Bacterial non-homologous end joining

Species-neutral bacterial module for Ku/LigD-mediated repair of DNA double-strand breaks by non-homologous end joining. The module covers the compact prokaryotic system in which Ku binds broken double-stranded DNA ends, protects and aligns them, and recruits the multifunctional LigD enzyme for end processing and ATP-dependent ligation. It excludes homologous recombination, mismatch repair, nucleotide excision repair, and eukaryotic multi-protein NHEJ factors.

MODULE:bacterial_nonhomologous_end_joiningDRAFTCONCRETEBiological Processmodules/bacterial_nonhomologous_end_joining.yaml
double-strand break repair via nonhomologous end joiningGO:0006303
KEGG:ppu03450
Pseudomonas putida KT2440 non-homologous end joining
The local PSEPK pathway partition assigns ku/PP_3255 and ligD/PP_3260 as the two primary genes in the compact KEGG ppu03450 NHEJ bucket.
GO:0006303
double-strand break repair via nonhomologous end joining
GO:0006303 captures repair of double-strand breaks by ligating DNA ends without a homologous template.
file:PSEPK/ku/ku-uniprot.txt
UniProtKB entry for PSEPK ku
Q88HU8 is a P. putida KT2440 prokaryotic Ku protein. UniProt describes it as acting with LigD in NHEJ, binding linear double-stranded DNA ends, and recruiting/stimulating LigD.
file:PSEPK/ligD/ligD-uniprot.txt
UniProtKB entry for PSEPK ligD
Q88HU3 is a P. putida KT2440 LigD-family protein with ATP-dependent DNA ligase, polymerase, phosphoesterase, and NHEJ-family domain signatures.

First-pass PSEPK interpretation: ku and ligD satisfy the compact bacterial NHEJ module. LigD carries several catalytic domains, but this module should not be expanded with unrelated ligases, RecA-dependent homologous recombination proteins, or mismatch-repair/excision-repair enzymes unless curating a broader DNA double-strand break response module.

3Nodes
2Parts
0Variant Sets
0Variants
2Annotons
1Connections

Derived QC

Recommended-field compliance

60.0% recommended fields populated
  • module.knowledge_gaps[0] · status (0/1)
  • module.knowledge_gaps[0] · provenance (0/1)

Module deep research

✓ present

  • bacterial_nonhomologous_end_joining-deep-research-openscientist.md (openscientist)

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Gene-review completeness (2/2 grounded genes reviewed)

2 complete review(s) · 0 with deep research · 0 missing review · 2 reviewed but lacking deep research

Gene Review Complete Deep research
ku Q88HU8 ✓ ✓ ✗
ligD Q88HU3 ✓ ✓ ✗

Details

Context
bacteriaNCBITaxon:2
cytoplasmGO:0005737
Bacterial non-homologous end joiningBiological Processbacterial_nonhomologous_end_joining
double-strand break repair via nonhomologous end joiningGO:0006303
Context
bacteriaNCBITaxon:2
cytoplasmGO:0005737

Connections

Ku-bound DNA ends and Ku-LigD recruitment provide the substrate context for LigD-mediated end processing and sealing.
Part 1: double-stranded DNA end recognition
Ku DNA-end binding and LigD recruitmentReactionku_dna_end_binding

Ku binds linear double-stranded DNA ends generated by a break, protects and aligns the ends, and recruits LigD to the break site.

Annotons

ku: prokaryotic Ku DNA-end binding factor
ku_dsdna_end_binding
Participant: Family: prokaryotic Ku family
Family:
prokaryotic Ku familyPANTHER:PTHR41251
Representative Members: PSEPK ku exemplarUniProtKB:Q88HU8

Function

double-stranded DNA bindingGO:0003690
Substrates: linear double-stranded DNA break end

Processes

double-strand break repair via nonhomologous end joiningGO:0006303

Locations

cytoplasmGO:0005737

DNA-end recognition and recruitment tier that positions LigD at broken DNA ends for end processing and sealing.

Part 2: DNA end processing and ligation
LigD end processing and ATP-dependent ligationReactionligd_end_processing_ligation

Multifunctional LigD processes incompatible or gapped DNA ends and seals repair intermediates by ATP-dependent phosphodiester bond formation.

Annotons

ligD: NHEJ DNA ligase/polymerase
ligd_ligation_and_processing
Participant: Family: bacterial LigD family
Family:
bacterial LigD familyPANTHER:PTHR42705
Representative Members: PSEPK ligD exemplarUniProtKB:Q88HU3

Function

DNA ligase (ATP) activityGO:0003910
Substrates: ATP 3-prime hydroxyl DNA end 5-prime phosphate DNA end
Products: repaired phosphodiester-linked DNA AMP diphosphate

Processes

double-strand break repair via nonhomologous end joiningGO:0006303

Locations

cytoplasmGO:0005737

Multifunctional NHEJ enzyme that performs DNA end processing and the ATP-dependent ligation step needed to complete repair.