P0A809 · RUVA_ECOLI
- ProteinHolliday junction branch migration complex subunit RuvA
- GeneruvA
- StatusUniProtKB reviewed (Swiss-Prot)
- Organism
- Amino acids203 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
The RuvA-RuvB-RuvC complex processes Holliday junction (HJ) DNA during genetic recombination and DNA repair (PubMed:21531731, PubMed:6374379).
The RuvA-RuvB complex plays an important role in the rescue of blocked DNA replication forks via replication fork reversal (RFR); RFR and homologous recombination required for UV light survival can be separated (PubMed:16424908, PubMed:18942176, PubMed:21531731, PubMed:9814711).
The RuvA-RuvB complex promotes Holliday junction (HJ) branch migration. RuvA binds to HJ cruciform DNA, conferring on it an open structure (PubMed:10890893, PubMed:7885479, PubMed:9628481).
In the presence of RuvB, ATP and Mg2+ the junction is dissociated; hydrolyzable (d)NTPs can replace ATP but other analogs cannot (PubMed:10772859, PubMed:10890893, PubMed:1608954, PubMed:1617728, PubMed:1833759, PubMed:7885479, PubMed:8393934, PubMed:9628481).
The RuvB hexamer acts as a pump, pulling dsDNA into and through the RuvAB complex (PubMed:9078376).
Can bypass UV-induced lesions (PubMed:1617728) and physically cross-linked DNA strands (PubMed:10662672).
RuvA gives specificity by binding to cruciform junctions, while the RuvB ATPase provides the motor force for branch migration; excess RuvB can promote branch migration in the absence of RuvA (PubMed:10662672, PubMed:1617728).
Overexpression of RuvA alone leads to UV sensitivity (PubMed:2164626).
RuvA stimulates the weak ATPase activity of RuvB in the presence of DNA; the addition of HJ DNA further stimulates ATPase about 10-fold (PubMed:1435721, PubMed:1833759, PubMed:8393934).
Inhibits RuvC endoDNase activity by binding to HJ DNA, including DNA to which RuvC is already bound (PubMed:9000618).
Does not bind dsDNA (PubMed:11080172).
May act as a collar that slides at HJ which promotes branch migration while inhibiting other DNA remodeling activities (Probable)
The RuvA-RuvB complex plays an important role in the rescue of blocked DNA replication forks via replication fork reversal (RFR); RFR and homologous recombination required for UV light survival can be separated (PubMed:16424908, PubMed:18942176, PubMed:21531731, PubMed:9814711).
The RuvA-RuvB complex promotes Holliday junction (HJ) branch migration. RuvA binds to HJ cruciform DNA, conferring on it an open structure (PubMed:10890893, PubMed:7885479, PubMed:9628481).
In the presence of RuvB, ATP and Mg2+ the junction is dissociated; hydrolyzable (d)NTPs can replace ATP but other analogs cannot (PubMed:10772859, PubMed:10890893, PubMed:1608954, PubMed:1617728, PubMed:1833759, PubMed:7885479, PubMed:8393934, PubMed:9628481).
The RuvB hexamer acts as a pump, pulling dsDNA into and through the RuvAB complex (PubMed:9078376).
Can bypass UV-induced lesions (PubMed:1617728) and physically cross-linked DNA strands (PubMed:10662672).
RuvA gives specificity by binding to cruciform junctions, while the RuvB ATPase provides the motor force for branch migration; excess RuvB can promote branch migration in the absence of RuvA (PubMed:10662672, PubMed:1617728).
Overexpression of RuvA alone leads to UV sensitivity (PubMed:2164626).
RuvA stimulates the weak ATPase activity of RuvB in the presence of DNA; the addition of HJ DNA further stimulates ATPase about 10-fold (PubMed:1435721, PubMed:1833759, PubMed:8393934).
Inhibits RuvC endoDNase activity by binding to HJ DNA, including DNA to which RuvC is already bound (PubMed:9000618).
