Bacterial RuvABC Holliday-junction processing

A reusable bacterial homologous-recombination module in which RuvA recognizes and opens a four-way Holliday junction, RuvB uses ATP to drive branch migration, and RuvC cleaves the migrated junction to produce duplex recombination products. RecG supplies a mechanistically parallel branch-migration route in bacteria that encode it. Presynaptic RecFOR and RecBCD processing, RecA strand exchange, replication restart, and DNA ligation are neighboring modules.

MODULE:bacterial_ruvabc_holliday_junction_processingDRAFTCONCRETEBiological Processmodules/bacterial_ruvabc_holliday_junction_processing.yaml
recombinational repairGO:0000725
GO:0000725
recombinational repair
Defines the homology-directed repair process in which Holliday-junction processing operates.
GO:0000400
four-way junction DNA binding
Defines the structure-specific junction-recognition activity supplied by RuvA.
GO:0009378
four-way junction helicase activity
Defines ATP-dependent junction branch migration by the RuvB motor.
GO:0008821
crossover junction DNA endonuclease activity
Defines the structure-specific cleavage reaction supplied by RuvC.
RHEA:13065
ATP hydrolysis reaction
Defines the chemistry that powers the RuvB and RecG motors.
PANTHER:PTN000349951
PAINT RuvB-family branch-migration node
The local PTHR42848 PAINT table assigns four-way-junction helicase activity, Holliday-junction complexes, and recombinational repair to this ancestral node.
PMID:9501105
Functional interactions between the holliday junction resolvase and the branch migration motor of Escherichia coli
Primary E. coli biochemistry assigns junction loading to RuvA, branch migration to the RuvB motor, and resolution to RuvC.
branch migration is catalysed by the RuvB protein, a hexameric DNA helicase that is loaded onto the junction by RuvA, whereas resolution is promoted by the RuvC endonuclease
PMID:7923356
Atomic structure of the RuvC resolvase: a holliday junction-specific endonuclease from E. coli
RuvC structure and mutational analysis establish a dimeric acidic catalytic center positioned to cleave Holliday-junction DNA.
the catalytic center, comprising four acidic residues, lies at the bottom of a cleft that nicely fits a DNA duplex
PMID:18375550
Repair and antirepair DNA helicases in Helicobacter pylori
Comparative genetics supports RecG and RuvABC as separate branch-migration routes while showing that their repair outcomes and downstream resolution can be taxon-dependent.
independent pathways that branch migrate Holliday junctions during recombinational DNA repair
file:projects/P_PUTIDA/deep-research/PSEPK__ruvabc-holliday-junction-processing__ppu03440-deep-research-openscientist.md
OpenScientist PSEPK RuvABC Holliday-junction-processing synthesis
Species-aware retrieval resolves the contiguous KT2440 ruvCAB locus, the parallel RecG route, the intact RuvC active site, and the spurious PP_0151 resolvase name.

The module is species-neutral. Pseudomonas putida KT2440 supplies a concrete representative for every role, while reviewed E. coli proteins provide canonical bacterial exemplars. RecG is an alternative branch-migration motor, not a RuvABC subunit and not a resolvase. The broad PTHR47964 family is not used to select RecG because its reviewed membership also contains Mfd; an ortholog-of selector anchored to reviewed E. coli RecG is safer. RuvA is handled analogously because no PANTHER family is assigned to the KT2440 protein. A RusA-like backup resolvase is not universally expected.

5Nodes
4Parts
0Variant Sets
0Variants
4Annotons
3Connections

Derived QC

Recommended-field compliance

53.8% 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.knowledge_gaps[2] · status (0/1)
  • module.knowledge_gaps[2] · provenance (0/1)

Module deep research

✗ none found

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

Leaf nodes lacking representative members

2 leaf node(s) with no concrete protein grounding:

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.

  • ruva_junction_recognition → ruvb_branch_migration [NOT_CHECKED]
    RuvA opens the junction and recruits the RuvB motor before canonical branch migration.

