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_processingCOMPLETECONCRETEBiological 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:8428576
Dissociation of synthetic Holliday junctions by E. coli RecG protein
RecG provides a branch-migration activity alternative to RuvAB.
We suggest that RecG and RuvAB provide alternative activities than can promote branch migration of Holliday junctions in recombination and DNA repair
PMID:18375550
Repair and antirepair DNA helicases in Helicobacter pylori
Orthologs of RecG and RuvABC are conserved across prokaryotes and form separate branch-migration routes; their repair outcomes and downstream resolution are 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: RuvABC and RecG are conserved across bacteria. Escherichia coli K-12 supplies the experimentally characterized exemplar for every role (RuvA, RuvB, RuvC and RecG biochemistry, structures and mutants), and Pseudomonas putida KT2440 (contiguous ruvCAB locus PP_1215-PP_1217 and recG/PP_5310) is kept as a homology-grade second exemplar. Other lineages are not added as representatives because no further gene reviews are needed to orient the roles. RecG is an alternative branch-migration motor, not a RuvABC subunit and not a resolvase. Family groundings follow the family reviews: RuvB is grounded to PANTHER PTHR42848:SF1 (PTHR42848 itself is unnamed, and SF1 is the whole family) and RuvC to PTHR30194:SF3 (the whole family). RuvA is grounded to InterPro IPR000085 rather than to PANTHER PTHR33796, because PTHR33796 classifies only a minority of RuvA proteins and KT2440 RuvA (Q88NJ1) has no PANTHER assignment. RecG is grounded to InterPro IPR004609 rather than to PANTHER PTHR47964, because PTHR47964:SF1 also holds Mfd (transcription-repair coupling factor) by the UniProt/InterPro assignments and no PANTHER subfamily separates RecG from Mfd; the RecG-specific PAINT node is PTN002773745 (DNA helicase activity). The RuvA four-way junction helicase assertion at PAINT node PTN008659601 (PTHR33796) is read as a contribution: RuvA confers junction specificity, RuvB is the ATPase. A RusA-type backup resolvase is lineage-restricted (present in E. coli as a cryptic prophage gene, not identified in the KT2440 candidate set) and is not part of the conserved module. The RuvA and RecG steps are grounded to InterPro families, which have no structured family review of their own; module QC reports that as an informational notice. The PANTHER families those proteins also belong to are reviewed (PTHR33796 for RuvA, PTHR47964 for RecG and Mfd), and the representatives have complete gene reviews. The RecG step requires four-way junction helicase activity (GO:0009378), not only 3'-5' DNA helicase activity, so that the selector does not admit other 3'-5' helicases such as UvrD, PcrA or Rep.

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

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:bacterial_ruvabc_holliday_junction_processing 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.

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

Function consistency and core coverage

8 gene-function check(s) reflected in core functions · 0 conflict(s) · 2 evidence or coverage gap(s) (12 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
ruva_binding_activity ruvA (Escherichia coli K-12)
UniProtKB:P0A809
Family Representative 		four-way junction DNA binding
GO:0000400 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ruva_binding_activity ruvA (Pseudomonas putida KT2440)
UniProtKB:Q88NJ1
Family Representative 		four-way junction DNA binding
GO:0000400 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ruvb_motor_activity ruvB (Pseudomonas putida KT2440)
UniProtKB:Q88NJ0
Family Representative 		four-way junction helicase activity
GO:0009378 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ruvb_motor_activity ruvB (Escherichia coli K-12)
UniProtKB:P0A812
Family Representative 		four-way junction helicase activity
GO:0009378 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
recg_motor_activity recG (Escherichia coli K-12)
UniProtKB:P24230
Family Representative 		four-way junction helicase activity (RecG, 3-prime-to-5-prime)
GO:0009378 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
recg_motor_activity recG (Pseudomonas putida KT2440)
UniProtKB:Q88C73
Family Representative 		four-way junction helicase activity (RecG, 3-prime-to-5-prime)
GO:0009378 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ruvc_nuclease_activity ruvC (Pseudomonas putida KT2440)
UniProtKB:Q88NJ2
Family Representative 		crossover junction DNA endonuclease activity
GO:0008821 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ruvc_nuclease_activity ruvC (Escherichia coli K-12)
UniProtKB:P0A814
Family Representative 		crossover junction DNA endonuclease activity
GO:0008821 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ruva_binding_activity RuvA family
InterPro:IPR000085
Family 		four-way junction DNA binding
GO:0000400 		Family Review Missing
No supported structured family review is available for InterPro:IPR000085.
ruvb_motor_activity RuvB family
PANTHER:PTHR42848:SF1
Family 		four-way junction helicase activity
GO:0009378 		Family Supported
Family review supports GO:0009378 FAMILY_WIDE. Ancestral at the bacterial root and the defining activity of every member.
recg_motor_activity RecG family
InterPro:IPR004609
Family 		four-way junction helicase activity (RecG, 3-prime-to-5-prime)
GO:0009378 		Family Review Missing
No supported structured family review is available for InterPro:IPR004609.
ruvc_nuclease_activity RuvC family
PANTHER:PTHR30194:SF3
Family 		crossover junction DNA endonuclease activity
GO:0008821 		Family Supported
Family review supports GO:0008821 FAMILY_WIDE. The defining activity of RuvC, assayed for E. coli RuvC and other bacterial RuvCs; the acidic catalytic residues are conserved across the family (they are annotated in KT2440 RuvC).

