 -
RIMFNETFAEMKKPTGEWK Q6PBL1 92 30 -
RISFKQSFAEMNKGSSEWK CX41_THUOB 83 30 -
RASFCQTIAEVQAGSGEWK Q7YZE4 96 29 -
RASFCQTIAEVQAGSGEWK Q7YZF0 96 29 -
RASFCQTIAEVQAGSGEWK Q7YZF1 96 29 -
RASFCQTIAEVQAGSGEWK Q9VIQ8 96 29 -
HIKFNKTYAEMNKPSNEWK Q6PH92 88 30 -
HIKFNQTYAEINRPSNEWK Q6DJG5 88 30 -
RLMFCQTYSEMKQPSSEWK CX42_THUOB 91 30 -
RLQFNETFAEMNRRSNEWK CX42_HUMAN 85 30 -
RLQFHETFAEMNHRSNEWK CX42_MOUSE 86 30 -
RLQFHETFAEMNHRSNEWK CX42_RAT 86 30 -
RASFRETYSEMKAPNGEWK Q27123 101 29 -
RYSFCQTYAEFQHITPEWK Q8T4H8 91 29 -
RYSFRQTLSEFEAPTGYWK Q9U329 90 29 -

Motif 3 width=14
Element Seqn Id St Int Rpt
YVYGPIPHTFDRDW CX41_MOUSE 124 22 -
YVYGPIPHTFDRDW CX41_RAT 124 22 -
YVYGPIPHTFDKEW CX41_RABIT 124 22 -
YVYGPIPHTFEEEW CX41_BOVIN 124 22 -
YVYGPLPQSFDKEW CX41_HUMAN 124 22 -
YVYGPLPQSFDKEW Q6P666 124 22 -
YVYGDVPHTFSEDW Q66L34 124 22 -
YMYGPIPHTFSDEW Q71SZ7 126 22 -
YVYGDVPHTFSEDW Q6GN62 124 22 -
YVYGDVPNTFDPEY Q6TNV0 124 22 -
YVYPPQPHTFGDEW Q6PBL1 133 22 -
YVYGAVPHTFDPEY CX41_THUOB 124 22 -
FVYDELPVTFDEEH Q7YZE4 137 22 -
FVYDELPVTFDEEH Q7YZF0 137 22 -
FVYDELPVTFDEEH Q7YZF1 137 22 -
FVYDELPVTFDEEH Q9VIQ8 137 22 -
YVYPPKPHTLADDW Q6PH92 129 22 -
YVYPPQPHTLADDW Q6DJG5 129 22 -
YVYPPRPRTFDDEW CX42_THUOB 132 22 -
YVFPPKPITLTDER CX42_HUMAN 126 22 -
YVFPKKVVTLTEER CX42_MOUSE 127 22 -
YVFPKKVVTLTEER CX42_RAT 127 22 -
NVYPPLPHTINEEY Q27123 142 22 -
VLYGKLPDTFNDER Q8T4H8 132 22 -
CVYPELPPTFQNEY Q9U329 131 22 -

Motif 4 width=17
Element Seqn Id St Int Rpt
PIQGFSAKWDYDKNEWK CX41_MOUSE 152 14 -
PIQGFSAKWDYNKNEWK CX41_RAT 152 14 -
PIQGFSAKWDYNKNEWR CX41_RABIT 152 14 -
PIQGFSAKWDYDKNEWK CX41_BOVIN 152 14 -
PIQGLASKWDYEKNEWK CX41_HUMAN 152 14 -
PIQGLASKWDYEKNEWK Q6P666 152 14 -
PVQGFSAQWDYEKNEWK Q66L34 152 14 -
PVQGISSQWDYEKNEWK Q71SZ7 154 14 -
PVQGFSSQWDYDKKEWK Q6GN62 152 14 -
PVQGFAAKWDYENNAWK Q6TNV0 152 14 -
PVQGFAAKWDYEKGQWK Q6PBL1 161 14 -
PVEGFSAHWDYENKQWK CX41_THUOB 152 14 -
PVTGLTSKWDYENKKWK Q7YZE4 165 14 -
PVTGLTSKWDYENKKWK Q7YZF0 165 14 -
PVTGLTSKWDYENKKWK Q7YZF1 165 14 -
PVTGLTSKWDYENKKWK Q9VIQ8 165 14 -
PIQGFASKWDYEKNEWK Q6PH92 157 14 -
PIQGFSSNWDYEKNEWK Q6DJG5 157 14 -
PIEGFSAKWDYEKGQWK CX42_THUOB 160 14 -
PVQGLASHWDYEKKQWK CX42_HUMAN 154 14 -
PIQGLAAHWDYEKKEWK CX42_MOUSE 155 14 -
PIQGLSAHWDYEKKEWK CX42_RAT 155 14 -
PITGVASKYDYENNRWK Q27123 170 14 -
PITGLASKWCYRENKWK Q8T4H8 160 14 -
QFLGAPTHYDYENKKWK Q9U329 159 14 -