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P0ABJ9

- CYDA_ECOLI

UniProt

P0ABJ9 - CYDA_ECOLI

Protein

Cytochrome bd-I ubiquinol oxidase subunit 1

Gene

cydA

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 83 (01 Oct 2014)
      Sequence version 1 (25 Oct 2005)
      Previous versions | rss
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    Functioni

    A terminal oxidase that produces a proton motive force by the vectorial transfer of protons across the inner membrane. It is the component of the aerobic respiratory chain of E.coli that predominates when cells are grown at low aeration. Generates a proton motive force using protons and electrons from opposite sides of the membrane to generate H2O, transferring 1 proton/electron.5 Publications

    Catalytic activityi

    2 ubiquinol + O2 + 4 H+(Side 1) = 2 ubiquinone + 2 H2O + 4 H+(Side 2).

    Cofactori

    Binds 1 protoheme IX center (heme b558) per subunit.
    Binds 1 protoheme IX center (heme b595, originally called cytochrome a1) per heterodimer, in conjunction with CydB.
    Binds 1 iron-chlorin (heme d or cytochrome d) per heterodimer, in conjunction with CydB.

    Enzyme regulationi

    90% inhibited by cyanide and 2-heptyl-4-hydroxyquinoline N-oxide, at 1 mM and 40 µM respectively.1 Publication

    Kineticsi

    pH 7.0, 37 degrees Celsius.

    1. KM=0.1 mM for ubiquinol-11 Publication
    2. KM=0.28 mM for 2,3,5,6-tetramethyl-p-phenylenediamine1 Publication
    3. KM=0.68 mM for N,N,N',N'-tetramethyl-p-phenylenediamine1 Publication

    Vmax=383 µmol/min/mg enzyme for ubiquinol-11 Publication

    Vmax=270 µmol/min/mg enzyme for 2,3,5,6-tetramethyl-p-phenylenediamine1 Publication

    Vmax=126 µmol/min/mg enzyme for N,N,N',N'-tetramethyl-p-phenylenediamine1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi19 – 191Iron (heme b595 axial ligand)Sequence Analysis
    Metal bindingi186 – 1861Iron (heme b558 axial ligand)
    Metal bindingi393 – 3931Iron (heme b558 axial ligand)

    GO - Molecular functioni

    1. electron carrier activity Source: EcoCyc
    2. heme binding Source: EcoCyc
    3. metal ion binding Source: UniProtKB-KW
    4. oxidoreductase activity, acting on diphenols and related substances as donors Source: EcoCyc
    5. protein binding Source: IntAct

    GO - Biological processi

    1. aerobic electron transport chain Source: EcoCyc
    2. oxidative phosphorylation Source: UniProtKB-UniPathway

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Electron transport, Transport

    Keywords - Ligandi

    Heme, Iron, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:CYDA-MONOMER.
    ECOL316407:JW0722-MONOMER.
    MetaCyc:CYDA-MONOMER.
    UniPathwayiUPA00705.

    Protein family/group databases

    TCDBi3.D.4.3.2. the proton-translocating cytochrome oxidase (cox) superfamily.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Cytochrome bd-I ubiquinol oxidase subunit 1 (EC:1.10.3.14)
    Alternative name(s):
    Cytochrome bd-I oxidase subunit I
    Cytochrome d ubiquinol oxidase subunit I
    Gene namesi
    Name:cydA
    Synonyms:cyd-1
    Ordered Locus Names:b0733, JW0722
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10173. cydA.

    Subcellular locationi

    Cell inner membrane 2 Publications; Multi-pass membrane protein 2 Publications

    GO - Cellular componenti

    1. cytochrome complex Source: EcoCyc
    2. integral component of plasma membrane Source: EcoCyc
    3. membrane Source: UniProtKB
    4. plasma membrane Source: EcoCyc

    Keywords - Cellular componenti

    Cell inner membrane, Cell membrane, Membrane

    Pathology & Biotechi

    Disruption phenotypei

    A double cydA/cydB deletion shows increased sensitivity to reductant (beta-mercapoethanol).3 Publications

