Bacterial nucleotide-excision repair system

A reusable bacterial nucleotide-excision repair module in which UvrA and UvrB recognize bulky, helix-distorting DNA lesions, UvrC incises the damaged strand on both sides of the lesion, UvrD releases the damage-containing oligonucleotide, DNA polymerase I fills the resulting gap, and an NAD-dependent DNA ligase seals the nick. Mfd supplies an optional transcription-coupled entry route by removing lesion-stalled RNA polymerase and recruiting the Uvr machinery. Base-excision repair, mismatch repair, homologous-recombination repair, translesion synthesis, and eukaryotic XPD/TFIIH excision repair are outside this module.

MODULE:bacterial_nucleotide_excision_repairDRAFTCONCRETEBiological Processmodules/bacterial_nucleotide_excision_repair.yaml
nucleotide-excision repairGO:0006289
GO:0006289
nucleotide-excision repair
Defines the UvrABC lesion-excision and repair-synthesis process represented here.
GO:0009381
excinuclease ABC activity
Defines the collective activity of the assembled UvrABC machinery; the individual UvrA, UvrB, and UvrC annotons below carry their own molecular functions rather than this complex-level term.
PMID:33480355
Structural basis for transcription complex disruption by the Mfd translocase.
Structural work on E. coli Mfd establishes ATP-dependent removal of lesion-stalled RNA polymerase and recruitment of UvrABC in bacterial TCR.
Mfd mediates TCR in bacteria by removing the stalled RNAP concealing the lesion and recruiting Uvr(A)BC.
RHEA:13065
ATP hydrolysis reaction
Defines the ATPase chemistry used by UvrD and Mfd to remodel DNA repair intermediates.
RHEA:22508
DNA-directed DNA polymerase reaction
Defines repair-gap filling by bacterial DNA polymerase I.
PANTHER:PTN000116141
PAINT UvrD-family helicase node
The local PTHR11070 PAINT table assigns 3-prime-to-5-prime DNA helicase activity to this ancestral node using experimentally characterized UvrD/PcrA-family seeds.
file:projects/P_PUTIDA/deep-research/PSEPK__bacterial-nucleotide-excision-repair__ppu03420-deep-research-openscientist.md
OpenScientist PSEPK bacterial nucleotide-excision repair synthesis
Species-aware retrieval identifies a complete seven-role KT2440 NER relay and distinguishes three KEGG-bucket proteins that are not required core components.

The module is species-neutral and represents both global-genome NER and the Mfd-dependent transcription-coupled entry route. Pseudomonas putida KT2440 supplies a concrete representative for every role. Mfd is optional for the global-genome route. Cho-family alternative incision proteins and lineage-specific UvrA2 accessory paralogs are not universal requirements. PolA and LigA are shared with replication and other DNA-repair pathways. GO:0009381 describes the assembled UvrABC activity and is retained only as module-level evidence; each subunit leaf is represented by its distinguishable activity.

8Nodes
7Parts
0Variant Sets
0Variants
7Annotons
6Connections

Derived QC

Recommended-field compliance

55.6% recommended fields populated
  • module.knowledge_gaps[0] · status (0/1)
  • module.knowledge_gaps[0] · provenance (0/1)
  • module.knowledge_gaps[1] · status (0/1)
  • module.knowledge_gaps[1] · provenance (0/1)

Module deep research

✗ none found

No MODULE:bacterial_nucleotide_excision_repair deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Reaction chaining (advisory)

✓ every PRECEDES step chains, or its break is acknowledged via chaining_status.

  • mfd_coupling → uvra_recognition [NOT_CHECKED]
    Mfd supplies the transcription-coupled entry route by recruiting UvrA to lesion-stalled transcription complexes.
  • uvra_recognition → uvrb_verification [NOT_CHECKED]
    UvrA loads UvrB at a candidate lesion and dissociates after verification.
  • uvrb_verification → uvrc_incision [NOT_CHECKED]
    Lesion-bound UvrB recruits and positions UvrC for dual incision.
  • uvrc_incision → uvrd_release [NOT_CHECKED]
    Dual incision creates the damage-containing oligonucleotide released by UvrD.
  • uvrd_release → pola_synthesis [NOT_CHECKED]
    Oligonucleotide release exposes a repair gap with a usable 3-prime hydroxyl.
  • pola_synthesis → liga_sealing [NOT_CHECKED]
    DNA polymerase I gap filling leaves the nick sealed by LigA.

Gene-review completeness (6/14 grounded genes reviewed)

6 complete review(s) · 3 with deep research · 8 missing review · 3 reviewed but lacking deep research

Gene Review Complete Deep research
ligA Q88F25 ✓ ✓ ✗
mfd Q88KZ1 ✓ ✓ ✗
E. coli PolA P00582 ✗ — —
E. coli UvrD P03018 ✗ — —
E. coli UvrA P0A698 ✗ — —
E. coli UvrB P0A8F8 ✗ — —
E. coli UvrC P0A8G0 ✗ — —
E. coli LigA P15042 ✗ — —
E. coli Mfd P30958 ✗ — —
PSEPK PolA Q88RK6 ✗ — —
uvrA Q88QK7 ✓ ✓ ✗
uvrB Q88LF9 ✓ ✓ ✓
uvrC Q88FJ7 ✓ ✓ ✓
uvrD Q88C31 ✓ ✓ ✓

Details

Bacterial nucleotide-excision repair systemBiological Processbacterial_nucleotide_excision_repair
nucleotide-excision repairGO:0006289