Does not bind dsDNA (PubMed:11080172).
May act as a collar that slides at HJ which promotes branch migration while inhibiting other DNA remodeling activities (Probable)
An in vitro resolvase system that forms and processes HJ has been reconstituted with DNA substrates, RuvA, RuvB and RuvC. RuvA-RuvB increases the rate of strand exchange (branch migration), dissociates the RecA filament and allows RuvC to cleave in both orientations at the cruciform junction (PubMed:10421637, PubMed:9160752).
HJ-RuvA-RuvB-RuvC complexes resolve Holliday junctions and also undergo branch migration, providing evidence for a coupled branch migration/HJ resolution reaction (PubMed:10421637).
HJ-RuvA-RuvB-RuvC complexes resolve Holliday junctions and also undergo branch migration, providing evidence for a coupled branch migration/HJ resolution reaction (PubMed:10421637).
Cofactor
Note: Branch migration by the RuvA-RuvB complex requires Mg2+.
Features
Showing features for binding site.
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | cytoplasm | |
Cellular Component | Holliday junction helicase complex | |
Cellular Component | Holliday junction resolvase complex | |
Molecular Function | ATP binding | |
Molecular Function | four-way junction DNA binding | |
Molecular Function | four-way junction helicase activity | |
Molecular Function | identical protein binding | |
Biological Process | recombinational repair | |
Biological Process | response to radiation | |
Biological Process | SOS response |
Keywords
- Molecular function
- Biological process
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameHolliday junction branch migration complex subunit RuvA
Gene names
Organism names
- Organism
- Strains
- Taxonomic lineageBacteria > Pseudomonadota > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Escherichia
Accessions
- Primary accessionP0A809
- Secondary accessions
Proteomes
Subcellular Location
UniProt Annotation
GO Annotation
Note: In 15% of cell localizes to discrete nucleoid foci (probable DNA damage sites) upon treatment with mitomycin C (MMC) for 2 hours.
Keywords
- Cellular component
Phenotypes & Variants
Disruption phenotype
Sensitive to radiation, filamentous growth after transient inhibition of DNA synthesis, little effect on conjugal recombination in wild-type strains (PubMed:6374379).
Increased sensitivity to mitomycin and UV light (PubMed:10772859, PubMed:18942176, PubMed:2164626, PubMed:2693946, PubMed:9493263).
Suppresses lethality in recB-recC and dnaB temperature-sensitive mutants (PubMed:9814711).
Increased sensitivity to mitomycin and UV light (PubMed:10772859, PubMed:18942176, PubMed:2164626, PubMed:2693946, PubMed:9493263).
Suppresses lethality in recB-recC and dnaB temperature-sensitive mutants (PubMed:9814711).
