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P0ABJ9 (CYDA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 81. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
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 bd-I ubiquinol oxidase subunit 1

EC=1.10.3.10
Alternative name(s):
Cytochrome bd-I oxidase subunit I
Cytochrome d ubiquinol oxidase subunit I
Gene names
Name:cydA
Synonyms:cyd-1
Ordered Locus Names:b0733, JW0722
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length522 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.6 Ref.10 Ref.13 Ref.17 Ref.18

Catalytic activity

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

Cofactor

Binds 1 protoheme IX center (heme b558) per subunit. Ref.6 Ref.7 Ref.8 Ref.10 Ref.13

Binds 1 protoheme IX center (heme b595, originally called cytochrome a1) per heterodimer, in conjunction with CydB. Ref.6 Ref.7 Ref.8 Ref.10 Ref.13

Binds 1 iron-chlorin (heme d or cytochrome d) per heterodimer, in conjunction with CydB. Ref.6 Ref.7 Ref.8 Ref.10 Ref.13

Enzyme regulation

90% inhibited by cyanide and 2-heptyl-4-hydroxyquinoline N-oxide, at 1 mM and 40 µM respectively. Ref.6

Pathway

Energy metabolism; oxidative phosphorylation.

Subunit structure

Heterodimer of subunits I and II. Probably interacts with CydX, and overexpressed AppX. Ref.5 Ref.6 Ref.15 Ref.19

Subcellular location

Cell inner membrane; Multi-pass membrane protein Ref.14 Ref.15.

Induction

Under conditions of low aeration, in stationary phase (at protein level). Ref.6

Post-translational modification

The N-terminus is blocked.

Disruption phenotype

A double cydA/cydB deletion shows increased sensitivity to reductant (beta-mercapoethanol). Ref.17 Ref.18 Ref.19

Sequence similarities

Belongs to the cytochrome ubiquinol oxidase subunit 1 family.

Biophysicochemical properties

Kinetic parameters:

pH 7.0, 37 degrees Celsius.

KM=0.1 mM for ubiquinol-1 Ref.6

KM=0.28 mM for 2,3,5,6-tetramethyl-p-phenylenediamine

KM=0.68 mM for N,N,N',N'-tetramethyl-p-phenylenediamine

Vmax=383 µmol/min/mg enzyme for ubiquinol-1

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

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 522522Cytochrome bd-I ubiquinol oxidase subunit 1
PRO_0000183919

Regions

Topological domain1 – 1515Periplasmic Probable
Transmembrane16 – 3520Helical; Probable
Topological domain36 – 5419Cytoplasmic Probable
Transmembrane55 – 6915Helical; Probable
Topological domain70 – 9627Periplasmic Probable
Transmembrane97 – 11418Helical; Probable
Topological domain115 – 12814Cytoplasmic Probable
Transmembrane129 – 14618Helical; Probable
Topological domain147 – 18640Periplasmic Probable
Transmembrane187 – 20317Helical; Probable
Topological domain204 – 21916Cytoplasmic Probable
Transmembrane220 – 23516Helical; Probable
Topological domain236 – 390155Periplasmic Probable
Transmembrane391 – 40717Helical; Probable
Topological domain408 – 42316Cytoplasmic Probable
Transmembrane424 – 44118Helical; Probable
Topological domain442 – 47231Periplasmic Probable
Transmembrane473 – 48715Helical; Probable
Topological domain488 – 52235Cytoplasmic Probable

Sites

Metal binding191Iron (heme b595 axial ligand) Potential
Metal binding1861Iron (heme b558 axial ligand)
Metal binding3931Iron (heme b558 axial ligand)

Amino acid modifications

Modified residue11N-formylmethionine

Experimental info

Mutagenesis191H → L or R: Loss of cytochrome b595 and heme d, no aerobic growth, complex assembles. Ref.10
Mutagenesis861H → R: No effect. Ref.10
Mutagenesis1261H → P: Loss of all cofactors, no aerobic growth, complex assembles. Ref.10
Mutagenesis1261H → R: No effect. Ref.10
Mutagenesis1861H → L: Loss of cytochrome b558, no aerobic growth, complex assembles, this subunit is more susceptible to proteolysis. Ref.10
Mutagenesis3141H → L: Grows aerobically, has altered cytochrome b/d ratio, complex assembles. Ref.10
Mutagenesis3141H → P: Loss of cytochrome b595 and heme d, no aerobic growth, loss of complex. Ref.10
Mutagenesis3931M → L: Cytochrome b558 shifts to a high spin configuration, complex assembles. Retains about 1% quinol oxidoreductase activity after purification.
Mutagenesis5101H → L: No effect. Ref.10
Sequence conflict2131F → L in AAA18804. Ref.1

Sequences

Sequence LengthMass (Da)Tools
P0ABJ9 [UniParc].

