LigD (PA2138) is the multifunctional DNA ligase of the bacterial non-homologous end-joining (NHEJ) pathway that, with the end-binding protein Ku, repairs DNA double-strand breaks. The 840-residue protein has three autonomous catalytic modules. An N-terminal 3'-phosphoesterase domain removes 3'-terminal ribonucleotides from DNA ends in two Mn2+-dependent steps, a 3'-ribonuclease that leaves a 3'-phosphate and a 3'-phosphatase that converts it to 3'-OH. A central ATP-dependent DNA ligase domain (EC 6.5.1.1) seals nicks through a lysyl-AMP intermediate. A C-terminal polymerase/primase domain performs templated primer extension and gap filling (best on gaps with a distal 5'-phosphate) and adds one or two non-templated nucleotides, preferring rNTPs, to blunt or single-stranded DNA ends. Ku stimulates the polymerase and promotes end joining of plasmid double-strand breaks by full-length LigD.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003887 DNA-directed DNA polymerase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN001627042 (LigD clade, 15 leaf IBAs in 10 taxa), seeded by M. tuberculosis LigD (P9WNV3, IDA) and by PaeLigD itself (PseudoCAP and UniProt IDA, PMID:15520014). The self-seed is expected, not circular. Reason: The LigD Pol domain performs templated primer extension and gap filling, shown with purified PaeLigD. The IBD stands on the Mtb seed alone and the term suits the clade. Supporting Evidence: PMID:15520014 (iii) templated extension of a 5'-tailed duplex DNA primer-template PMID:20018881 Here, we characterized the gap repair activity of Pseudomonas LigD POL, which is more efficient than simple templated primer extension |
| GO:0003887 DNA-directed DNA polymerase activity | IDA PMID:15520014 A primer-dependent polymerase function of pseudomonas aerugi... | ACCEPT | Summary: PseudoCAP (and UniProt) IDA; seed of the PTN001627042 polymerase IBD. Seed verdict SOUND. Reason: Purified LigD and its isolated C-terminal domain extend a primer-template; the activity is abolished by D669A/D671A in the metal-binding site. Supporting Evidence: PMID:15520014 (iii) templated extension of a 5'-tailed duplex DNA primer-template PMID:15520014 The polymerase activity is abolished by alanine substitution for two aspartates (Asp-669 and Asp-671) within the putative metal-binding site. |
| GO:0003910 DNA ligase (ATP) activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN001627042, seeded by Mtb LigD (P9WNV3, several IDAs) and by PaeLigD itself (PMID:15520014). Reason: ATP-dependent nick sealing is the defining LigD activity, and the IBD stands on the Mtb seed alone. Supporting Evidence: PMID:20018881 We find that Pseudomonas Ku stimulates POL-catalyzed ribonucleotide addition to a plasmid DSB end and promotes plasmid end joining by full-length Pseudomonas LigD. file:PSEAE/ligD/ligD-uniprot.txt N6-AMP-lysine intermediate |
| GO:0003910 DNA ligase (ATP) activity | IDA PMID:15520014 A primer-dependent polymerase function of pseudomonas aerugi... | ACCEPT | Summary: PseudoCAP (and UniProt) IDA; seed of the PTN001627042 ligase IBD. Seed verdict SOUND. Reason: The paper purifies LigD and defines an autonomous DNA ligase domain. The abstract does not spell out the nick-sealing assay, but the curated UniProt entry ties the ligase-domain finding to this paper and later work shows LigD-catalysed end joining. Deferred to the curators. Supporting Evidence: PMID:15520014 Here we purify LigD and show that it possesses an intrinsic polymerase function resident within an autonomous C-terminal polymerase domain, LigD-(533-840), that flanks an autonomous DNA ligase domain, LigD-(188-527). file:PSEAE/ligD/ligD-uniprot.txt The central ATP-dependent ligase domain (Lig) functions as an independent domain. |
| GO:0003910 DNA ligase (ATP) activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA from the ATP-dependent DNA ligase domains and EC 6.5.1.1. Reason: Consistent with the experimental and IBA rows. Supporting Evidence: file:PSEAE/ligD/ligD-uniprot.txt N6-AMP-lysine intermediate |
| GO:0004532 RNA exonuclease activity | IDA PMID:15897197 Novel 3'-ribonuclease and 3'-phosphatase activities of the b... | MODIFY | Summary: PseudoCAP (and UniProt) IDA for the 3'-ribonuclease activity of the PE domain. Reason: Correct but general. The PE domain removes the 3'-terminal ribonucleoside from a primer strand, stepping in from the 3' end, which is 3'-5'-RNA exonuclease activity (GO:0000175, is_a GO:0004532). The companion 3'-phosphatase step is proposed as a NEW row. Proposed replacements: 3'-5'-RNA exonuclease activity Supporting Evidence: PMID:15897197 (i) the 3'-terminal nucleoside is first removed to yield a primer strand with a ribonucleoside 3'-PO4 terminus, and (ii) the 3'-PO4 is hydrolyzed to a 3'-OH |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO from the ATP-dependent ligase domain. Reason: The ligase domain uses ATP to form the lysyl-AMP intermediate, so ATP binding is true; the informative activity is the ligase itself. Supporting Evidence: file:PSEAE/ligD/ligD-uniprot.txt N6-AMP-lysine intermediate |
