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Protein

Cytochrome bd-I ubiquinol oxidase subunit 2

Gene

cydB

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.3 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 b595, originally called cytochrome a1) per heterodimer, in conjunction with CydA.
  • heme d cis-diolNote: Binds 1 iron-chlorin (heme d or cytochrome d) per heterodimer, in conjunction with CydA.

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: oxidative phosphorylation

This protein is involved in the pathway oxidative phosphorylation, which is part of Energy metabolism.
View all proteins of this organism that are known to be involved in the pathway oxidative phosphorylation and in Energy metabolism.

GO - Molecular functioni

  • electron carrier activity Source: EcoCyc
  • heme binding Source: EcoCyc
  • metal ion binding Source: UniProtKB-KW
  • oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor Source: EcoCyc

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:CYDB-MONOMER.
ECOL316407:JW0723-MONOMER.
MetaCyc:CYDB-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 2 (EC:1.10.3.14)
Alternative name(s):
Cytochrome bd-I oxidase subunit II
Cytochrome d ubiquinol oxidase subunit II
Gene namesi
Name:cydB
Synonyms:cyd-2
Ordered Locus Names:b0734, JW0723
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10174. cydB.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 88CytoplasmicCurated
Transmembranei9 – 2820HelicalCuratedAdd
BLAST
Topological domaini29 – 7951PeriplasmicCuratedAdd
BLAST
Transmembranei80 – 9920HelicalCuratedAdd
BLAST
Topological domaini100 – 12223CytoplasmicCuratedAdd
BLAST
Transmembranei123 – 14220HelicalCuratedAdd
BLAST
Topological domaini143 – 16422PeriplasmicCuratedAdd
BLAST
Transmembranei165 – 18420HelicalCuratedAdd
BLAST
Topological domaini185 – 20521CytoplasmicCuratedAdd
BLAST
Transmembranei206 – 22520HelicalCuratedAdd
BLAST
Topological domaini226 – 26237PeriplasmicCuratedAdd
BLAST
Transmembranei263 – 28220HelicalCuratedAdd
BLAST
Topological domaini283 – 29210CytoplasmicCurated
Transmembranei293 – 31220HelicalCuratedAdd
BLAST
Topological domaini313 – 33624PeriplasmicCuratedAdd
BLAST
Transmembranei337 – 35620HelicalCuratedAdd
BLAST
Topological domaini357 – 37923CytoplasmicCuratedAdd
BLAST

GO - Cellular componenti

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

Keywords - Cellular componenti

Cell inner membrane, Cell membrane, Membrane

Pathology & Biotechi

Disruption phenotypei

Loss of cytochrome b595 and d from enzyme preparations (PubMed:3013298). A double cydA/cydB deletion shows increased sensitivity to reductant (beta-mercapoethanol) (PubMed:23749980). Greatly increased resistance to hydroxyurea, probably due to decreased OH radical formation as an electron transport chain is disrupted (PubMed:20005847).5 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi56 – 561H → L: No effect. 1 Publication
Mutagenesisi197 – 1971H → L: No effect. 1 Publication
Mutagenesisi237 – 2371H → L or R: No effect. 1 Publication
Mutagenesisi376 – 3761H → P: No effect. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 379379Cytochrome bd-I ubiquinol oxidase subunit 2PRO_0000183925Add
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

PaxDbiP0ABK2.
PRIDEiP0ABK2.

Expressioni

Inductioni

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

Interactioni

Subunit structurei

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

Binary interactionsi

WithEntry#Exp.IntActNotes
cydAP0ABJ95EBI-1213195,EBI-906928

Protein-protein interaction databases

BioGridi4263540. 347 interactions.
IntActiP0ABK2. 2 interactions.
STRINGi511145.b0734.

Structurei

3D structure databases

ProteinModelPortaliP0ABK2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG4105CFY. Bacteria.
COG1294. LUCA.
HOGENOMiHOG000084824.
InParanoidiP0ABK2.
KOiK00426.
OMAiFLWGVAF.
OrthoDBiEOG6K4031.
PhylomeDBiP0ABK2.

Family and domain databases

InterProiIPR003317. Cyt-d_oxidase_su2.
[Graphical view]
PfamiPF02322. Cyt_bd_oxida_II. 1 hit.
[Graphical view]
PIRSFiPIRSF000267. Cyt_oxidse_sub2. 1 hit.
TIGRFAMsiTIGR00203. cydB. 1 hit.

Sequencei

Sequence statusi: Complete.

