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xthA exodeoxyribonuclease III [ Escherichia coli str. K-12 substr. MG1655 ]

Gene ID: 946254, updated on 17-Dec-2024

Summary

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Official Symbol
xthA
Official Full Name
exodeoxyribonuclease III
Primary source
ECOCYC:EG11073
Locus tag
b1749
See related
ASAP:ABE-0005829
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
ECK1747; xth
Summary
Exonuclease III (XthA) is one of two 5' apurinic/apyrimidinic (AP) endonucleases (along with endonuclease IV) in Escherichia coli which function in the repair of DNA at sites where damaged bases have been removed by the activity of DNA glycosylases or where bases have been spontaneously lost. [More information is available at EcoCyc: EG11073].
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Genomic context

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Sequence:
NC_000913.3 (1832428..1833234)

NC_000913.3Genomic Context describing neighboring genes Neighboring gene N-succinylarginine dihydrolase Neighboring gene aldehyde dehydrogenase Neighboring gene arginine N-succinyltransferase Neighboring gene succinylornithine transaminase Neighboring gene DedA family protein YdjX Neighboring gene 4Fe-4S ferredoxin-type domain-containing protein YdjY

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. Exonuclease III (XthA) Enforces In Vivo DNA Cloning of Escherichia coli To Create Cohesive Ends. Nozaki S, et al. J Bacteriol, 2019 Mar 1. PMID 30530516, Free PMC Article
  2. Properties of the main endonuclease specific for apurinic sites of Escherichia coli (endonuclease VI). Mechanism of apurinic site excision from DNA. Gossard F, et al. Eur J Biochem, 1978 Jan 16. PMID 342234
  3. Solid-phase synthesis of oligo(2'-deoxyxylonucleotides) and PCR amplification of base-modified DNA fragments. Seela F, et al. Nucleic Acids Symp Ser, 1991. PMID 1668697
  4. The use of thioglycollate to demonstrate DNA AP (apurinic/apyrimidinic-site) lyase activities. Biological consequences of thiol addition to the 5' product of a beta-elimination reaction at an AP site in DNA. Bricteux-Grégoire S, et al. Biochem J, 1991 Feb 1. PMID 1705116, Free PMC Article
  5. Exonuclease III and endonuclease IV remove 3' blocks from DNA synthesis primers in H2O2-damaged Escherichia coli. Demple B, et al. Proc Natl Acad Sci U S A, 1986 Oct. PMID 2429316, Free PMC Article

See all (54) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Bacterial exonuclease III expands its enzymatic activities on single-stranded DNA.
    Title: Bacterial exonuclease III expands its enzymatic activities on single-stranded DNA.
  2. XthA resects the 3' ends of linear DNA fragments that are introduced into Escherichia coli cells, resulting in exposure of the single-stranded 5' overhangs.
    Title: Exonuclease III (XthA) Enforces In Vivo DNA Cloning of Escherichia coli To Create Cohesive Ends.
  3. This increased MMS sensitivity was not suppressed by the presence of multi-copy holC. Addition of the yoaA disruption increased the methyl methanesulfonate (MMS) sensitivity of xthA single-deletion or xthA nfo double-deletion mutants.
    Title: Systematic identification of synthetic lethal mutations with reduced-genome Escherichia coli: synthetic genetic interactions among yoaA, xthA and holC related to survival from MMS exposure.
  4. Xth may act in a complementary repair pathway to nucleotide excision repair to remove S-cdA adducts from 3' DNA termini.
    Title: Insight into mechanisms of 3'-5' exonuclease activity and removal of bulky 8,5'-cyclopurine adducts by apurinic/apyrimidinic endonucleases.
  5. It is shown (paradoxically) that in xthA mutants, RecA-GFP loading is predominantly RecBCD-dependent and that xthA recB double mutants are viable.
    Title: XthA (Exonuclease III) regulates loading of RecA onto DNA substrates in log phase Escherichia coli cells.
  6. Endonuclease IV and Exonuclease III have roles in counteracting DNA damage induced by the oxidative counterpart of UVB in E.coli
    Title: Endonuclease IV and exonuclease III are involved in the repair and mutagenesis of DNA lesions induced by UVB in Escherichia coli.
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General gene information

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Homology

Gene Ontology Provided by EcoCyc

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables double-stranded DNA 3'-5' DNA exonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables double-stranded DNA 3'-5' DNA exonuclease activity IEA
Inferred from Electronic Annotation
more info
  
enables endonuclease activity IEA
Inferred from Electronic Annotation
more info
  
enables exonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables exonuclease activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within DNA damage response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in DNA repair IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
exodeoxyribonuclease III
NP_416263.1

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
    1832428..1833234
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NP_416263.1 exodeoxyribonuclease III [Escherichia coli str. K-12 substr. MG1655]

    See identical proteins and their annotated locations for NP_416263.1

    Status: PROVISIONAL

    UniProtKB/TrEMBL
    A0A0H3EWK5, A0A140N7B9, A0A1X3JGK3, A0AAN3MER4
    Conserved Domains (1) summary
    PRK11756
    Location:1 → 267
    PRK11756; exonuclease III; Provisional
Nucleotide Protein
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