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi19 – 191H → L or R: Loss of cytochrome b595 and heme d, no aerobic growth, complex assembles. 1 Publication
    Mutagenesisi86 – 861H → R: No effect. 1 Publication
    Mutagenesisi126 – 1261H → P: Loss of all cofactors, no aerobic growth, complex assembles. 1 Publication
    Mutagenesisi126 – 1261H → R: No effect. 1 Publication
    Mutagenesisi186 – 1861H → L: Loss of cytochrome b558, no aerobic growth, complex assembles, this subunit is more susceptible to proteolysis. 1 Publication
    Mutagenesisi314 – 3141H → L: Grows aerobically, has altered cytochrome b/d ratio, complex assembles. 1 Publication
    Mutagenesisi314 – 3141H → P: Loss of cytochrome b595 and heme d, no aerobic growth, loss of complex. 1 Publication
    Mutagenesisi393 – 3931M → L: Cytochrome b558 shifts to a high spin configuration, complex assembles. Retains about 1% quinol oxidoreductase activity after purification.
    Mutagenesisi510 – 5101H → L: No effect. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 522522Cytochrome bd-I ubiquinol oxidase subunit 1PRO_0000183919Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei1 – 11N-formylmethionine1 Publication

    Post-translational modificationi

    The N-terminus is blocked.

    Keywords - PTMi

    Formylation

    Proteomic databases

    PaxDbiP0ABJ9.
    PRIDEiP0ABJ9.

    Expressioni

    Inductioni

    Under conditions of low aeration, in stationary phase (at protein level).1 Publication

    Gene expression databases

    GenevestigatoriP0ABJ9.

    Interactioni

    Subunit structurei

    Heterodimer of subunits I and II. Probably interacts with CydX, and overexpressed AppX.4 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    cydBP0ABK25EBI-906928,EBI-1213195

    Protein-protein interaction databases

    DIPiDIP-36181N.
    IntActiP0ABJ9. 4 interactions.
    STRINGi511145.b0733.

    Structurei

    3D structure databases

    ProteinModelPortaliP0ABJ9.
    ModBaseiSearch...
    MobiDBiSearch...

    Topological domain

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Topological domaini1 – 1515PeriplasmicCuratedAdd
    BLAST
    Topological domaini36 – 5419CytoplasmicCuratedAdd
    BLAST
    Topological domaini70 – 9627PeriplasmicCuratedAdd
    BLAST
    Topological domaini115 – 12814CytoplasmicCuratedAdd
    BLAST
    Topological domaini147 – 18640PeriplasmicCuratedAdd
    BLAST
    Topological domaini204 – 21916CytoplasmicCuratedAdd
    BLAST
    Topological domaini236 – 390155PeriplasmicCuratedAdd
    BLAST
    Topological domaini408 – 42316CytoplasmicCuratedAdd
    BLAST
    Topological domaini442 – 47231PeriplasmicCuratedAdd
    BLAST
    Topological domaini488 – 52235CytoplasmicCuratedAdd
    BLAST

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei16 – 3520HelicalCuratedAdd
    BLAST
    Transmembranei55 – 6915HelicalCuratedAdd
    BLAST
    Transmembranei97 – 11418HelicalCuratedAdd
    BLAST
    Transmembranei129 – 14618HelicalCuratedAdd
    BLAST
    Transmembranei187 – 20317HelicalCuratedAdd
    BLAST
    Transmembranei220 – 23516HelicalCuratedAdd
    BLAST
    Transmembranei391 – 40717HelicalCuratedAdd
    BLAST
    Transmembranei424 – 44118HelicalCuratedAdd
    BLAST
    Transmembranei473 – 48715HelicalCuratedAdd
    BLAST

    Family & Domainsi

    Sequence similaritiesi

    Keywords - Domaini

    Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiCOG1271.
    HOGENOMiHOG000084938.
    KOiK00425.
    OMAiGWDRFSK.
    OrthoDBiEOG600DNV.
    PhylomeDBiP0ABJ9.

    Family and domain databases

    InterProiIPR002585. Cyt-d_ubiquinol_oxidase_suI.
    [Graphical view]
    PfamiPF01654. Bac_Ubq_Cox. 1 hit.
    [Graphical view]
    PIRSFiPIRSF006446. Cyt_quinol_oxidase_1. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P0ABJ9-1 [UniParc]FASTAAdd to Basket