Gene-review completeness (2/6 grounded genes reviewed)

2 complete review(s) · 1 with deep research · 4 missing review · 1 reviewed but lacking deep research

Gene Review Complete Deep research
E. coli RuvA P0A809 ✗ — —
E. coli RuvB P0A812 ✗ — —
E. coli RuvC P0A814 ✗ — —
E. coli RecG P24230 ✗ — —
ruvB Q88NJ0 ✓ ✓ ✓
ruvC Q88NJ2 ✓ ✓ ✗

Details

Bacterial RuvABC Holliday-junction processingBiological Processbacterial_ruvabc_holliday_junction_processing
recombinational repairGO:0000725

Connections

Part 1: four-way-junction recognition and branch-migration-motor loading
RuvA recognition and opening of the Holliday junctionBiological Processruva_junction_recognition

Annotons

RuvA four-way-junction binding
ruva_binding_activity
Participant: Ortholog Of: E. coli RuvA
Ortholog Of:
E. coli RuvAUniProtKB:P0A809 Orthologs of the reviewed canonical bacterial RuvA exemplar that retain four-way-junction binding and motor-loading function.
Required Function:
four-way junction DNA bindingGO:0000400

Function

four-way junction DNA bindingGO:0000400
Substrates: Holliday-junction DNA
Products: opened RuvA-bound Holliday junction

Processes

recombinational repairGO:0000725

Recognizes the crossover, opens the junction, and creates the platform on which RuvB rings assemble.

UniProtKB:Q88NJ1
KT2440 implementation ruvA/PP_1216; the reviewed entry assigns the exact RuvA family and junction-binding mechanism.
Part 2: canonical ATP-dependent Holliday-junction branch migration
RuvB-driven Holliday-junction branch migrationReactionruvb_branch_migration

Annotons

RuvB four-way-junction helicase
ruvb_motor_activity
Participant: Family: RuvB family
Family:
RuvB familyPANTHER:PTHR42848:SF1
Representative Members: PSEPK RuvBUniProtKB:Q88NJ0 E. coli RuvBUniProtKB:P0A812
Required Function:
four-way junction helicase activityGO:0009378

Function

four-way junction helicase activityGO:0009378
Substrates: ATP RuvA-bound Holliday-junction DNA
Products: ADP phosphate branch-migrated Holliday junction

Processes

recombinational repairGO:0000725

Uses ATP hydrolysis to pull duplex DNA through RuvAB and move the junction crossover point.

Part 2: alternative ATP-dependent branched-DNA migration
RecG-dependent alternative branch migrationReactionrecg_branch_migration

Annotons

RecG directional DNA helicase
recg_motor_activity
Participant: Ortholog Of: E. coli RecG
Ortholog Of:
E. coli RecGUniProtKB:P24230 Orthologs of the reviewed canonical bacterial RecG exemplar that retain the RecG-specific wedge and directional helicase domains.
Required Function:
3-prime-to-5-prime DNA helicase activityGO:0043138

Function

3-prime-to-5-prime DNA helicase activityGO:0043138
Substrates: ATP branched DNA intermediate
Products: ADP phosphate branch-migrated DNA intermediate

Processes

recombinational repairGO:0000725

Provides an RuvAB-independent route for migrating Holliday junctions and remodeling stalled forks.

UniProtKB:Q88C73
KT2440 implementation recG/PP_5310 with the exact RecG InterPro family and directional ATP-dependent helicase mechanism.
Part 3: symmetric cleavage and Holliday-junction resolution
RuvC cleavage and resolution of the Holliday junctionReactionruvc_junction_resolution

Annotons

RuvC crossover-junction endonuclease
ruvc_nuclease_activity
Participant: Family: RuvC family
Family:
RuvC familyPANTHER:PTHR30194:SF3
Representative Members: PSEPK RuvCUniProtKB:Q88NJ2 E. coli RuvCUniProtKB:P0A814
Required Function:
crossover junction DNA endonuclease activityGO:0008821

Function

crossover junction DNA endonuclease activityGO:0008821
Substrates: branch-migrated Holliday-junction DNA
Products: nicked duplex recombination products with 5-prime phosphate and 3-prime hydroxyl ends

Processes

recombinational repairGO:0000725

Cleaves opposing junction strands at symmetrical positions to resolve the four-way intermediate.