Last modified October 25, 2005. Version 1.
Checksum: E757442068BCFCFE

FASTA52258,205
        10         20         30         40         50         60 
MLDIVELSRL QFALTAMYHF LFVPLTLGMA FLLAIMETVY VLSGKQIYKD MTKFWGKLFG 

        70         80         90        100        110        120 
INFALGVATG LTMEFQFGTN WSYYSHYVGD IFGAPLAIEG LMAFFLESTF VGLFFFGWDR 

       130        140        150        160        170        180 
LGKVQHMCVT WLVALGSNLS ALWILVANGW MQNPIASDFN FETMRMEMVS FSELVLNPVA 

       190        200        210        220        230        240 
QVKFVHTVAS GYVTGAMFIL GISAWYMLKG RDFAFAKRSF AIAASFGMAA VLSVIVLGDE 

       250        260        270        280        290        300 
SGYEMGDVQK TKLAAIEAEW ETQPAPAAFT LFGIPDQEEE TNKFAIQIPY ALGIIATRSV 

       310        320        330        340        350        360 
DTPVIGLKEL MVQHEERIRN GMKAYSLLEQ LRSGSTDQAV RDQFNSMKKD LGYGLLLKRY 

       370        380        390        400        410        420 
TPNVADATEA QIQQATKDSI PRVAPLYFAF RIMVACGFLL LAIIALSFWS VIRNRIGEKK 

       430        440        450        460        470        480 
WLLRAALYGI PLPWIAVEAG WFVAEYGRQP WAIGEVLPTA VANSSLTAGD LIFSMVLICG 

       490        500        510        520 
LYTLFLVAEL FLMFKFARLG PSSLKTGRYH FEQSSTTTQP AR 

« Hide

References

« Hide 'large scale' references
[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]"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map."
Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. expand/collapse author list , Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M., Horiuchi T.
DNA Res. 3:137-155(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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]"Protein complexes of the Escherichia coli cell envelope."
Stenberg F., Chovanec P., Maslen S.L., Robinson C.V., Ilag L., von Heijne G., Daley D.O.
J. Biol. Chem. 280:34409-34419(2005) [PubMed] [Europe PMC] [Abstract]
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]"The cytochrome bd respiratory oxygen reductases."
Borisov V.B., Gennis R.B., Hemp J., Verkhovsky M.I.
Biochim. Biophys. Acta 1807:1398-1413(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
J03939 Unassigned DNA. Translation: AAA18804.1.
U00096 Genomic DNA. Translation: AAC73827.2.
AP009048 Genomic DNA. Translation: BAA35399.1.
RefSeqNP_415261.2. NC_000913.3.
YP_489012.1. NC_007779.1.

3D structure databases

ProteinModelPortalP0ABJ9.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-36181N.
IntActP0ABJ9. 3 interactions.
STRING511145.b0733.

Protein family/group databases

TCDB3.D.4.3.2. the proton-translocating cytochrome oxidase (cox) superfamily.

Proteomic databases

PaxDbP0ABJ9.
PRIDEP0ABJ9.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC73827; AAC73827; b0733.
BAA35399; BAA35399; BAA35399.
GeneID12934545.
945341.
KEGGecj:Y75_p0712.
eco:b0733.
PATRIC32116663. VBIEscCol129921_0764.

Organism-specific databases

EchoBASEEB0170.
EcoGeneEG10173. cydA.

Phylogenomic databases

eggNOGCOG1271.
HOGENOMHOG000084938.
KOK00425.
OMAGWDRFSK.
OrthoDBEOG600DNV.
PhylomeDBP0ABJ9.

Enzyme and pathway databases

BioCycEcoCyc:CYDA-MONOMER.
ECOL316407:JW0722-MONOMER.
MetaCyc:CYDA-MONOMER.
UniPathwayUPA00705.

Gene expression databases

GenevestigatorP0ABJ9.

Family and domain databases

InterProIPR002585. Cyt-d_ubiquinol_oxidase_suI.
[Graphical view]
PfamPF01654. Bac_Ubq_Cox. 1 hit.
[Graphical view]
PIRSFPIRSF006446. Cyt_quinol_oxidase_1. 1 hit.
ProtoNetSearch...

Other

PROP0ABJ9.

Entry information

Entry nameCYDA_ECOLI
AccessionPrimary (citable) accession number: P0ABJ9
Secondary accession number(s): P11026, P75754, P76823
Entry history
Integrated into UniProtKB/Swiss-Prot: October 25, 2005
Last sequence update: October 25, 2005
Last modified: July 9, 2014
This is version 81 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene