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    sbcD ATP-dependent structure-specific DNA nuclease - SbcD subunit [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 945049, updated on 3-Dec-2024

    Summary

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    Official Symbol
    sbcD
    Official Full Name
    ATP-dependent structure-specific DNA nuclease - SbcD subunit
    Primary source
    ECOCYC:EG11094
    Locus tag
    b0398
    See related
    ASAP:ABE-0001383
    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
    ECK0392; yajA
    Summary
    SbcCD can cleave dsDNA 5' ends sealed by a hairpin or by covalent linkage to a protein. [More information is available at EcoGene: EG11094]. sbcD encodes a component of the SbcCD exonuclease . [More information is available at EcoCyc: EG11094].
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    Genomic context

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    Sequence:
    NC_000913.3 (415750..416952, complement)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene fructokinase Neighboring gene putative transport protein AraJ Neighboring gene ATP-dependent structure-specific DNA nuclease - SbcC subunit Neighboring gene DNA-binding transcriptional dual regulator PhoB Neighboring gene sensor histidine kinase PhoR

    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. Structural basis for DNA recognition and nuclease processing by the Mre11 homologue SbcD in double-strand breaks repair. Liu S, et al. Acta Crystallogr D Biol Crystallogr, 2014 Feb. PMID 24531464
    2. Structural and functional similarities between the SbcCD proteins of Escherichia coli and the RAD50 and MRE11 (RAD32) recombination and repair proteins of yeast. Sharples GJ, et al. Mol Microbiol, 1995 Sep. PMID 8594339
    3. DNA cleavage and degradation by the SbcCD protein complex from Escherichia coli. Connelly JC, et al. Nucleic Acids Res, 1999 Feb 15. PMID 9927737, Free PMC Article
    4. Evidence for two mechanisms of palindrome-stimulated deletion in Escherichia coli: single-strand annealing and replication slipped mispairing. Bzymek M, et al. Genetics, 2001 Jun. PMID 11404319, Free PMC Article
    5. Nucleolytic processing of a protein-bound DNA end by the E. coli SbcCD (MR) complex. Connelly JC, et al. DNA Repair (Amst), 2003 Jul 16. PMID 12826280

    See all (39) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The E. coli Mre11-Rad50 homolog SbcC/SbcD can detect and process diverse DNA ends.
      Title: Mechanism of DNA End Sensing and Processing by the Mre11-Rad50 Complex.
    2. Data show that replication forks form a palindrome-like structural intermediate that requires nucleolytic processing by SbcC-SbcD and exonuclease I (ExoI) before chromosome replication can be completed.
      Title: SbcC-SbcD and ExoI process convergent forks to complete chromosome replication.
    3. The results suggest that SbcCD processes hairpin and linear dsDNA ends with a novel DNA end-dependent binary endonuclease activity in response to substrate length.
      Title: A novel mode of nuclease action is revealed by the bacterial Mre11/Rad50 complex.
    4. The SbcD monomer exhibits single-stranded DNA endonuclease activity and double-stranded DNA exonuclease activity.
      Title: Structural basis for DNA recognition and nuclease processing by the Mre11 homologue SbcD in double-strand breaks repair.
    5. By initiating or participating in double-strand break repair, SbcCD may provide DNA substrates for Pol IV polymerase activity.
      Title: The SMC-like protein complex SbcCD enhances DNA polymerase IV-dependent spontaneous mutation in Escherichia coli.
    6. In sbcCD mutants, RecA4142 can bind other DNA substrates by itself that are normally degraded by the SbcCD nuclease.
      Title: RecA4142 causes SOS constitutive expression by loading onto reversed replication forks in Escherichia coli K-12.
    7. Study found that functions of SbcCD, a DNA structure specific nuclease, were needed in the RNase E-dependent lacZ expression of the GAA repeats.
      Title: The roles of SbcCD and RNaseE in the transcription of GAA x TTC repeats in Escherichia coli.
    8. The absence of SbcC and SbcD in sbcB15 cells decreased stationary-phase mutation.
      Title: Role of single-strand DNA 3'-5' exonuclease ExoI and nuclease SbcCD in stationary-phase mutation in Escherichia coli K-12.
    9. N-terminus verified by Edman degradation on complete protein
      Title: Overexpression, purification, and characterization of the SbcCD protein from Escherichia coli.
    10. Transcription of the sbcDC operon is shown to be dependent on starvation and RpoS protein, and SbcD protein is distributed through the cytoplasm.
      Title: SbcCD regulation and localization in 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 3'-5' exonuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA exonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA exonuclease activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables double-stranded DNA endonuclease activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables endonuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables exonuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables single-stranded DNA endodeoxyribonuclease activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA recombination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA recombination NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in DNA repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within DNA repair IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in DNA repair NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within DNA replication IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in DNA replication IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within DNA replication termination EXP
    Inferred from Experiment
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of DNA repair complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ATP-dependent structure-specific DNA nuclease - SbcD subunit

    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
      415750..416952 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_414932.1 ATP-dependent structure-specific DNA nuclease - SbcD subunit [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_414932.1

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A2H4TPP2, A0A8S7JU23
      Conserved Domains (1) summary
      PRK10966
      Location:1 → 400
      PRK10966; exonuclease subunit SbcD; Provisional
    Nucleotide Protein
    Heading Accession and Version

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