| GO:0006269 DNA replication, synthesis of primer | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: IBA from PTN001627042, seeded only by Mtb LigD (P9WNV3, MTBBASE IDA, PMID:16023671). ligD is not a seed of this IBD. Reason: The LigD Pol domain has primase-like and primer-extension activities in vitro, but LigD acts in NHEJ repair of double-strand breaks with Ku, not in chromosomal replication, where primers are made by DnaG. The process term claims a replication role that has not been shown for any LigD. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: ROLE CONFLATION Sources checked: PANTHER:PTN001627042 · PTN001627042 SUPPORTS SOURCE BUT NOT TARGET LigD clade; the activity is real but the replication-process term does not suit an NHEJ enzyme clade. The topology (panther_tree.py, 2026-11-05) shows a homogeneous clade of LigD-type ATP-dependent ligases, so there is no subclade with a replicative role to move the term to. UniProtKB:P9WNV3 · LigD (M. tuberculosis) SUPPORTS SOURCE BUT NOT TARGET In vitro primase activity, coded as a replication process. Paper not read here. Supporting Evidence: PMID:20018881 Many bacterial pathogens, including Pseudomonas aeruginosa, have a nonhomologous end joining (NHEJ) system of DNA double strand break (DSB) repair driven by Ku and DNA ligase D (LigD). |
| GO:0006281 DNA repair | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO from the ATP-dependent ligase domains. Reason: True, but double-strand break repair via nonhomologous end joining (GO:0006303), accepted in this review, is a descendant and entails it. Supporting Evidence: PMID:20018881 Many bacterial pathogens, including Pseudomonas aeruginosa, have a nonhomologous end joining (NHEJ) system of DNA double strand break (DSB) repair driven by Ku and DNA ligase D (LigD). |
| GO:0006303 double-strand break repair via nonhomologous end joining | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN001627042, seeded by Mtb LigD (P9WNV3, several IDAs). Reason: LigD is the NHEJ ligase of bacteria. For PaeLigD, Ku stimulates the polymerase and promotes Ku-dependent end joining of plasmid double-strand breaks by full-length LigD; the curated UniProt function also places it in NHEJ with Ku. Supporting Evidence: PMID:20018881 We find that Pseudomonas Ku stimulates POL-catalyzed ribonucleotide addition to a plasmid DSB end and promotes plasmid end joining by full-length Pseudomonas LigD. PMID:20018881 Many bacterial pathogens, including Pseudomonas aeruginosa, have a nonhomologous end joining (NHEJ) system of DNA double strand break (DSB) repair driven by Ku and DNA ligase D (LigD). |
| GO:0006310 DNA recombination | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: InterPro2GO from the generic ATP-dependent DNA ligase domains. Reason: The mapping is made for all ATP-dependent DNA ligases. PaeLigD has a repair role (NHEJ), and no recombination function has been shown for it. In GO, NHEJ is classified under DNA repair, not DNA recombination. Supporting Evidence: PMID:20018881 Many bacterial pathogens, including Pseudomonas aeruginosa, have a nonhomologous end joining (NHEJ) system of DNA double strand break (DSB) repair driven by Ku and DNA ligase D (LigD). |
| GO:0016779 nucleotidyltransferase activity | IDA PMID:15520014 A primer-dependent polymerase function of pseudomonas aerugi... | TOO GENERAL | Summary: PseudoCAP (and UniProt) IDA for nucleotidyltransferase activity (nucleotide addition by Pol). Reason: True, but DNA-directed DNA polymerase activity (GO:0003887), accepted from the same paper, is a descendant and entails it. Supporting Evidence: PMID:15520014 (i) non-templated nucleotide addition to a blunt-ended duplex DNA primer |
| GO:0071897 DNA biosynthetic process | IDA PMID:15520014 A primer-dependent polymerase function of pseudomonas aerugi... | TOO GENERAL | Summary: PseudoCAP IDA for DNA synthesis by the Pol domain in vitro. Reason: True but uninformative. DNA-directed DNA polymerase activity (GO:0003887), accepted here, is part_of DNA biosynthetic process, and the biological role of the synthesis is NHEJ gap filling (GO:0006303). Supporting Evidence: PMID:15520014 (iii) templated extension of a 5'-tailed duplex DNA primer-template |
| GO:0046403 polynucleotide 3'-phosphatase activity | IDA PMID:15897197 Novel 3'-ribonuclease and 3'-phosphatase activities of the b... | NEW | Summary: Proposed. The PE domain hydrolyses the 3'-phosphate left by its 3'-ribonuclease step to a 3'-OH, and UniProt records the 3'-phosphatase as also acting, more actively, on DNA 3'-phosphate ends. Reason: Direct biochemical evidence with purified PaeLigD and the isolated PE domain, with active-site mutants (D50, R52, H84) that abolish it. This 3'-end healing activity is part of the core end-processing function and has no GO row yet. Supporting Evidence: PMID:15897197 (i) the 3'-terminal nucleoside is first removed to yield a primer strand with a ribonucleoside 3'-PO4 terminus, and (ii) the 3'-PO4 is hydrolyzed to a 3'-OH PMID:15897197 which are essential for the 3'-ribonuclease and 3'-phosphatase reactions |
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Download this section (compressed HTML)Q: Should the PTN001627042 IBD for GO:0006269 DNA replication, synthesis of primer be removed, since LigD polymerase/primase activity serves NHEJ rather than chromosomal replication?
Experiment: Measure ionizing-radiation or desiccation survival and plasmid end-joining fidelity in P. aeruginosa ligD and ku deletion mutants, with ligD alleles inactivating each domain (K238A ligase, D669A/D671A polymerase, H84A phosphoesterase), to establish which activities NHEJ needs in vivo.
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