Features
Showing features for mutagenesis.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Mutagenesis | 28 | Defective replication fork reversal (RFR), UV light resistant, resistant to mitomycin C (MMC). | ||||
Sequence: V → G | ||||||
Mutagenesis | 36 | Partially complements deletion, tetramerizes, binds RuvB, branch migration by RuvA-RuvB is normal. | ||||
Sequence: Y → A | ||||||
Mutagenesis | 55 | Does not bind dsDNA, slightly increases HJ resolution with RuvAB, 20% decreased chi resolution with RuvABC, no effect in vivo. | ||||
Sequence: E → D | ||||||
Mutagenesis | 55 | Reduced binding of HJDNA, binds dsDNA, increases HJ resolution with RuvAB, 40% decreased chi resolution with RuvABC, 100-fold decrease in UV resistance. | ||||
Sequence: E → Q | ||||||
Mutagenesis | 55 | Binds dsDNA, increases HJ resolution with RuvAB, 1000-fold decrease in UV resistance. | ||||
Sequence: E → R | ||||||
Mutagenesis | 55-56 | Reduced binding of Holliday junction (HJ) DNA, binds dsDNA, decreases HJ resolution with RuvAB, inhibits chi resolution with RuvABC, nearly 10000-fold decrease in UV resistance. | ||||
Sequence: ED → RK | ||||||
Mutagenesis | 56 | Binds dsDNA, increases HJ resolution with RuvAB, no chi resolution with RuvABC. | ||||
Sequence: D → K | ||||||
Mutagenesis | 56 | Reduced binding of HJDNA, binds dsDNA, increases HJ resolution with RuvAB. | ||||
Sequence: D → N | ||||||
Mutagenesis | 89 | Defective RFR, UV light resistant, sensitive to MMC. | ||||
Sequence: I → N | ||||||
Mutagenesis | 110 | Does not complement deletion, tetramerizes, binds RuvB, does not bind DNA, no migration by RuvA-RuvB. | ||||
Sequence: L → A | ||||||
Mutagenesis | 114 | Defective RFR, UV light resistant, resistant to MMC, may interact poorly with RuvB. | ||||
Sequence: P → S | ||||||
Mutagenesis | 119-127 | In RuvA2KaP; tetramerizes, weakly octamerizes, binds RuvB, binds HJDNA, makes weak complex II on HJ, 50% stimulation of RuvBATPase, poor branch migration, does not inhibit RuvC, no defect in HJ processing in vivo, does not promote RFR in vivo. | ||||
Sequence: KTAERLIVE → ATAERLIVR | ||||||
Mutagenesis | 120 | Suppresses the RuvB 'P220S' mutation, restores wild-type phenotype. | ||||
Sequence: T → N | ||||||
Mutagenesis | 122-130 | In RuvA3m; does not make complex II with HJ, tetramerizes, binds HJDNA, binds RuvB and stimulates its helicase activity, has decreased branch migration activity, alters RuvA-RuvC interaction, does not complement a deletion mutant, has extra abnormal DNA-binding. | ||||
Sequence: ERLIVEMKD → RRLIVRMKR | ||||||
Mutagenesis | 164 | Defective RFR, UV light resistant, resistant to MMC, may interact poorly with RuvB. | ||||
Sequence: V → I | ||||||
Mutagenesis | 167 | Does not complement deletion, tetramerizes, does not bind RuvB, dominant negative to wild-type (wt). | ||||
Sequence: L → A | ||||||
Mutagenesis | 170 | Does not complement deletion, tetramerizes, does not bind RuvB, dominant negative to wt. Alters conformation of isolated domain III. | ||||
Sequence: L → A | ||||||
Mutagenesis | 172 | Does not complement deletion, tetramerizes, does not bind RuvB, dominant negative to wt. | ||||
Sequence: Y → A | ||||||
Mutagenesis | 199 | Does not complement deletion, tetramerizes, does not bind RuvB, dominant negative to wt. | ||||
Sequence: L → A |
PTM/Processing
Features
Showing features for chain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000094629 | 1-203 | Holliday junction branch migration complex subunit RuvA | |||
Sequence: MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLLYGFNNKQERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKDRFKGLHGDLFTPAADLVLTSPASPATDDAEQEAVAALVALGYKPQEASRMVSKIARPDASSETLIREALRAAL |
Proteomic databases
Expression
Induction
Part of the ruvA-ruvB operon. Expression of the ruv region is induced by damage to DNA and is regulated by LexA as part of the SOS response. RuvA and RuvB are also involved in mutagenesis induced by UV and X irradiation and by some chemicals (PubMed:2842314, PubMed:3279394).
Induced by hydroxyurea (PubMed:20005847).
Induced by hydroxyurea (PubMed:20005847).
Interaction
Subunit
Homotetramer (PubMed:10772859, PubMed:10890893, PubMed:1435721, PubMed:7885479, PubMed:8832889, PubMed:9493263, PubMed:9628481).