P0ABK2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIDYEVLRFI WWLLVGVLLI GFAVTDGFDM GVGMLTRFLG RNDTERRIMI
60 70 80 90 100
NSIAPHWDGN QVWLITAGGA LFAAWPMVYA AAFSGFYVAM ILVLASLFFR
110 120 130 140 150
PVGFDYRSKI EETRWRNMWD WGIFIGSFVP PLVIGVAFGN LLQGVPFNVD
160 170 180 190 200
EYLRLYYTGN FFQLLNPFGL LAGVVSVGMI ITQGATYLQM RTVGELHLRT
210 220 230 240 250
RATAQVAALV TLVCFALAGV WVMYGIDGYV VKSTMDHYAA SNPLNKEVVR
260 270 280 290 300
EAGAWLVNFN NTPILWAIPA LGVVLPLLTI LTARMDKAAW AFVFSSLTLA
310 320 330 340 350
CIILTAGIAM FPFVMPSSTM MNASLTMWDA TSSQLTLNVM TWVAVVLVPI
360 370
ILLYTAWCYW KMFGRITKED IERNTHSLY
Length:379
Mass (Da):42,453
Last modified:October 25, 2005 - v1
Checksum:iA3775AC95F713D0C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J03939 Unassigned DNA. Translation: AAA18805.1.
U00096 Genomic DNA. Translation: AAC73828.1.
AP009048 Genomic DNA. Translation: BAA35400.1.
U30934 Genomic DNA. Translation: AAA74397.1.
PIRiB28940.
RefSeqiNP_415262.1. NC_000913.3.
WP_000568275.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73828; AAC73828; b0734.
BAA35400; BAA35400; BAA35400.
GeneIDi945347.
KEGGiecj:JW0723.
eco:b0734.
PATRICi32116665. VBIEscCol129921_0765.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J03939 Unassigned DNA. Translation: AAA18805.1.
U00096 Genomic DNA. Translation: AAC73828.1.
AP009048 Genomic DNA. Translation: BAA35400.1.
U30934 Genomic DNA. Translation: AAA74397.1.
PIRiB28940.
RefSeqiNP_415262.1. NC_000913.3.
WP_000568275.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP0ABK2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263540. 347 interactions.
IntActiP0ABK2. 2 interactions.
STRINGi511145.b0734.

Protein family/group databases

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

Proteomic databases

PaxDbiP0ABK2.
PRIDEiP0ABK2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73828; AAC73828; b0734.
BAA35400; BAA35400; BAA35400.
GeneIDi945347.
KEGGiecj:JW0723.
eco:b0734.
PATRICi32116665. VBIEscCol129921_0765.

Organism-specific databases

EchoBASEiEB0171.
EcoGeneiEG10174. cydB.

Phylogenomic databases

eggNOGiENOG4105CFY. Bacteria.
COG1294. LUCA.
HOGENOMiHOG000084824.
InParanoidiP0ABK2.
KOiK00426.
OMAiFLWGVAF.
OrthoDBiEOG6K4031.
PhylomeDBiP0ABK2.

Enzyme and pathway databases

UniPathwayiUPA00705.
BioCyciEcoCyc:CYDB-MONOMER.
ECOL316407:JW0723-MONOMER.
MetaCyc:CYDB-MONOMER.
BRENDAi1.10.3.14. 2026.

Miscellaneous databases

PROiP0ABK2.

Family and domain databases

InterProiIPR003317. Cyt-d_oxidase_su2.
[Graphical view]
PfamiPF02322. Cyt_bd_oxida_II. 1 hit.
[Graphical view]
PIRSFiPIRSF000267. Cyt_oxidse_sub2. 1 hit.
TIGRFAMsiTIGR00203. cydB. 1 hit.
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. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 361-379.
    Strain: K12 / MG1655 / ATCC 47076.
  7. "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.
  8. "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: DISRUPTION PHENOTYPE.
  9. "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.
  10. "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.
  11. "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: COFACTOR, MUTAGENESIS OF HIS-56; HIS-197; HIS-237 AND HIS-376.
  12. "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.
  13. Cited for: SUBUNIT, SUBCELLULAR LOCATION.
    Strain: BL21-DE3.
  14. "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.
  15. "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.
  16. "Hydroxyurea induces hydroxyl radical-mediated cell death in Escherichia coli."
    Davies B.W., Kohanski M.A., Simmons L.A., Winkler J.A., Collins J.J., Walker G.C.
    Mol. Cell 36:845-860(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ROLE IN HYDROXYUREA RESISTANCE, DISRUPTION PHENOTYPE.
    Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
  17. "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.
  18. "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.
  19. Cited for: REVIEW.

Entry informationi

Entry nameiCYDB_ECOLI
AccessioniPrimary (citable) accession number: P0ABK2
Secondary accession number(s): P11027
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 25, 2005
Last sequence update: October 25, 2005
Last modified: January 20, 2016
This is version 88 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

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 one 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.