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P98002

- COX1B_PARDE

UniProt

P98002 - COX1B_PARDE

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Protein

Cytochrome c oxidase subunit 1-beta

Gene

ctaDII

Organism
Paracoccus denitrificans
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

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 activityi

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

Cofactori

Protein has several cofactor binding sites:
  • Cu2+Note: Binds 1 copper B ion per subunit.
  • hemeNote: Binds 2 heme groups per subunit.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi94 – 941Iron (heme A axial ligand)
Metal bindingi276 – 2761Copper B
Metal bindingi280 – 2801Copper B
Metal bindingi325 – 3251Copper B
Metal bindingi326 – 3261Copper B
Metal bindingi411 – 4111Iron (heme A3 axial ligand)
Metal bindingi413 – 4131Iron (heme A axial ligand)

GO - Molecular functioni

  1. copper ion binding Source: InterPro
  2. cytochrome-c oxidase activity Source: UniProtKB-EC
  3. heme binding Source: InterPro
  4. iron ion binding Source: InterPro

GO - Biological processi

  1. aerobic respiration Source: InterPro
  2. electron transport chain Source: InterPro
  3. oxidative phosphorylation Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Electron transport, Hydrogen ion transport, Ion transport, Respiratory chain, Transport

Keywords - Ligandi

Copper, Heme, Iron, Metal-binding

Enzyme and pathway databases

UniPathwayiUPA00705.

Protein family/group databases

TCDBi3.D.4.6.1. the proton-translocating cytochrome oxidase (cox) superfamily.

Names & Taxonomyi

Protein namesi
Recommended 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 namesi
Name:ctaDII
OrganismiParacoccus denitrificans
Taxonomic identifieri266 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaeParacoccus

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 2828CytoplasmicAdd
BLAST
Transmembranei29 – 5931Helical; Name=IAdd
BLAST
Topological domaini60 – 8223PeriplasmicAdd
BLAST
Transmembranei83 – 12038Helical; Name=IIAdd
BLAST
Topological domaini121 – 1266Cytoplasmic
Transmembranei127 – 15125Helical; Name=IIIAdd
BLAST
Topological domaini152 – 17625PeriplasmicAdd
BLAST
Transmembranei177 – 20630Helical; Name=IVAdd
BLAST
Topological domaini207 – 21711CytoplasmicAdd
BLAST
Transmembranei218 – 25134Helical; Name=VAdd
BLAST
Topological domaini252 – 26211PeriplasmicAdd
BLAST
Transmembranei263 – 29937Helical; Name=VIAdd
BLAST
Topological domaini300 – 3034Cytoplasmic
Transmembranei304 – 33128Helical; Name=VIIAdd
BLAST
Topological domaini332 – 3321Periplasmic
Transmembranei333 – 36432Helical; Name=VIIIAdd
BLAST
Topological domaini365 – 3695Cytoplasmic
Transmembranei370 – 39526Helical; Name=IXAdd
BLAST
Topological domaini396 – 4049Periplasmic
Transmembranei405 – 43733Helical; Name=XAdd
BLAST
Topological domaini438 – 4403Cytoplasmic
Transmembranei441 – 46929Helical; Name=XIAdd
BLAST
Topological domaini470 – 4789Periplasmic
Transmembranei479 – 51436Helical; Name=XIIAdd
BLAST
Topological domaini515 – 55844CytoplasmicAdd
BLAST

GO - Cellular componenti

  1. integral component of membrane Source: UniProtKB-KW
  2. plasma membrane Source: UniProtKB-KW
  3. respiratory chain Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cell inner membrane, Cell membrane, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 558558Cytochrome c oxidase subunit 1-betaPRO_0000183456Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi66 ↔ 80
Cross-linki276 ↔ 2801'-histidyl-3'-tyrosine (His-Tyr)

Post-translational modificationi

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.

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

DIPiDIP-6088N.

Structurei

Secondary structure

1
558
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi19 – 213Combined sources
Turni22 – 243Combined sources
Helixi28 – 5730Combined sources
Beta strandi59 – 613Combined sources
Beta strandi63 – 664Combined sources
Beta strandi76 – 783Combined sources
Helixi84 – 10118Combined sources
Helixi103 – 1075Combined sources
Turni108 – 1103Combined sources
Helixi111 – 1199Combined sources
Helixi128 – 15023Combined sources
Beta strandi151 – 1533Combined sources
Helixi154 – 1563Combined sources
Beta strandi157 – 1593Combined sources
Turni163 – 1664Combined sources
Helixi170 – 1734Combined sources
Beta strandi175 – 1773Combined sources
Helixi178 – 20629Combined sources
Helixi214 – 2163Combined sources
Helixi219 – 25032Combined sources
Beta strandi254 – 2563Combined sources
Helixi258 – 2603Combined sources
Helixi264 – 29835Combined sources
Helixi305 – 31814Combined sources
Helixi323 – 3264Combined sources
Helixi328 – 3303Combined sources
Helixi334 – 34512Combined sources
Helixi348 – 36215Combined sources
Helixi371 – 39424Combined sources
Helixi396 – 4027Combined sources
Beta strandi403 – 4053Combined sources
Helixi406 – 41712Combined sources
Helixi420 – 43617Combined sources
Beta strandi437 – 4393Combined sources
Helixi442 – 46019Combined sources
Helixi462 – 4687Combined sources
Beta strandi472 – 4743Combined sources
Helixi480 – 4823Combined sources
Helixi483 – 51331Combined sources
Beta strandi514 – 5163Combined sources
Helixi530 – 5334Combined sources
Beta strandi540 – 5423Combined sources
Helixi549 – 5524Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1AR1X-ray2.70A1-558[»]
1QLEX-ray3.00A17-554[»]
1ZYYmodel-A17-545[»]
3EHBX-ray2.32A1-558[»]
3HB3X-ray2.25A1-558[»]
ProteinModelPortaliP98002.
SMRiP98002. Positions 17-554.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP98002.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

KOiK02274.
OrthoDBiEOG6B35XR.

