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    dinB DNA polymerase IV [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 944922, updated on 11-Apr-2024

    Summary

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    Gene symbol
    dinB
    Gene description
    DNA polymerase IV
    Primary source
    ASAP:ABE-0000789
    Locus tag
    b0231
    See related
    ECOCYC:G6115
    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
    dinP; ECK0232
    Summary
    Part of dinB-yafNOP operon. [More information is available at EcoGene: EG13141]. dinB encodes DNA polymerase IV (DNA pol IV), which belongs to the Y family of DNA polymerases . [More information is available at EcoCyc: G6115].
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    Genomic context

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    Sequence:
    NC_000913.3 (250898..251953)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene pseudo Neighboring gene pseudo Neighboring gene antitoxin YafN Neighboring gene ribosome-dependent mRNA interferase toxin YafO

    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. Residues in the fingers domain of the translesion DNA polymerase DinB enable its unique participation in error-prone double-strand break repair. Tashjian TF, et al. J Biol Chem, 2019 May 10. PMID 30872406, Free PMC Article
    2. DNA polymerase IV primarily operates outside of DNA replication forks in Escherichia coli. Henrikus SS, et al. PLoS Genet, 2018 Jan. PMID 29351274, Free PMC Article
    3. Persistent damaged bases in DNA allow mutagenic break repair in Escherichia coli. Moore JM, et al. PLoS Genet, 2017 Jul. PMID 28727736, Free PMC Article
    4. Processing closely spaced lesions during Nucleotide Excision Repair triggers mutagenesis in E. coli. Janel-Bintz R, et al. PLoS Genet, 2017 Jul. PMID 28686598, Free PMC Article
    5. DNA polymerase IV mediates efficient and quick recovery of replication forks stalled at N2-dG adducts. Ikeda M, et al. Nucleic Acids Res, 2014 Jul. PMID 24957605, Free PMC Article

    See all (146) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB).
      Title: Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB).
    2. Single-molecule live-cell imaging reveals RecB-dependent function of DNA polymerase IV in double strand break repair.
      Title: Single-molecule live-cell imaging reveals RecB-dependent function of DNA polymerase IV in double strand break repair.
    3. the amino acid patch of highly conserved residues in DinB-like proteins provides a mechanistic explanation for DinB's function in strand exchange and improves our understanding of recombination by providing evidence that RecA plays a role in facilitating DinB's activity during strand exchange.
      Title: Residues in the fingers domain of the translesion DNA polymerase DinB enable its unique participation in error-prone double-strand break repair.
    4. In an SOS-constitutive mutant that expresses high levels of pol IV, few foci are observed in the absence of damage, indicating that within cells access of pol IV to DNA is dependent on the presence of damage, as opposed to concentration-driven competition for binding sites.
      Title: DNA polymerase IV primarily operates outside of DNA replication forks in Escherichia coli.
    5. We hypothesize that damaged bases allow the switch to use of Pol IV during MBR by pausing the replicative polymerase to allow polymerase exchange in the replisome. The findings suggest that spontaneous mutation by MBR is regulated by regulation of the intracellular level of ROS
      Title: Persistent damaged bases in DNA allow mutagenic break repair in Escherichia coli.
    6. A mathematical model let us define the geometry (infer the structure) of the toxic intermediate as being formed when NER incises a lesion that resides in close proximity of another lesion in the complementary strand. This critical NER intermediate requires Pol IV / Pol II for repair, it is either lethal if left unrepaired or mutation-prone when repaired
      Title: Processing closely spaced lesions during Nucleotide Excision Repair triggers mutagenesis in E. coli.
    7. although lagging-strand synthesis is still perturbed in holD trkA mutants, the trkA mutation allows HolD-less Pol III HE to resist increased levels of the SOS-induced bypass polymerase DinB
      Title: Mutations Affecting Potassium Import Restore the Viability of the Escherichia coli DNA Polymerase III holD Mutant.
    8. The steric gate is crucial for rNTP discrimination because of its role in specifically promoting a dNTP-induced conformational change and that rNTP discrimination occurs in a relatively closed state of the polymerases.
      Title: Steric gate residues of Y-family DNA polymerases DinB and pol kappa are crucial for dNTP-induced conformational change.
    9. The structural dynamics of DinB changes upon substrate binding, noncognate DNA damage prevents the formation of the active conformation of DINB.
      Title: Noncognate DNA damage prevents the formation of the active conformation of the Y-family DNA polymerases DinB and DNA polymerase κ.
    10. A DeltadinB mutation that sensitizes Escherichia coli to the lethal effects of UV- and X-radiation.
      Title: A ΔdinB mutation that sensitizes Escherichia coli to the lethal effects of UV- and X-radiation.
    Submit: New GeneRIF Correction See all GeneRIFs (40)

    General gene information

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    Gene Ontology Provided by EcoCyc

    Function Evidence Code Pubs
    NOT enables 3'-5'-DNA exonuclease activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-directed DNA polymerase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-directed DNA polymerase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-directed DNA polymerase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables damaged DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables magnesium ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables magnesium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleotidyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA damage response IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within DNA damage response IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in DNA repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA replication IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within DNA synthesis involved in DNA repair IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in DNA-templated DNA replication IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in SOS response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in SOS response IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within SOS response IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within error-free translesion synthesis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within error-free translesion synthesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in error-prone translesion synthesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within error-prone translesion synthesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IC
    Inferred by Curator
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    DNA polymerase IV
    NP_414766.1

    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
      250898..251953
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_414766.1 DNA polymerase IV [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_414766.1

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A8S7YHA5
      Conserved Domains (1) summary
      PRK02406
      Location:9 → 351
      PRK02406; DNA polymerase IV; Validated
    Nucleotide Protein
    Heading Accession and Version

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