    « Hide

    MLDIVELSRL QFALTAMYHF LFVPLTLGMA FLLAIMETVY VLSGKQIYKD    50
    MTKFWGKLFG INFALGVATG LTMEFQFGTN WSYYSHYVGD IFGAPLAIEG 100
    LMAFFLESTF VGLFFFGWDR LGKVQHMCVT WLVALGSNLS ALWILVANGW 150
    MQNPIASDFN FETMRMEMVS FSELVLNPVA QVKFVHTVAS GYVTGAMFIL 200
    GISAWYMLKG RDFAFAKRSF AIAASFGMAA VLSVIVLGDE SGYEMGDVQK 250
    TKLAAIEAEW ETQPAPAAFT LFGIPDQEEE TNKFAIQIPY ALGIIATRSV 300
    DTPVIGLKEL MVQHEERIRN GMKAYSLLEQ LRSGSTDQAV RDQFNSMKKD 350
    LGYGLLLKRY TPNVADATEA QIQQATKDSI PRVAPLYFAF RIMVACGFLL 400
    LAIIALSFWS VIRNRIGEKK WLLRAALYGI PLPWIAVEAG WFVAEYGRQP 450
    WAIGEVLPTA VANSSLTAGD LIFSMVLICG LYTLFLVAEL FLMFKFARLG 500
    PSSLKTGRYH FEQSSTTTQP AR 522
    Length:522
    Mass (Da):58,205
    Last modified:October 25, 2005 - v1
    Checksum:iE757442068BCFCFE
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti213 – 2131F → L in AAA18804. (PubMed:2843510)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J03939 Unassigned DNA. Translation: AAA18804.1.
    U00096 Genomic DNA. Translation: AAC73827.2.
    AP009048 Genomic DNA. Translation: BAA35399.1.
    RefSeqiNP_415261.2. NC_000913.3.
    YP_489012.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73827; AAC73827; b0733.
    BAA35399; BAA35399; BAA35399.
    GeneIDi12934545.
    945341.
    KEGGiecj:Y75_p0712.
    eco:b0733.
    PATRICi32116663. VBIEscCol129921_0764.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    J03939 Unassigned DNA. Translation: AAA18804.1 .
    U00096 Genomic DNA. Translation: AAC73827.2 .
    AP009048 Genomic DNA. Translation: BAA35399.1 .
    RefSeqi NP_415261.2. NC_000913.3.
    YP_489012.1. NC_007779.1.

    3D structure databases

    ProteinModelPortali P0ABJ9.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-36181N.
    IntActi P0ABJ9. 4 interactions.
    STRINGi 511145.b0733.

    Protein family/group databases

    TCDBi 3.D.4.3.2. the proton-translocating cytochrome oxidase (cox) superfamily.

    Proteomic databases

    PaxDbi P0ABJ9.
    PRIDEi P0ABJ9.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC73827 ; AAC73827 ; b0733 .
    BAA35399 ; BAA35399 ; BAA35399 .
    GeneIDi 12934545.
    945341.
    KEGGi ecj:Y75_p0712.
    eco:b0733.
    PATRICi 32116663. VBIEscCol129921_0764.

    Organism-specific databases

    EchoBASEi EB0170.
    EcoGenei EG10173. cydA.

    Phylogenomic databases

    eggNOGi COG1271.
    HOGENOMi HOG000084938.
    KOi K00425.
    OMAi GWDRFSK.
    OrthoDBi EOG600DNV.
    PhylomeDBi P0ABJ9.

    Enzyme and pathway databases

    UniPathwayi UPA00705 .
    BioCyci EcoCyc:CYDA-MONOMER.
    ECOL316407:JW0722-MONOMER.
    MetaCyc:CYDA-MONOMER.

    Miscellaneous databases

    PROi P0ABJ9.

    Gene expression databases

    Genevestigatori P0ABJ9.