Forms a stable RuvA-RuvB-Holliday junction (HJ) complex in the presence of non-hydrolyzable (d)NTPs; in the presence of hydrolyzable (d)NTPs branch migration occurs (PubMed:7885479, PubMed:8393934).
In electron microscopic images the complex is formed by 2 oppositely facing RuvB hexamers sandwiching possibly 2 RuvA tetramers at cruciform DNA structures (PubMed:7885479, PubMed:9047358).
In E.coli X-ray structures only 1 RuvA tetramer binds to HJ (complex I); however in M.leprae and T.thermophilus, 2 RuvA tetramers bind the HJ (complex II) (PubMed:10890893, PubMed:9628481).
Mutagenesis experiments that prevent RuvA complex II formation on HJ DNA have impaired function, suggesting both complex I and complex II are physiologically important. Y-junction resolution is normal in these mutants, further suggesting each RuvA tetramer supports the activity of one RuvB hexamer. Mutants that don't make complex II are impaired in replication fork reversal (RFR), suggesting complex II exists in vivo (PubMed:15556943, PubMed:21531731).
Forms a complex with RuvB without DNA; RuvA-RuvC complexes were not detected in the absence of DNA (PubMed:9160752).
Can form complexes with RuvC and HJ DNA which inhibits RuvC activity (PubMed:15556943, PubMed:21531731, PubMed:9000618, PubMed:9637927).
In the presence of HJ DNA a DNA-RuvA-RuvB-RuvC complex forms with 2 rings of RuvB that resolves upon addition of ATP. Upon HJ resolution the protein complex dissociates from DNA (PubMed:10421637, PubMed:9637927).
Forms a stable RuvA-RuvB-Holliday junction (HJ) complex in the presence of non-hydrolyzable (d)NTPs; in the presence of hydrolyzable (d)NTPs branch migration occurs (PubMed:7885479, PubMed:8393934).
In electron microscopic images the complex is formed by 2 oppositely facing RuvB hexamers sandwiching possibly 2 RuvA tetramers at cruciform DNA structures (PubMed:7885479, PubMed:9047358).
In E.coli X-ray structures only 1 RuvA tetramer binds to HJ (complex I); however in M.leprae and T.thermophilus, 2 RuvA tetramers bind the HJ (complex II) (PubMed:10890893, PubMed:9628481).
Mutagenesis experiments that prevent RuvA complex II formation on HJ DNA have impaired function, suggesting both complex I and complex II are physiologically important. Y-junction resolution is normal in these mutants, further suggesting each RuvA tetramer supports the activity of one RuvB hexamer. Mutants that don't make complex II are impaired in replication fork reversal (RFR), suggesting complex II exists in vivo (PubMed:15556943, PubMed:21531731).
Forms a complex with RuvB without DNA; RuvA-RuvC complexes were not detected in the absence of DNA (PubMed:9160752).
Can form complexes with RuvC and HJ DNA which inhibits RuvC activity (PubMed:15556943, PubMed:21531731, PubMed:9000618, PubMed:9637927).
In the presence of HJ DNA a DNA-RuvA-RuvB-RuvC complex forms with 2 rings of RuvB that resolves upon addition of ATP. Upon HJ resolution the protein complex dissociates from DNA (PubMed:10421637, PubMed:9637927).
