DinB (DNA polymerase IV, Pol IV) is a Y-family translesion DNA polymerase that performs template-directed, error-prone DNA synthesis. It is a poorly processive, low-fidelity nucleotidyltransferase (EC 2.7.7.7) that lacks 3'-5' exonuclease proofreading activity and uses a two-metal-ion mechanism dependent on Mg(2+). Pol IV extends primers at stalled replication forks, including mismatched or misaligned primer ends, and can bypass DNA lesions in conjunction with the beta clamp of DNA polymerase III, contributing to translesion synthesis and untargeted mutagenesis. It acts in the cytoplasm as a monomer and is part of the cellular response to DNA damage, with homologs across bacteria induced as part of the SOS regulon. It belongs to the DNA polymerase type-Y (UmuC/DinB) family.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000287 magnesium ion binding | IEA GO_REF:0000104 | MARK AS OVER ANNOTATED | Summary: Mg(2+) is the catalytic cofactor of Pol IV, bound via a two-metal-ion mechanism. This is supportable but a generic cofactor-binding term that is non-core relative to the polymerase activity. Reason: Magnesium ion binding is a general cofactor-binding term. While accurate (Pol IV binds 2 Mg(2+) per subunit), the informative molecular function is the DNA-directed DNA polymerase activity, so this should not be treated as a core function. Supporting Evidence: file:PSEPK/dinB/dinB-uniprot.txt Binds 2 magnesium ions per subunit. |
| GO:0003677 DNA binding | IEA GO_REF:0000104 | MARK AS OVER ANNOTATED | Summary: Pol IV binds DNA (template/primer), but DNA binding is a broad parent of the more informative damaged DNA binding term that is also annotated. Reason: DNA binding is correct but uninformative given that the specific damaged DNA binding term (GO:0003684) is present and better captures the lesion-bypass function. Supporting Evidence: file:PSEPK/dinB/dinB-uniprot.txt May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII. |
| GO:0003684 damaged DNA binding | IEA GO_REF:0000002 | ACCEPT | Summary: Core molecular function. As a Y-family translesion polymerase, Pol IV binds damaged/lesion-containing DNA templates to perform lesion bypass. Reason: Damaged DNA binding accurately reflects the lesion-bypass role of Pol IV and is consistent with its UmuC/DinB Y-family domain architecture. Supporting Evidence: file:PSEPK/dinB/dinB-uniprot.txt May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII. |
| GO:0003887 DNA-directed DNA polymerase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Core molecular function. Pol IV is a template-directed (DNA-directed) DNA polymerase, EC 2.7.7.7, catalyzing primer extension by addition of dNTPs. Reason: This is the central catalytic activity of Pol IV, directly supported by the UniProt FUNCTION and CATALYTIC ACTIVITY (EC 2.7.7.7) records. Supporting Evidence: file:PSEPK/dinB/dinB-uniprot.txt Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. file:PSEPK/dinB/dinB-uniprot.txt PTHR11076:SF33; DNA POLYMERASE KAPPA |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: Consistent with the UniProt subcellular location. Pol IV acts on the bacterial chromosome in the cytoplasm. Reason: UniProt records cytoplasmic localization, appropriate for a bacterial DNA polymerase. Supporting Evidence: file:PSEPK/dinB/dinB-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm |
| GO:0005829 cytosol | IEA GO_REF:0000118 | KEEP AS NON CORE | Summary: Cytosol is a correct, if broad, location for this soluble monomeric polymerase. Reason: Pol IV is a soluble monomer with a UniProt cytoplasmic subcellular location and no membrane or nucleoid-restricted architecture, so the TreeGrafter cytosol call is true rather than an over-annotation; a bacterial cell has no organelles to exclude, and redundancy with the parent cytoplasm term is not grounds for rejection. It is kept as non-core because the informative annotations are the polymerase activity and the translesion-synthesis/DNA-repair processes. Supporting Evidence: file:PSEPK/dinB/dinB-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm |
| GO:0006259 DNA metabolic process | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: Very broad parent term. Pol IV participates in DNA metabolism, but more specific terms (DNA repair, translesion synthesis) are present. Reason: DNA metabolic process is a high-level parent of the specific DNA repair and translesion synthesis terms already annotated, so it adds no informative content. Supporting Evidence: file:PSEPK/dinB/dinB-uniprot.txt May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII. |
| GO:0006261 DNA-templated DNA replication | IEA GO_REF:0000104 | MARK AS OVER ANNOTATED | Summary: Pol IV is not a replicative polymerase; its biological role is lesion bypass and untargeted mutagenesis at stalled forks, not bulk genome replication. Reason: This term is derived electronically from the generic polymerase reaction. Pol IV is a translesion polymerase that extends misaligned/mismatched primers and bypasses lesions rather than carrying out chromosomal replication; DNA repair and translesion synthesis are the biologically accurate process terms. Supporting Evidence: file:PSEPK/dinB/dinB-uniprot.txt Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. |
| GO:0006281 DNA repair | IEA GO_REF:0000120 | ACCEPT | Summary: Core biological process. Pol IV contributes to DNA repair through translesion synthesis as part of the DNA damage response. Reason: DNA repair accurately reflects the role of Pol IV in lesion tolerance/bypass, consistent with HAMAP-Rule annotation and Y-family polymerase function. Supporting Evidence: file:PSEPK/dinB/dinB-uniprot.txt May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII. |
| GO:0009432 SOS response | IEA GO_REF:0000120 | ACCEPT | Summary: dinB is a classic SOS regulon member; Pol IV is induced as part of the bacterial SOS response to DNA damage. Accepted as a core damage-response process. Reason: The dinB gene (formerly dinP, DNA-damage-inducible) is part of the SOS response in bacteria, and this term is well supported by the conserved family annotation. Supporting Evidence: file:PSEPK/dinB/dinB-uniprot.txt Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. |
| GO:0034061 DNA polymerase activity | IEA GO_REF:0000116 | MARK AS OVER ANNOTATED | Summary: Broad parent of DNA-directed DNA polymerase activity (GO:0003887), which is also annotated and more informative. Reason: DNA polymerase activity is the parent term; the specific DNA-directed DNA polymerase activity (GO:0003887) is present and should be used as the core molecular function instead. Supporting Evidence: file:PSEPK/dinB/dinB-uniprot.txt Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. |
| GO:0042276 error-prone translesion synthesis | IEA GO_REF:0000118 | ACCEPT | Summary: Core biological process. Pol IV performs error-prone translesion synthesis, bypassing lesions with low fidelity and contributing to untargeted mutagenesis. Reason: Error-prone translesion synthesis is the most specific and accurate process term for Pol IV, directly matching its error-prone, untargeted-mutagenesis role and lack of proofreading. Supporting Evidence: file:PSEPK/dinB/dinB-uniprot.txt Exhibits no 3'-5' exonuclease (proofreading) activity. |
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Download this section (compressed HTML)Q: Does P. putida KT2440 Pol IV contribute to stress-induced (adaptive) mutagenesis and antibiotic resistance acquisition under environmental stress, and is its expression LexA/SOS-regulated in this organism?
Q: What spectrum of DNA lesions (e.g., N2-dG adducts, oxidative lesions) does P. putida Pol IV bypass most efficiently, and how does this shape the mutational signature in this environmentally important bacterium?
Experiment: Construct a dinB (PP_1203) deletion and overexpression strain and measure spontaneous and DNA-damage-induced mutation frequencies (e.g., rifampicin-resistance rates) to quantify Pol IV's contribution to mutagenesis in P. putida.
Type: Genetic mutagenesis assay
Experiment: Purify recombinant Pol IV and assay template-directed polymerase activity, fidelity, Mg(2+) dependence, and lesion-bypass efficiency on defined lesion-containing primer/template substrates, with and without the beta clamp.
Type: In vitro biochemical characterization
Experiment: Monitor dinB induction following DNA-damaging treatments (e.g., UV, mitomycin C) and in a lexA background to confirm SOS regulation of Pol IV in P. putida KT2440.
Type: Transcriptional reporter / RT-qPCR
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