    Family and domain databases

    InterProi IPR002585. Cyt-d_ubiquinol_oxidase_suI.
    [Graphical view ]
    Pfami PF01654. Bac_Ubq_Cox. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF006446. Cyt_quinol_oxidase_1. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "The nucleotide sequence of the cyd locus encoding the two subunits of the cytochrome d terminal oxidase complex of Escherichia coli."
      Green G.N., Fang H., Lin R.-J., Newton G., Mather M., Georgiou C.D., Gennis R.B.
      J. Biol. Chem. 263:13138-13143(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    5. "The active form of the cytochrome d terminal oxidase complex of Escherichia coli is a heterodimer containing one copy of each of the two subunits."
      Miller M.J., Hermodson M., Gennis R.B.
      J. Biol. Chem. 263:5235-5240(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-6, FORMYLATION AT MET-1, SUBUNIT.
      Strain: MR43L/F152.
    6. "The purification and characterization of the cytochrome d terminal oxidase complex of the Escherichia coli aerobic respiratory chain."
      Miller M.J., Gennis R.B.
      J. Biol. Chem. 258:9159-9165(1983) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS AN OXIDASE, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, COFACTOR, SUBUNIT, INDUCTION.
      Strain: MR43L/F152.
    7. "Specific overproduction and purification of the cytochrome b558 component of the cytochrome d complex from Escherichia coli."
      Green G.N., Lorence R.M., Gennis R.B.
      Biochemistry 25:2309-2314(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: COFACTOR.
    8. "Coulometric and spectroscopic analysis of the purified cytochrome d complex of Escherichia coli: evidence for the identification of 'cytochrome a1' as cytochrome b595."
      Lorence R.M., Koland J.G., Gennis R.B.
      Biochemistry 25:2314-2321(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: COFACTOR.
      Strain: MR43L/F152.
    9. "Beta-galactosidase gene fusions as probes for the cytoplasmic regions of subunits I and II of the membrane-bound cytochrome d terminal oxidase from Escherichia coli."
      Georgiou C.D., Dueweke T.J., Gennis R.B.
      J. Biol. Chem. 263:13130-13137(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: TOPOLOGY.
    10. "Location of heme axial ligands in the cytochrome d terminal oxidase complex of Escherichia coli determined by site-directed mutagenesis."
      Fang H., Lin R.J., Gennis R.B.
      J. Biol. Chem. 264:8026-8032(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, COFACTOR, MUTAGENESIS OF HIS-19; HIS-86; HIS-126; HIS-186; HIS-314 AND HIS-510.
    11. "Epitopes of monoclonal antibodies which inhibit ubiquinol oxidase activity of Escherichia coli cytochrome d complex localize functional domain."
      Dueweke T.J., Gennis R.B.
      J. Biol. Chem. 265:4273-4277(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: DOMAINS.
    12. "Analysis of the topology of the cytochrome d terminal oxidase complex of Escherichia coli by alkaline phosphatase fusions."
      Newton G., Yun C.H., Gennis R.B.
      Mol. Microbiol. 5:2511-2518(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: TOPOLOGY.
    13. "Methionine-393 is an axial ligand of the heme b558 component of the cytochrome bd ubiquinol oxidase from Escherichia coli."
      Kaysser T.M., Ghaim J.B., Georgiou C., Gennis R.B.
      Biochemistry 34:13491-13501(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, COFACTOR, MUTAGENSIS OF MET-393.
    14. "Gene fusions with beta-lactamase show that subunit I of the cytochrome bd quinol oxidase from E. coli has nine transmembrane helices with the O2 reactive site near the periplasmic surface."
      Zhang J., Barquera B., Gennis R.B.
      FEBS Lett. 561:58-62(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION, TOPOLOGY.
    15. Cited for: SUBUNIT, SUBCELLULAR LOCATION.
      Strain: BL21-DE3.
    16. "Global topology analysis of the Escherichia coli inner membrane proteome."
      Daley D.O., Rapp M., Granseth E., Melen K., Drew D., von Heijne G.
      Science 308:1321-1323(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: TOPOLOGY [LARGE SCALE ANALYSIS].
      Strain: K12 / MG1655 / ATCC 47076.
    17. "Respiration of Escherichia coli can be fully uncoupled via the nonelectrogenic terminal cytochrome bd-II oxidase."
      Bekker M., de Vries S., Ter Beek A., Hellingwerf K.J., de Mattos M.J.
      J. Bacteriol. 191:5510-5517(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN PROTON TRANSLOCATION, DISRUPTION PHENOTYPE.
      Strain: K12.
    18. "Aerobic respiratory chain of Escherichia coli is not allowed to work in fully uncoupled mode."
      Borisov V.B., Murali R., Verkhovskaya M.L., Bloch D.A., Han H., Gennis R.B., Verkhovsky M.I.
      Proc. Natl. Acad. Sci. U.S.A. 108:17320-17324(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN PROTON TRANSLOCATION, DISRUPTION PHENOTYPE.
      Strain: K12.
    19. "The Escherichia coli CydX protein is a member of the CydAB cytochrome bd oxidase complex and is required for cytochrome bd oxidase activity."
      Vanorsdel C.E., Bhatt S., Allen R.J., Brenner E.P., Hobson J.J., Jamil A., Haynes B.M., Genson A.M., Hemm M.R.
      J. Bacteriol. 195:3640-3650(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROBABLE INTERACTION WITH CYDX, POSSIBLE INTERACTION WITH APPX, SUBUNIT, DISRUPTION PHENOTYPE.
      Strain: K12 / MG1655 / ATCC 47076.
    20. Cited for: REVIEW.

    Entry informationi

    Entry nameiCYDA_ECOLI
    AccessioniPrimary (citable) accession number: P0ABJ9
    Secondary accession number(s): P11026, P75754, P76823
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 25, 2005
    Last sequence update: October 25, 2005
    Last modified: October 1, 2014
    This is version 83 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

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3