Gene-review completeness (8/8 grounded genes reviewed)

8 complete review(s) · 1 with deep research · 0 missing review · 7 reviewed but lacking deep research

Gene Review Complete Deep research
recG P24230 ✓ ✓ ✗
recG Q88C73 ✓ ✓ ✗
ruvA P0A809 ✓ ✓ ✗
ruvA Q88NJ1 ✓ ✓ ✗
ruvB P0A812 ✓ ✓ ✗
ruvB Q88NJ0 ✓ ✓ ✓
ruvC P0A814 ✓ ✓ ✗
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: Family: RuvA family
Family:
RuvA familyInterPro:IPR000085 RuvA proteins (TIGR00084). PANTHER PTHR33796:SF1 classifies only part of this family and does not include KT2440 RuvA.
Representative Members: ruvA (Escherichia coli K-12)UniProtKB:P0A809 ruvA (Pseudomonas putida KT2440)UniProtKB:Q88NJ1
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.

PMID:1617728
ATP-dependent branch migration of Holliday junctions promoted by the RuvA and RuvB proteins of E. coli
RuvA supplies junction specificity and lowers the RuvB requirement; RuvB is the motor.
RuvA protein provides specificity by binding to the Holliday junction, thereby reducing the requirement for RuvB by 50-fold
PANTHER:PTN008659601
PTHR33796 PAINT places four-way junction helicase activity at this RuvA node (seeds E. coli and M. tuberculosis RuvA); read as RuvA's contribution to the RuvAB helicase.
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: ruvB (Pseudomonas putida KT2440)UniProtKB:Q88NJ0 ruvB (Escherichia coli K-12)UniProtKB: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 junction-specific DNA helicase
recg_motor_activity
Participant: Family: RecG family
Family:
RecG familyInterPro:IPR004609 RecG helicases with the RecG wedge domain (TIGR00643); excludes Mfd, which shares PANTHER PTHR47964:SF1 by the UniProt assignments.
Representative Members: recG (Escherichia coli K-12)UniProtKB:P24230 recG (Pseudomonas putida KT2440)UniProtKB:Q88C73
Required Function:
four-way junction helicase activityGO:0009378

Function

four-way junction helicase activity (RecG, 3-prime-to-5-prime)GO:0009378
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.

PMID:7957087
Branch migration of Holliday junctions: identification of RecG protein as a junction specific DNA helicase
E. coli RecG is a junction-specific helicase with 3'-5' polarity.
The unwinding proceeds with a clear 3' to 5' polarity with respect to the single strand bound by RecG
PANTHER:PTN002773745
PTHR47964 PAINT places DNA helicase activity and DNA repair at this RecG-only node (seeds B. subtilis, E. coli, M. tuberculosis and P. aeruginosa RecG).
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: ruvC (Pseudomonas putida KT2440)UniProtKB:Q88NJ2 ruvC (Escherichia coli K-12)UniProtKB: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.