Connections

Part 1: transcription-coupled lesion recognition (optional)
Mfd-dependent transcription-repair couplingBiological Processmfd_coupling

Annotons

Transcription-repair-coupling factor
mfd_activity
Participant: Family: RecG/Mfd ATP-dependent DNA translocase family
Family:
RecG/Mfd ATP-dependent DNA translocase familyPANTHER:PTHR47964
Representative Members: PSEPK MfdUniProtKB:Q88KZ1 E. coli MfdUniProtKB:P30958
Required Function:
DNA translocase activityGO:0015616
Required Domain:
Mfd transcription-repair coupling factor domainInterPro:IPR004576

Function

DNA translocase activityGO:0015616

Processes

transcription-coupled nucleotide-excision repair, DNA damage recognitionGO:0000716

Removes lesion-stalled RNA polymerase and recruits the Uvr machinery to the transcribed strand.

Part 2: global-genome damage recognition
UvrA-dependent lesion recognitionBiological Processuvra_recognition

Annotons

UvrA damage-recognition ATPase
uvra_activity
Participant: Family: canonical UvrA family
Family:
canonical UvrA familyPANTHER:PTHR43152:SF3
Representative Members: PSEPK UvrAUniProtKB:Q88QK7 E. coli UvrAUniProtKB:P0A698
Required Function:
damaged DNA bindingGO:0003684

Function

damaged DNA bindingGO:0003684

Processes

nucleotide-excision repairGO:0006289

Scans duplex DNA with UvrB and initiates recognition of helix-distorting lesions.

Part 3: lesion verification and preincision-complex formation
UvrB-dependent lesion verificationBiological Processuvrb_verification

Annotons

UvrB lesion-verification ATPase
uvrb_activity
Participant: Family: UvrB family
Family:
UvrB familyPANTHER:PTHR24029:SF0
Representative Members: PSEPK UvrBUniProtKB:Q88LF9 E. coli UvrBUniProtKB:P0A8F8
Required Function:
ATP hydrolysis activityGO:0016887

Function

ATP hydrolysis activityGO:0016887
Substrates: ATP water
Products: ADP phosphate

Processes

nucleotide-excision repairGO:0006289

Verifies the lesion, locally opens DNA, and forms the UvrB-DNA preincision complex.

Part 4: dual incision of the damaged strand
UvrC dual-incision reactionReactionuvrc_incision

Annotons

UvrC dual-incision endonuclease
uvrc_activity
Participant: Family: UvrC family
Family:
UvrC familyPANTHER:PTHR30562:SF1
Representative Members: PSEPK UvrCUniProtKB:Q88FJ7 E. coli UvrCUniProtKB:P0A8G0
Required Function:
DNA endonuclease activityGO:0004520

Function

DNA endonuclease activityGO:0004520
Substrates: damaged-strand UvrB-DNA preincision complex
Products: DNA incised on both sides of the lesion

Processes

nucleotide-excision repairGO:0006289

Cleaves the damaged strand on the 3-prime and 5-prime sides of the lesion.

Part 5: damage-containing oligonucleotide release
UvrD-dependent excised-oligonucleotide releaseReactionuvrd_release

Annotons

UvrD 3-prime-to-5-prime DNA helicase
uvrd_activity
Participant: Family: UvrD/PcrA DNA helicase family
Family:
UvrD/PcrA DNA helicase familyPANTHER:PTHR11070
Representative Members: PSEPK UvrDUniProtKB:Q88C31 E. coli UvrDUniProtKB:P03018
Required Function:
3-prime-to-5-prime DNA helicase activityGO:0043138

Function

3-prime-to-5-prime DNA helicase activityGO:0043138
Substrates: ATP incised lesion-containing duplex DNA
Products: ADP phosphate released damage-containing oligonucleotide

Processes

nucleotide-excision repairGO:0006289

Unwinds the incised duplex to release the lesion-containing oligonucleotide and UvrB.

Part 6: repair-gap filling
DNA polymerase I repair synthesisReactionpola_synthesis

Annotons

DNA polymerase I
pola_activity
Participant: Family: bacterial DNA polymerase I family
Family:
bacterial DNA polymerase I familyPANTHER:PTHR10133
Representative Members: PSEPK PolAUniProtKB:Q88RK6 E. coli PolAUniProtKB:P00582
Required Function:
DNA-directed DNA polymerase activityGO:0003887

Function

DNA-directed DNA polymerase activityGO:0003887
Substrates: gapped DNA with a 3-prime hydroxyl deoxyribonucleoside triphosphates
Products: repaired nicked DNA diphosphate

Processes

nucleotide-excision repairGO:0006289

Restores the excised DNA tract using the undamaged strand as template.

Part 7: repair-nick sealing
NAD-dependent DNA ligationReactionliga_sealing

Annotons

NAD-dependent DNA ligase
liga_activity
Participant: Family: canonical bacterial LigA family
Family:
canonical bacterial LigA familyPANTHER:PTHR23389:SF9
Representative Members: PSEPK LigAUniProtKB:Q88F25 E. coli LigAUniProtKB:P15042
Required Function:
DNA ligase (NAD+) activityGO:0003911

Function

DNA ligase (NAD+) activityGO:0003911
Substrates: NAD+ nicked duplex DNA
Products: sealed duplex DNA AMP nicotinamide mononucleotide

Processes

nucleotide-excision repairGO:0006289

Seals the remaining phosphodiester nick after repair synthesis.