Binary interactions
Type | Entry 1 | Entry 2 | Number of experiments | Intact | |
---|---|---|---|---|---|
BINARY | P0A809 | ruvA P0A809 | 5 | EBI-555119, EBI-555119 | |
BINARY | P0A809 | ruvB P0A812 | 5 | EBI-555119, EBI-557878 | |
BINARY | P0A809 | ruvC P0A814 | 4 | EBI-555119, EBI-1123014 |
Protein-protein interaction databases
Structure
Family & Domains
Features
Showing features for region, motif.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Region | 1-64 | Domain I | ||||
Sequence: MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLLYGFN | ||||||
Region | 1-144 | N-terminal proteolytic domain, tetramerizes and binds DNA, does not bind RuvB | ||||
Sequence: MIGRLRGIIIEKQPPLVLIEVGGVGYEVHMPMTCFYELPEAGQEAIVFTHFVVREDAQLLYGFNNKQERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKDRFKGLHGDLFTPAA | ||||||
Motif | 55-56 | Acidic pin | ||||
Sequence: ED | ||||||
Region | 65-142 | Domain II | ||||
Sequence: NKQERTLFKELIKTNGVGPKLALAILSGMSAQQFVNAVEREEVGALVKLPGIGKKTAERLIVEMKDRFKGLHGDLFTP | ||||||
Region | 143-155 | Flexible linker | ||||
Sequence: AADLVLTSPASPA | ||||||
Region | 156-203 | Domain III | ||||
Sequence: TDDAEQEAVAALVALGYKPQEASRMVSKIARPDASSETLIREALRAAL |
Domain
Has three domains with a flexible linker between the domains II and III, and assumes an 'L' shape. Domain III has weak interactions with the adjacent subunit (PubMed:10890893, PubMed:8832889, PubMed:9493263, PubMed:9628481).
In complex with Holliday junction (HJ) DNA, an approximately square planar DNA molecule is bound to the tetramer's concave face, with the DNA accessible to solution on one side. Domain III moves 4-5 Angstroms toward the protein-DNA interface upon DNA binding (PubMed:10890893, PubMed:9628481).
The isolated N-terminus (domains I and II) forms tetramers and binds HJ DNA but does not bind RuvB (PubMed:10772859, PubMed:9493263).
Alterations of bulky residues on the surface of domain III prevent binding to RuvB (PubMed:9493263).
Domains I and II crystallize with the same tetrameric structure and are dominant negative to wild-type in vivo. In intact protein, domain III is quite flexible in solution. Isolated domain III inhibits the ATPase activity of RuvB (PubMed:10772859).
The acidic pin (Glu-55 and Asp-56) seems to push the DNA backbone away from the HJ/RuvA complex center. It prevents binding to non-HJ dsDNA and constrains the rate of branch migration (PubMed:10890893, PubMed:11080172).
In complex with Holliday junction (HJ) DNA, an approximately square planar DNA molecule is bound to the tetramer's concave face, with the DNA accessible to solution on one side. Domain III moves 4-5 Angstroms toward the protein-DNA interface upon DNA binding (PubMed:10890893, PubMed:9628481).
The isolated N-terminus (domains I and II) forms tetramers and binds HJ DNA but does not bind RuvB (PubMed:10772859, PubMed:9493263).
Alterations of bulky residues on the surface of domain III prevent binding to RuvB (PubMed:9493263).
Domains I and II crystallize with the same tetrameric structure and are dominant negative to wild-type in vivo. In intact protein, domain III is quite flexible in solution. Isolated domain III inhibits the ATPase activity of RuvB (PubMed:10772859).
The acidic pin (Glu-55 and Asp-56) seems to push the DNA backbone away from the HJ/RuvA complex center. It prevents binding to non-HJ dsDNA and constrains the rate of branch migration (PubMed:10890893, PubMed:11080172).
Sequence similarities
Belongs to the RuvA family.
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length203
- Mass (Da)22,086
- Last updated2005-06-07 v1
- Checksum805DDB79DC5A8385
Features
Showing features for sequence conflict.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Sequence conflict | 166 | in Ref. 1; CAA30119 | ||||
Sequence: A → R |
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
X07091 EMBL· GenBank· DDBJ | CAA30119.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
M21298 EMBL· GenBank· DDBJ | AAA24612.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
U00096 EMBL· GenBank· DDBJ | AAC74931.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
AP009048 EMBL· GenBank· DDBJ | BAA15672.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
D10165 EMBL· GenBank· DDBJ | BAA01034.1 EMBL· GenBank· DDBJ | Genomic DNA |