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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 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
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)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. 347 interactors.
IntActiP0ABK2. 2 interactors.
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.
OMAiYFLPQVW.
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 interactors.
IntActiP0ABK2. 2 interactors.
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.
OMAiYFLPQVW.
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...

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: November 2, 2016
This is version 91 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.