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Protein

Cytochrome bd-I ubiquinol oxidase subunit 1

Gene

cydA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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

Protein has several cofactor binding sites:
  • heme bNote: Binds 1 protoheme IX center (heme b558) per subunit.
  • heme bNote: Binds 1 protoheme IX center (heme b595, originally called cytochrome a1) per heterodimer, in conjunction with CydB.
  • heme d cis-diolNote: 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
  1. Vmax=383 µmol/min/mg enzyme for ubiquinol-11 Publication
  2. Vmax=270 µmol/min/mg enzyme for 2,3,5,6-tetramethyl-p-phenylenediamine1 Publication
  3. 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

GO - Biological processi

  • aerobic electron transport chain Source: EcoCyc
  • oxidative phosphorylation Source: UniProtKB-UniPathway
Complete GO annotation...

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.
BRENDAi1.10.3.14. 2026.
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 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10173. cydA.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 1515PeriplasmicCuratedAdd
BLAST
Transmembranei16 – 3520HelicalCuratedAdd
BLAST
Topological domaini36 – 5419CytoplasmicCuratedAdd
BLAST
Transmembranei55 – 6915HelicalCuratedAdd
BLAST
Topological domaini70 – 9627PeriplasmicCuratedAdd
BLAST
Transmembranei97 – 11418HelicalCuratedAdd
BLAST
Topological domaini115 – 12814CytoplasmicCuratedAdd
BLAST
Transmembranei129 – 14618HelicalCuratedAdd
BLAST
Topological domaini147 – 18640PeriplasmicCuratedAdd
BLAST
Transmembranei187 – 20317HelicalCuratedAdd
BLAST
Topological domaini204 – 21916CytoplasmicCuratedAdd
BLAST
Transmembranei220 – 23516HelicalCuratedAdd
BLAST
Topological domaini236 – 390155PeriplasmicCuratedAdd
BLAST
Transmembranei391 – 40717HelicalCuratedAdd
BLAST
Topological domaini408 – 42316CytoplasmicCuratedAdd
BLAST
Transmembranei424 – 44118HelicalCuratedAdd
BLAST
Topological domaini442 – 47231PeriplasmicCuratedAdd
BLAST
Transmembranei473 – 48715HelicalCuratedAdd
BLAST
Topological domaini488 – 52235CytoplasmicCuratedAdd
BLAST

GO - Cellular componenti

  • cytochrome complex Source: EcoCyc
  • integral component of plasma membrane Source: EcoCyc
  • membrane Source: UniProtKB
  • plasma membrane Source: EcoCyc
Complete GO annotation...

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...

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiCOG1271.
HOGENOMiHOG000084938.
InParanoidiP0ABJ9.
KOiK00425.
OMAiGWDRFSK.
OrthoDBiEOG600DNV.
PhylomeDBiP0ABJ9.

Family and domain databases

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

Sequencei

Sequence statusi: Complete.

P0ABJ9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLDIVELSRL QFALTAMYHF LFVPLTLGMA FLLAIMETVY VLSGKQIYKD
60 70 80 90 100
MTKFWGKLFG INFALGVATG LTMEFQFGTN WSYYSHYVGD IFGAPLAIEG
110 120 130 140 150
LMAFFLESTF VGLFFFGWDR LGKVQHMCVT WLVALGSNLS ALWILVANGW
160 170 180 190 200
MQNPIASDFN FETMRMEMVS FSELVLNPVA QVKFVHTVAS GYVTGAMFIL
210 220 230 240 250
GISAWYMLKG RDFAFAKRSF AIAASFGMAA VLSVIVLGDE SGYEMGDVQK
260 270 280 290 300
TKLAAIEAEW ETQPAPAAFT LFGIPDQEEE TNKFAIQIPY ALGIIATRSV
310 320 330 340 350
DTPVIGLKEL MVQHEERIRN GMKAYSLLEQ LRSGSTDQAV RDQFNSMKKD
360 370 380 390 400
LGYGLLLKRY TPNVADATEA QIQQATKDSI PRVAPLYFAF RIMVACGFLL
410 420 430 440 450
LAIIALSFWS VIRNRIGEKK WLLRAALYGI PLPWIAVEAG WFVAEYGRQP
460 470 480 490 500
WAIGEVLPTA VANSSLTAGD LIFSMVLICG LYTLFLVAEL FLMFKFARLG
510 520
PSSLKTGRYH FEQSSTTTQP AR
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:
EMBLi
GenBanki
DDBJi
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.

Genome annotation databases

EnsemblBacteriaiAAC73827; AAC73827; b0733.
BAA35399; BAA35399; BAA35399.
GeneIDi945341.
KEGGiecj:Y75_p0712.
eco:b0733.
PATRICi32116663. VBIEscCol129921_0764.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

ProteinModelPortaliP0ABJ9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

Protein family/group databases

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

Proteomic databases

PaxDbiP0ABJ9.
PRIDEiP0ABJ9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73827; AAC73827; b0733.
BAA35399; BAA35399; BAA35399.
GeneIDi945341.
KEGGiecj:Y75_p0712.
eco:b0733.
PATRICi32116663. VBIEscCol129921_0764.

Organism-specific databases

EchoBASEiEB0170.
EcoGeneiEG10173. cydA.

Phylogenomic databases

eggNOGiCOG1271.
HOGENOMiHOG000084938.
InParanoidiP0ABJ9.
KOiK00425.
OMAiGWDRFSK.
OrthoDBiEOG600DNV.
PhylomeDBiP0ABJ9.

Enzyme and pathway databases

UniPathwayiUPA00705.
BioCyciEcoCyc:CYDA-MONOMER.
ECOL316407:JW0722-MONOMER.
MetaCyc:CYDA-MONOMER.
BRENDAi1.10.3.14. 2026.

Miscellaneous databases

PROiP0ABJ9.

Gene expression databases

GenevestigatoriP0ABJ9.

Family and domain databases

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

Publicationsi

« Hide 'large scale' publications
  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: May 27, 2015
This is version 89 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.