cydB:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

CydB

Synonyms

cytochrome d terminal oxidase, subunit II[1], B0734[2][1], CydB[2][1] , ECK0722, JW0723, b0734

Product description

cytochrome bd-I terminal oxidase subunit II[2][3];

Component of cytochrome bd-I terminal oxidase[2][3]

Cytochrome d (bd-I) terminal oxidase subunit II; upregulated in biofilms and microaerobic conditions; aerobically repressed by H-NS; anaerobically repressed by Fnr[4]

EC number (for enzymes)

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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0005506

iron ion binding

PMID:10393326[5]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0997

C

Seeded from EcoCyc (v14.0)

complete

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-1003

C

Seeded from EcoCyc (v14.0)

complete

GO:0006810

transport

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0813

P

Seeded from EcoCyc (v14.0)

complete

GO:0009055

electron carrier activity

PMID:16299377[6]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003317

C

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0472

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0812

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9909

C

Seeded from EcoCyc (v14.0)

complete

GO:0016682

oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor

PMID:6321507[7]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0017004

cytochrome complex assembly

PMID:2856143[8]

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

GO:0020037

heme binding

PMID:8516338[9]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0022900

electron transport chain

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0249

P

Seeded from EcoCyc (v14.0)

complete

GO:0031224

intrinsic to membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

C

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003317

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

P

Seeded from EcoCyc (v14.0)

complete

Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

Subunits of [[:Category:Complex:cytochrome bd-I terminal oxidase|cytochrome bd-I terminal oxidase]]

could be indirect


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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes

plasma membrane

C-terminus localized in the cytoplasm with 8 predicted transmembrane domains

Daley et al. (2005) [10]


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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc

MIDYEVLRFI WWLLVGVLLI GFAVTDGFDM GVGMLTRFLG RNDTERRIMI NSIAPHWDGN
QVWLITAGGA LFAAWPMVYA AAFSGFYVAM ILVLASLFFR PVGFDYRSKI EETRWRNMWD
WGIFIGSFVP PLVIGVAFGN LLQGVPFNVD EYLRLYYTGN FFQLLNPFGL LAGVVSVGMI
ITQGATYLQM RTVGELHLRT RATAQVAALV TLVCFALAGV WVMYGIDGYV VKSTMDHYAA
SNPLNKEVVR EAGAWLVNFN NTPILWAIPA LGVVLPLLTI LTARMDKAAW AFVFSSLTLA
CIILTAGIAM FPFVMPSSTM MNASLTMWDA TSSQLTLNVM TWVAVVLVPI ILLYTAWCYW
KMFGRITKED IERNTHSLY
Length

379

Mol. Wt

42.453 kDa

pI

7.2 (calculated)

Extinction coefficient

108,860 - 109,235 (calc based on 14 Y, 16 W, and 3 C residues)


Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Domain

6..363

PF02322 Cytochrome oxidase subunit II

PMID:19920124[11]

<motif_map/>

tmhmm.php?gene=cydB&show=pic&.jpg
Click the image to view raw output from TMHMM.

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=cydB taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16128709

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945347

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002501

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0ABK2

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10174

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10174

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945347

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000169

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0171

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. 1.0 1.1 1.2 1.3 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. 2.0 2.1 2.2 2.3 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. Tsubaki, M et al. (1999) Fluoride-binding to the Escherichia coli bd-type ubiquinol oxidase studied by visible absorption and EPR spectroscopies. J. Biochem. 126 98-103 PubMed
  6. Matsumoto, Y et al. (2006) Mass spectrometric analysis of the ubiquinol-binding site in cytochrome bd from Escherichia coli. J. Biol. Chem. 281 1905-12 PubMed
  7. Kita, K et al. (1984) Terminal oxidases of Escherichia coli aerobic respiratory chain. II. Purification and properties of cytochrome b558-d complex from cells grown with limited oxygen and evidence of branched electron-carrying systems. J. Biol. Chem. 259 3375-81 PubMed
  8. Miller, MJ & Gennis, RB (1986) Purification and reconstitution of the cytochrome d terminal oxidase complex from Escherichia coli. Meth. Enzymol. 126 87-94 PubMed
  9. Hill, JJ et al. (1993) Spectroscopic evidence for a heme-heme binuclear center in the cytochrome bd ubiquinol oxidase from Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 90 5863-7 PubMed
  10. Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
  11. Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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