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Protein

Cytochrome bd-I ubiquinol oxidase subunit 2

Gene

cydB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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(Side 2) + 4 H+(Side 2) = 2 ubiquinone + 2 H2O(Side 2) + 4 H+(Side 1).1 Publication

Cofactori

Protein has several cofactor binding sites:
  • heme b3 PublicationsNote: Binds 1 protoheme IX center (heme b595, originally called cytochrome a1) per heterodimer, in conjunction with CydA.3 Publications
  • heme d cis-diol3 PublicationsNote: Binds 1 iron-chlorin (heme d or cytochrome d) per heterodimer, in conjunction with CydA.3 Publications

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 transfer 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

Keywordsi

Molecular functionOxidoreductase
Biological processElectron transport, Transport
LigandHeme, Iron, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:CYDB-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:1.10.3.141 Publication)
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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10174 cydB

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 8CytoplasmicCurated8
Transmembranei9 – 28HelicalCuratedAdd BLAST20
Topological domaini29 – 79PeriplasmicCuratedAdd BLAST51
Transmembranei80 – 99HelicalCuratedAdd BLAST20
Topological domaini100 – 122CytoplasmicCuratedAdd BLAST23
Transmembranei123 – 142HelicalCuratedAdd BLAST20
Topological domaini143 – 164PeriplasmicCuratedAdd BLAST22
Transmembranei165 – 184HelicalCuratedAdd BLAST20
Topological domaini185 – 205CytoplasmicCuratedAdd BLAST21
Transmembranei206 – 225HelicalCuratedAdd BLAST20
Topological domaini226 – 262PeriplasmicCuratedAdd BLAST37
Transmembranei263 – 282HelicalCuratedAdd BLAST20
Topological domaini283 – 292CytoplasmicCurated10
Transmembranei293 – 312HelicalCuratedAdd BLAST20
Topological domaini313 – 336PeriplasmicCuratedAdd BLAST24
Transmembranei337 – 356HelicalCuratedAdd BLAST20
Topological domaini357 – 379CytoplasmicCuratedAdd BLAST23

GO - Cellular componenti

  • cytochrome complex Source: EcoCyc
  • integral component of plasma membrane Source: EcoCyc
  • membrane Source: EcoCyc
  • plasma membrane Source: EcoCyc

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)DescriptionActionsGraphical viewLength
Mutagenesisi56H → L: No effect. 1 Publication1
Mutagenesisi197H → L: No effect. 1 Publication1
Mutagenesisi237H → L or R: No effect. 1 Publication1
Mutagenesisi376H → P: No effect. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001839251 – 379Cytochrome bd-I ubiquinol oxidase subunit 2Add BLAST379

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-formylmethionine1 Publication1

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, 447 interactors
ComplexPortaliCPX-268 Cytochrome bd-I ubiquinol oxidase complex
IntActiP0ABK2, 2 interactors
MINTiP0ABK2
STRINGi316385.ECDH10B_0800

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
OMAiFLPQVWF
PhylomeDBiP0ABK2

Family and domain databases

InterProiView protein in InterPro
IPR003317 Cyt-d_oxidase_su2
PANTHERiPTHR43141 PTHR43141, 1 hit
PfamiView protein in Pfam
PF02322 Cyt_bd_oxida_II, 1 hit
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
PATRICifig|1411691.4.peg.1539

Similar proteinsi

Entry informationi

Entry nameiCYDB_ECOLI
AccessioniPrimary (citable) accession number: P0ABK2
Secondary accession number(s): P11027
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 25, 2005
Last sequence update: October 25, 2005
Last modified: June 20, 2018
This is version 101 of the entry and version 1 of the sequence. See 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

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