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cydB [ Escherichia coli str. K-12 substr. MG1655 ]

Gene ID: 945347, updated on 11-Sep-2024

Summary

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Official Symbol
cydB
Primary source
ECOCYC:EG10174
Locus tag
b0734
See related
ASAP:ABE-0002501
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Escherichia coli str. K-12 substr. MG1655 (strain: K-12, substrain: MG1655)
Lineage
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia
Also known as
cyd-2; ECK0722
Summary
Fnr and ArcA regulons. [More information is available at EcoGene: EG10174]. CydB is required for binding the heme b595 component and one heme d (iron-chlorin) component of cytochrome bd-I . [More information is available at EcoCyc: EG10174].
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Genomic context

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Sequence:
NC_000913.3 (773042..774181)

NC_000913.3Genomic Context describing neighboring genes Neighboring gene alpha-mannosidase Neighboring gene cytochrome bd-I subunit 1 Neighboring gene cytochrome bd-I accessory subunit CydX Neighboring gene PF09600 family protein YbgE

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_000913.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. The cytochrome bd-I respiratory oxidase augments survival of multidrug-resistant Escherichia coli during infection. Shepherd M, et al. Sci Rep, 2016 Oct 21. PMID 27767067, Free PMC Article
  2. Glutamate 107 in subunit I of the cytochrome bd quinol oxidase from Escherichia coli is protonated and near the heme d/heme b595 binuclear center. Yang K, et al. Biochemistry, 2007 Mar 20. PMID 17305364
  3. Fluoride-binding to the Escherichia coli bd-type ubiquinol oxidase studied by visible absorption and EPR spectroscopies. Tsubaki M, et al. J Biochem, 1999 Jul. PMID 10393326
  4. In vivo assembly of the cytochrome d terminal oxidase complex of Escherichia coli from genes encoding the two subunits expressed on separate plasmids. Newton G, et al. Biochim Biophys Acta, 1991 May 2. PMID 1851043
  5. Isolation and characterization of a new class of cytochrome d terminal oxidase mutants of Escherichia coli. Oden KL, et al. J Bacteriol, 1991 Oct. PMID 1655701, Free PMC Article

See all (78) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. structure of the E. coli cytochrome bd-I oxidase to a resolution of 2.7 angstroms; structure contains an accessory subunit CydH encoded by ynhF, the L-subfamily-specific Q-loop domain, a structural ubiquinone-8 cofactor, an active-site density interpreted as dioxygen, distinct water-filled proton channels, and an oxygen-conducting pathway
    Title: Active site rearrangement and structural divergence in prokaryotic respiratory oxidases.
  2. CydAB expression augments survival of multidrug-resistant Escherichia coli during infection.
    Title: The cytochrome bd-I respiratory oxidase augments survival of multidrug-resistant Escherichia coli during infection.
  3. Cytochrome bd oxidases split the O-O bond in a single four-electron transfer reaction without a peroxide intermediate.
    Title: Oxoferryl-porphyrin radical catalytic intermediate in cytochrome bd oxidases protects cells from formation of reactive oxygen species.
  4. E. coli can compensate for the loss of cytochrome bd-I activity and cytochrome bd-II-mediated quinol oxidation prevents the accumulation of NADH
    Title: Compensations for diminished terminal oxidase activity in Escherichia coli: cytochrome bd-II-mediated respiration and glutamate metabolism.
  5. The data support models of the catalytic cycle which do not include the fully oxidized form of cytochrome bd quinol oxidase as an intermediate.
    Title: The fully oxidized form of the cytochrome bd quinol oxidase from E. coli does not participate in the catalytic cycle: direct evidence from rapid kinetics studies.
  6. the N-terminal region of periplasmic loop VI/VII (Q-loop) of cytochrome bd is a part of the quinol oxidation site and the 2- and 3-methoxy groups of the quinone ring are in the close vicinity of I-Glu(280)
    Title: Mass spectrometric analysis of the ubiquinol-binding site in cytochrome bd from Escherichia coli.
Submit: New GeneRIF Correction

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Gene Ontology Provided by EcoCyc

Function Evidence Code Pubs
enables electron transfer activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables electron transfer activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor IBA
Inferred from Biological aspect of Ancestor
more info
  
enables oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in aerobic electron transport chain IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in aerobic electron transport chain IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in aerobic electron transport chain NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in oxidative phosphorylation IEA
Inferred from Electronic Annotation
more info
  
involved_in oxidative phosphorylation NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of cytochrome complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of cytochrome complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane ISM
Inferred from Sequence Model
more info
 PubMed 
located_in plasma membrane RCA
inferred from Reviewed Computational Analysis
more info
 PubMed 

General protein information

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Preferred Names
cytochrome bd-I subunit 2
NP_415262.1

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

  1. NC_000913.3 Reference assembly

    Range
    773042..774181
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NP_415262.1 cytochrome bd-I subunit 2 [Escherichia coli str. K-12 substr. MG1655]

    See identical proteins and their annotated locations for NP_415262.1

    Status: PROVISIONAL

    UniProtKB/TrEMBL
    A0A1V2G7J0
    Conserved Domains (1) summary
    PRK15003
    Location:1 → 379
    PRK15003; cytochrome d ubiquinol oxidase subunit II
Nucleotide Protein
Heading Accession and Version

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