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

Gene ID: 945049, updated on 11-Sep-2024

Summary

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Official Symbol
sbcD
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. Mechanism of DNA End Sensing and Processing by the Mre11-Rad50 Complex. Käshammer L, et al. Mol Cell, 2019 Nov 7. PMID 31492634
  3. A novel mode of nuclease action is revealed by the bacterial Mre11/Rad50 complex. Lim CT, et al. Nucleic Acids Res, 2015 Nov 16. PMID 26319016, Free PMC Article
  4. SbcCD regulation and localization in Escherichia coli. Darmon E, et al. J Bacteriol, 2007 Sep. PMID 17644583, 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 (40) 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.
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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 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
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