ligD (PP_3260) encodes the predicted multifunctional LigD enzyme of the Pseudomonas putida KT2440 bacterial non-homologous end joining system. The protein has ATP-dependent DNA ligase signatures and additional LigD polymerase and phosphoesterase/end-processing domains, allowing it to process damaged DNA ends and seal double-strand break repair intermediates recruited by Ku. Its central biological role is therefore DNA end processing and ATP-dependent ligation during Ku/LigD-mediated NHEJ. Loss of LigD alters stationary-phase mutation spectra in carbon-starved P. putida.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003910 DNA ligase (ATP) activity | IEA GO_REF:0000120 | ACCEPT | Summary: ATP-dependent DNA ligase activity is the core catalytic activity of the LigD ligase domain. Reason: UniProt records the EC 6.5.1.1 ATP-dependent DNA ligase reaction and conserved ATP-dependent DNA ligase domain signatures for Q88HU3. Supporting Evidence: file:PSEPK/ligD/ligD-uniprot.txt Reaction=ATP + (deoxyribonucleotide)n-3'-hydroxyl PMID:16023671 The ligase domain catalysed the sealing of nicked double-stranded DNA |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: ATP binding is correct for the ATP-dependent ligase reaction but is less informative than the catalytic DNA ligase activity. Reason: Retain as a supporting nucleotide-binding annotation; the core function is ATP-dependent DNA ligation. |
| GO:0006281 DNA repair | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: DNA repair is correct as a broad parent process for the LigD role. Reason: LigD functions in DNA repair, but the specific module context is bacterial non-homologous end joining. |
| GO:0006310 DNA recombination | IEA GO_REF:0000002 | MODIFY | Summary: DNA recombination is broad and potentially misleading for LigD because the compact Ku/LigD pathway repairs breaks without a homologous template. Reason: The annotation likely reflects legacy keyword/domain propagation. LigD is part of non-homologous end joining; GO:0006303 is a more specific and biologically clearer process term than generic DNA recombination. Note that NHEJ (GO:0006303) sits under DNA repair and is not an ontology child of DNA recombination (GO:0006310), so replacing this term is a lateral correction to the accurate process branch rather than a specialization within DNA recombination. Proposed replacements: double-strand break repair via nonhomologous end joining |
| GO:0003887 DNA-directed DNA polymerase activity | IEA file:PSEPK/ligD/ligD-uniprot.txt | NEW | Summary: LigD contains a polymerase domain and UniProt keyword/GO cross-references record DNA-directed DNA polymerase activity. Reason: Add as a secondary LigD end-processing activity that helps explain the NHEJ repair role, while keeping ATP-dependent DNA ligase activity as the primary core function. Supporting Evidence: file:PSEPK/ligD/ligD-uniprot.txt GO; GO:0003887; F:DNA-directed DNA polymerase activity PMID:20018881 Pseudomonas Ku stimulates POL-catalyzed ribonucleotide addition to a plasmid DSB end PMID:25942369 both phosphoesterase (PE) and polymerase (POL) domains |
| GO:0046403 polynucleotide 3'-phosphatase activity | ISS PMID:15897197 Novel 3'-ribonuclease and 3'-phosphatase activities of the b... | NEW | Summary: The central LigD phosphoesterase (PE) domain (IPR014144 / TIGR02777) is a 3'-phosphoesterase that removes 3'-phosphate (and 3'-ribonucleotide) groups to prepare broken DNA ends for ligation. This is the accurate end-processing activity of the PE domain, not a classic exonuclease. Reason: Replaces the imprecise UniProt-keyword-derived exonuclease cross-reference (GO:0004527). The LigD PE domain does not act as a processive exonuclease. It performs sequential terminal-ribonucleotide removal and 3'-phosphate hydrolysis on damaged DNA ends; GO:0046403 captures the phosphatase half. A general 3'-5' RNA exonuclease term is deliberately not added because the demonstrated substrate is a ribonucleotide-terminated DNA repair intermediate, not bulk RNA. Supporting Evidence: file:PSEPK/ligD/ligD-uniprot.txt InterPro; IPR014144; LigD_PE_domain. file:PSEPK/ligD/ligD-uniprot.txt NCBIfam; TIGR02777; LigD_PE_dom; 1. PMID:15897197 The 3'-ribonuclease and 3'-phosphatase activities are PMID:16023671 The nuclease domain did not function independently as a 3'-5' exonuclease. PMID:25942369 both phosphoesterase (PE) and polymerase (POL) domains |
| GO:0006303 double-strand break repair via nonhomologous end joining | ISS file:PSEPK/ligD/ligD-uniprot.txt | NEW | Summary: LigD is the catalytic partner of Ku in compact bacterial NHEJ. Reason: The UniProt entry identifies Q88HU3 as LigD/NHEJ DNA polymerase and records LigD NHEJ-family domains. The PTHR42705 PAINT export assigns GO:0006303 to PTN001627042 using experimentally characterized mycobacterial LigD, and pseudomonal biochemistry establishes the coupled Ku-LigD pathway. Supporting Evidence: file:PSEPK/ligD/ligD-uniprot.txt AltName: Full=NHEJ DNA polymerase file:PSEPK/ligD/ligD-uniprot.txt InterPro; IPR052171; NHEJ_LigD. PMID:20018881 repair driven by Ku and DNA ligase D (LigD). PMID:36475478 and LigD proteins involved in Non-Homologous End Joining (NHEJ). file:PSEPK/ligD/ligD-deep-research-openscientist.md Direct experimental (in-organism) |
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