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

Gene ID: 944922, updated on 17-Dec-2024

Summary

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Official Symbol
dinB
Official Full Name
DNA polymerase IV
Primary source
ECOCYC:G6115
Locus tag
b0231
See related
ASAP:ABE-0000789
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. Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB). Okeke DC, et al. Nucleic Acids Res, 2023 Jul 21. PMID 37260088, Free PMC Article
  2. The processivity factor beta controls DNA polymerase IV traffic during spontaneous mutagenesis and translesion synthesis in vivo. Lenne-Samuel N, et al. EMBO Rep, 2002 Jan. PMID 11751576, Free PMC Article
  3. Translesion DNA synthesis in eukaryotes: a one- or two-polymerase affair. Prakash S, et al. Genes Dev, 2002 Aug 1. PMID 12154119
  4. poliota-dependent lesion bypass in vitro. Vaisman A, et al. Mutat Res, 2002 Dec 29. PMID 12459439
  5. Formation of an F' plasmid by recombination between imperfectly repeated chromosomal Rep sequences: a closer look at an old friend (F'(128) pro lac). Kofoid E, et al. J Bacteriol, 2003 Jan. PMID 12511513, 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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Homology

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 polymerase activity 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 protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA damage response IEA
Inferred from Electronic Annotation
more info
  
involved_in DNA damage response IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in DNA metabolic process IEA
Inferred from Electronic Annotation
more info
  
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 IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in error-free translesion synthesis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in 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
  
involved_in 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
    A0A376MC11, A0AAN3IP62
    Conserved Domains (1) summary
    PRK02406
    Location:9 → 351
    PRK02406; DNA polymerase IV; Validated
Nucleotide Protein
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