Family and domain databases

Gene3Di1.20.210.10. 1 hit.
InterProiIPR000883. COX1.
IPR023615. Cyt_c_Oxase_su1_BS.
IPR023616. Cyt_c_Oxase_su1_dom.
IPR014241. Cyt_c_oxidase_su1_bac.
[Graphical view]
PANTHERiPTHR10422. PTHR10422. 1 hit.
PfamiPF00115. COX1. 1 hit.
[Graphical view]
PRINTSiPR01165. CYCOXIDASEI.
SUPFAMiSSF81442. SSF81442. 1 hit.
TIGRFAMsiTIGR02891. CtaD_CoxA. 1 hit.
PROSITEiPS50855. COX1. 1 hit.
PS00077. COX1_CUB. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P98002-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MADAAVHGHG DHHDTRGFFT RWFMSTNHKD IGILYLFTAG IVGLISVCFT
60 70 80 90 100
VYMRMELQHP GVQYMCLEGA RLIADASAEC TPNGHLWNVM ITYHGVLMMF
110 120 130 140 150
FVVIPALFGG FGNYFMPLHI GAPDMAFPRL NNLSYWMYVC GVALGVASLL
160 170 180 190 200
APGGNDQMGS GVGWVLYPPL STTEAGYSMD LAIFAVHVSG ASSILGAINI
210 220 230 240 250
ITTFLNMRAP GMTLFKVPLF AWSVFITAWL ILLSLPVLAG AITMLLMDRN
260 270 280 290 300
FGTQFFDPAG GGDPVLYQHI LWFFGHPEVY IIILPGFGII SHVISTFAKK
310 320 330 340 350
PIFGYLPMVL AMAAIGILGF VVWAHHMYTA GMSLTQQAYF MLATMTIAVP
360 370 380 390 400
TGIKVFSWIA TMWGGSIEFK TPMLWAFGFL FLFTVGGVTG VVLSQAPLDR
410 420 430 440 450
VYHDTYYVVA HFHYVMSLGA VFGIFAGVYY WIGKMSGRQY PEWAGQLHFW
460 470 480 490 500
MMFIGSNLIF FPQHFLGRQG MPRRYIDYPV EFAYWNNISS IGAYISFASF
510 520 530 540 550
LFFIGIVFYT LFAGKRVNVP NYWNEHADTL EWTLPSPPPE HTFETLPKRE

DWDRAHAH
Length:558
Mass (Da):62,439
Last modified:November 1, 1995 - v1
Checksum:iA8402453C0C0339E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y07533 Genomic DNA. Translation: CAA68821.1.
PIRiS08270.
RefSeqiYP_915727.1. NC_008686.1.

Genome annotation databases

GeneIDi4581060.
KEGGipde:Pden_1938.
PATRICi22854991. VBIParDen97112_1873.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y07533 Genomic DNA. Translation: CAA68821.1 .
PIRi S08270.
RefSeqi YP_915727.1. NC_008686.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1AR1 X-ray 2.70 A 1-558 [» ]
1QLE X-ray 3.00 A 17-554 [» ]
1ZYY model - A 17-545 [» ]
3EHB X-ray 2.32 A 1-558 [» ]
3HB3 X-ray 2.25 A 1-558 [» ]
ProteinModelPortali P98002.
SMRi P98002. Positions 17-554.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-6088N.

Protein family/group databases

TCDBi 3.D.4.6.1. the proton-translocating cytochrome oxidase (cox) superfamily.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 4581060.
KEGGi pde:Pden_1938.
PATRICi 22854991. VBIParDen97112_1873.

Phylogenomic databases

KOi K02274.
OrthoDBi EOG6B35XR.

Enzyme and pathway databases

UniPathwayi UPA00705 .

Miscellaneous databases

EvolutionaryTracei P98002.

Family and domain databases

Gene3Di 1.20.210.10. 1 hit.
InterProi IPR000883. COX1.
IPR023615. Cyt_c_Oxase_su1_BS.
IPR023616. Cyt_c_Oxase_su1_dom.
IPR014241. Cyt_c_oxidase_su1_bac.
[Graphical view ]
PANTHERi PTHR10422. PTHR10422. 1 hit.
Pfami PF00115. COX1. 1 hit.
[Graphical view ]
PRINTSi PR01165. CYCOXIDASEI.
SUPFAMi SSF81442. SSF81442. 1 hit.
TIGRFAMsi TIGR02891. CtaD_CoxA. 1 hit.
PROSITEi PS50855. COX1. 1 hit.
PS00077. COX1_CUB. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  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. Cited for: REVIEW.

Entry informationi

Entry nameiCOX1B_PARDE
AccessioniPrimary (citable) accession number: P98002
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: November 26, 2014
This is version 116 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3