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

    Gene ID: 945347, updated on 3-Dec-2024

    Summary

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    Official Symbol
    cydB
    Official Full Name
    cytochrome bd-I subunit 2
    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. 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
    3. 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
    4. 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
    5. 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

    See all (77) 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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    Homology

    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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