P08306 (COX2_PARDE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Cytochrome c oxidase subunit 2
EC=1.9.3.1

Alternative name(s):
Cytochrome aa3 subunit 2
Cytochrome c oxidase polypeptide II
Oxidase aa(3) subunit 2

Gene names

Name:	ctaC
Synonyms:	coiI, ctaB

Organism

Paracoccus denitrificans

Taxonomic identifier

266 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Alphaproteobacteria › Rhodobacterales › Rhodobacteraceae › Paracoccus

Protein attributes

Sequence length	298 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Subunits I and II form the functional core of the enzyme complex. Electrons originating in cytochrome c are transferred via heme a and Cu(A) to the binuclear center formed by heme a3 and Cu(B).
Catalytic activity	4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O.
Cofactor	Binds 2 copper A ions per subunit.
Subcellular location	Cell inner membrane; Multi-pass membrane protein.
Sequence similarities	Belongs to the cytochrome c oxidase subunit 2 family.

Ontologies

Keywords
Biological process	Electron transport Respiratory chain Transport
Cellular component	Cell inner membrane Cell membrane Membrane
Domain	Signal Transmembrane Transmembrane helix
Ligand	Copper Metal-binding
Molecular function	Oxidoreductase
PTM	Pyrrolidone carboxylic acid
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological_process	electron transport chain Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell respiratory chain Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	copper ion binding Inferred from electronic annotation. Source: InterPro cytochrome-c oxidase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 29

29

Chain

30 – 280

251

Cytochrome c oxidase subunit 2

PRO_0000006059

Propeptide

281 – 298

18

C-terminal propeptide

PRO_0000006060

Regions

Topological domain

30 – 55

26

Periplasmic

Transmembrane

56 – 88

33

Helical

Topological domain

89 – 103

15

Cytoplasmic

Transmembrane

104 – 134

31

Helical

Topological domain

135 – 280

146

Periplasmic

Sites

Metal binding

210

1

Copper A1

Metal binding

245

1

Copper A1

Metal binding

245

1

Copper A2

Metal binding

247

1

Copper A2; via carbonyl oxygen

Metal binding

249

1

Copper A1

Metal binding

249

1

Copper A2

Metal binding

253

1

Copper A2

Metal binding

256

1

Copper A1

Amino acid modifications

Modified residue

30

1

Pyrrolidone carboxylic acid

Experimental info

Sequence conflict

160 – 161

2

GV → AF AA sequence Ref.2

Secondary structure

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298

Helix Strand Turn

Details...

Turn

32 – 35

4

Beta strand

38 – 40

3

Helix

55 – 88

34

Turn

91 – 93

3

Beta strand

94 – 96

3

Helix

104 – 133

30

Beta strand

140 – 148

9

Beta strand

151 – 156

6

Turn

157 – 160

4

Beta strand

161 – 165

5

Helix

170 – 172

3

Helix

174 – 176

3

Helix

180 – 182

3

Turn

183 – 185

3

Beta strand

187 – 189

3

Beta strand

191 – 208

18

Beta strand

210 – 214

5

Helix

215 – 217

3

Beta strand

219 – 223

5

Beta strand

229 – 234

6

Beta strand

236 – 243

8

Turn

251 – 254

4

Beta strand

258 – 263

6

Helix

265 – 278

14

Sequences

	Sequence		Length	Mass (Da)
	P08306 [UniParc]. Last modified August 1, 1988. Version 1. Checksum: 918A64A9E3B93366	FASTA	298	32,539
	10 20 30 40 50 60 MMAIATKRRG VAAVMSLGVA TMTAVPALAQ DVLGDLPVIG KPVNGGMNFQ PASSPLAHDQ 70 80 90 100 110 120 QWLDHFVLYI ITAVTIFVCL LLLICIVRFN RRANPVPARF THNTPIEVIW TLVPVLILVA 130 140 150 160 170 180 IGAFSLPILF RSQEMPNDPD LVIKAIGHQW YWSYEYPNDG VAFDALMLEK EALADAGYSE 190 200 210 220 230 240 DEYLLATDNP VVVPVGKKVL VQVTATDVIH AWTIPAFAVK QDAVPGRIAQ LWFSVDQEGV 250 260 270 280 290 YFGQCSELCG INHAYMPIVV KAVSQEKYEA WLAGAKEEFA ADASDYLPAS PVKLASAE

References

[1]	"Isolation and analysis of the genes for cytochrome c oxidase in Paracoccus denitrificans." Raitio M., Jalli T., Saraste M. EMBO J. 6:2825-2833(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: S1657.
[2]	"Subunit II of cytochrome c oxidase from Paracoccus denitrificans. DNA sequence, gene expression and the protein." Steinruecke P., Steffens G.C.M., Panskus G., Buse G., Ludwig B. Eur. J. Biochem. 167:431-439(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE. Strain: ATCC 13543 / NRRL B-3784 / NRC 449.
[3]	"Structure at 2.8-A resolution of cytochrome c oxidase from Paracoccus denitrificans." Iwata S., Ostermeier C., Ludwig B., Michel H. Nature 376:660-669(1995) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
[4]	"Structure at 2.7-A resolution of the Paracoccus denitrificans two-subunit cytochrome c oxidase complexed with an antibody FV fragment." Ostermeier C., Harrenga A., Ermler U., Michel H. Proc. Natl. Acad. Sci. U.S.A. 94:10547-10553(1997) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X05828 Genomic DNA. Translation: CAA29268.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1AR1	X-ray	2.70	B	1-298	[»]
1QLE	X-ray	3.00	B	30-281	[»]
1ZYY	model	-	B	30-281	[»]
3EHB	X-ray	2.32	B	1-298	[»]
3HB3	X-ray	2.25	B	1-298	[»]

ProteinModelPortal

P08306.

SMR

P08306. Positions 30-281.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-6089N.

Protein family/group databases

TCDB

3.D.4.6.1. proton-translocating cytochrome oxidase (COX) superfamily.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

Gene3D

1.10.287.90. 1 hit.
2.60.40.420. 1 hit.

InterPro

IPR001505. Copper_CuA.
IPR008972. Cupredoxin.
IPR014222. Cyt_c_oxidase_su2.
IPR002429. Cyt_c_oxidase_su2_C.
IPR011759. Cyt_c_oxidase_su2_TM_dom.
[Graphical view]

Pfam

PF00116. COX2. 1 hit.
PF02790. COX2_TM. 1 hit.
[Graphical view]

SUPFAM

SSF49503. Cupredoxin. 1 hit.
SSF81464. Cyt_c_oxidase_II-like_TM. 1 hit.

TIGRFAMs

TIGR02866. CoxB. 1 hit.

PROSITE

PS00078. COX2. 1 hit.
PS50857. COX2_CUA. 1 hit.
PS50999. COX2_TM. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P08306.

Entry information

Entry name

COX2_PARDE

Accession

Primary (citable) accession number: P08306

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1988
Last sequence update:	August 1, 1988
Last modified:	May 1, 2013
This is version 111 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program