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P98002 (COX1B_PARDE) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 104. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
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to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Cytochrome c oxidase subunit 1-beta
EC=1.9.3.1
Alternative name(s):
Cytochrome aa3 subunit 1-beta
Cytochrome c oxidase polypeptide I-beta
Gene names
Name:ctaDII
OrganismParacoccus denitrificans
Taxonomic identifier266 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Alphaproteobacteria › Rhodobacterales › Rhodobacteraceae › Paracoccus

Protein attributes

Sequence length558 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Subunit 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). This cytochrome c oxidase shows proton pump activity across the membrane in addition to the electron transfer.

Catalytic activity

4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O.

Cofactor

Binds 1 copper B ion per subunit.

Binds 2 heme groups per subunit.

Pathway

Energy metabolism; oxidative phosphorylation.

Subcellular location

Cell inner membrane; Multi-pass membrane protein.

Post-translational modification

His-276 and Tyr-280 are involved in the formation of a copper-coordinated covalent cross-link at the active site of the catalytic subunit I.

Sequence similarities

Belongs to the heme-copper respiratory oxidase family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 558558Cytochrome c oxidase subunit 1-beta
PRO_0000183456

Regions

Topological domain1 – 2828Cytoplasmic
Transmembrane29 – 5931Helical; Name=I
Topological domain60 – 8223Periplasmic
Transmembrane83 – 12038Helical; Name=II
Topological domain121 – 1266Cytoplasmic
Transmembrane127 – 15125Helical; Name=III
Topological domain152 – 17625Periplasmic
Transmembrane177 – 20630Helical; Name=IV
Topological domain207 – 21711Cytoplasmic
Transmembrane218 – 25134Helical; Name=V
Topological domain252 – 26211Periplasmic
Transmembrane263 – 29937Helical; Name=VI
Topological domain300 – 3034Cytoplasmic
Transmembrane304 – 33128Helical; Name=VII
Topological domain3321Periplasmic
Transmembrane333 – 36432Helical; Name=VIII
Topological domain365 – 3695Cytoplasmic
Transmembrane370 – 39526Helical; Name=IX
Topological domain396 – 4049Periplasmic
Transmembrane405 – 43733Helical; Name=X
Topological domain438 – 4403Cytoplasmic
Transmembrane441 – 46929Helical; Name=XI
Topological domain470 – 4789Periplasmic
Transmembrane479 – 51436Helical; Name=XII
Topological domain515 – 55844Cytoplasmic

Sites

Metal binding941Iron (heme A axial ligand)
Metal binding2761Copper B
Metal binding2801Copper B
Metal binding3251Copper B
Metal binding3261Copper B
Metal binding4111Iron (heme A3 axial ligand)
Metal binding4131Iron (heme A axial ligand)

Amino acid modifications

Disulfide bond66 ↔ 80
Cross-link276 ↔ 2801'-histidyl-3'-tyrosine (His-Tyr)

Secondary structure

1 ........................................................................... 558
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P98002 [UniParc].

Last modified November 1, 1995. Version 1.
Checksum: A8402453C0C0339E

FASTA55862,439
        10         20         30         40         50         60 
MADAAVHGHG DHHDTRGFFT RWFMSTNHKD IGILYLFTAG IVGLISVCFT VYMRMELQHP 

        70         80         90        100        110        120 
GVQYMCLEGA RLIADASAEC TPNGHLWNVM ITYHGVLMMF FVVIPALFGG FGNYFMPLHI 

       130        140        150        160        170        180 
GAPDMAFPRL NNLSYWMYVC GVALGVASLL APGGNDQMGS GVGWVLYPPL STTEAGYSMD 

       190        200        210        220        230        240 
LAIFAVHVSG ASSILGAINI ITTFLNMRAP GMTLFKVPLF AWSVFITAWL ILLSLPVLAG 

       250        260        270        280        290        300 
AITMLLMDRN FGTQFFDPAG GGDPVLYQHI LWFFGHPEVY IIILPGFGII SHVISTFAKK 

       310        320        330        340        350        360 
PIFGYLPMVL AMAAIGILGF VVWAHHMYTA GMSLTQQAYF MLATMTIAVP TGIKVFSWIA 

       370        380        390        400        410        420 
TMWGGSIEFK TPMLWAFGFL FLFTVGGVTG VVLSQAPLDR VYHDTYYVVA HFHYVMSLGA 

       430        440        450        460        470        480 
VFGIFAGVYY WIGKMSGRQY PEWAGQLHFW MMFIGSNLIF FPQHFLGRQG MPRRYIDYPV 

       490        500        510        520        530        540 
EFAYWNNISS IGAYISFASF LFFIGIVFYT LFAGKRVNVP NYWNEHADTL EWTLPSPPPE 

       550 
HTFETLPKRE DWDRAHAH

« Hide

References

[1]"Are there isoenzymes of cytochrome c oxidase in Paracoccus denitrificans?"
Raitio M., Pispa J.M., Metso T., Saraste M.
FEBS Lett. 261:431-435(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: Pd 1222.
[2]"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).
[3]"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).
[4]"Evidence for a copper-coordinated histidine-tyrosine cross-link in the active site of cytochrome oxidase."
Buse G., Soulimane T., Dewor M., Meyer H.E., Blueggel M.
Protein Sci. 8:985-990(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: COVALENT BOND.
[5]"Cytochrome c oxidase."
Ostermeier C., Iwata S., Michel H.
Curr. Opin. Struct. Biol. 6:460-466(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		Y07533 Genomic DNA. Translation: CAA68821.1.
PIRS08270.
RefSeqYP_915727.1. NC_008686.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1AR1X-ray2.70A1-558[»]
1QLEX-ray3.00A17-554[»]
1ZYYmodel-A17-545[»]
3EHBX-ray2.32A1-558[»]
3HB3X-ray2.25A1-558[»]
ProteinModelPortalP98002.
SMRP98002. Positions 17-554.
ModBaseSearch...

Protein-protein interaction databases

DIPDIP-6088N.

Protein family/group databases

TCDB3.D.4.6.1. proton-translocating cytochrome oxidase (COX) superfamily.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID4581060.
KEGGpde:Pden_1938.
PATRIC22854991. VBIParDen97112_1873.

Phylogenomic databases

KOK02274.
ProtClustDBCLSK933538.

Enzyme and pathway databases

UniPathwayUPA00705.

Family and domain databases

Gene3D1.20.210.10. 1 hit.
InterProIPR000883. Cyt_c_Oxase_su1.
IPR023615. Cyt_c_Oxase_su1_BS.
IPR023616. Cyt_c_Oxase_su1_dom.
IPR014241. Cyt_c_oxidase_su1_bac.
[Graphical view]
PANTHERPTHR10422. PTHR10422. 1 hit.
PfamPF00115. COX1. 1 hit.
[Graphical view]
PRINTSPR01165. CYCOXIDASEI.
SUPFAMSSF81442. COX1. 1 hit.
TIGRFAMsTIGR02891. CtaD_CoxA. 1 hit.
PROSITEPS50855. COX1. 1 hit.
PS00077. COX1_CUB. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP98002.

Entry information

Entry nameCOX1B_PARDE
AccessionPrimary (citable) accession number: P98002
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: April 3, 2013
This is version 104 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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