ID A0A3N6PNF5_9BURK Unreviewed; 358 AA.
AC A0A3N6PNF5;
DT 13-FEB-2019, integrated into UniProtKB/TrEMBL.
DT 13-FEB-2019, sequence version 1.
DT 24-JAN-2024, entry version 21.
DE RecName: Full=Holliday junction branch migration complex subunit RuvB {ECO:0000256|HAMAP-Rule:MF_00016};
DE EC=3.6.4.12 {ECO:0000256|HAMAP-Rule:MF_00016};
GN Name=ruvB {ECO:0000256|HAMAP-Rule:MF_00016,
GN ECO:0000313|EMBL:RQH00656.1};
GN ORFNames=D1Y85_24475 {ECO:0000313|EMBL:RQH00656.1};
OS Paraburkholderia dinghuensis.
OC Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales;
OC Burkholderiaceae; Paraburkholderia.
OX NCBI_TaxID=2305225 {ECO:0000313|EMBL:RQH00656.1, ECO:0000313|Proteomes:UP000272778};
RN [1] {ECO:0000313|EMBL:RQH00656.1, ECO:0000313|Proteomes:UP000272778}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DHOA04 {ECO:0000313|EMBL:RQH00656.1,
RC ECO:0000313|Proteomes:UP000272778};
RA Gao Z.-H., Qiu L.-H., Fu J.-C.;
RT "Paraburkholderia sp. DHOA04, isolated from soil.";
RL Submitted (NOV-2018) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: The RuvA-RuvB-RuvC complex processes Holliday junction (HJ)
CC DNA during genetic recombination and DNA repair, while the RuvA-RuvB
CC complex plays an important role in the rescue of blocked DNA
CC replication forks via replication fork reversal (RFR). RuvA
CC specifically binds to HJ cruciform DNA, conferring on it an open
CC structure. The RuvB hexamer acts as an ATP-dependent pump, pulling
CC dsDNA into and through the RuvAB complex. RuvB forms 2 homohexamers on
CC either side of HJ DNA bound by 1 or 2 RuvA tetramers; 4 subunits per
CC hexamer contact DNA at a time. Coordinated motions by a converter
CC formed by DNA-disengaged RuvB subunits stimulates ATP hydrolysis and
CC nucleotide exchange. Immobilization of the converter enables RuvB to
CC convert the ATP-contained energy into a lever motion, pulling 2
CC nucleotides of DNA out of the RuvA tetramer per ATP hydrolyzed, thus
CC driving DNA branch migration. The RuvB motors rotate together with the
CC DNA substrate, which together with the progressing nucleotide cycle
CC form the mechanistic basis for DNA recombination by continuous HJ
CC branch migration. Branch migration allows RuvC to scan DNA until it
CC finds its consensus sequence, where it cleaves and resolves cruciform
CC DNA. {ECO:0000256|HAMAP-Rule:MF_00016}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.12;
CC Evidence={ECO:0000256|ARBA:ARBA00001665, ECO:0000256|HAMAP-
CC Rule:MF_00016};
CC -!- SUBUNIT: Homohexamer. Forms an RuvA(8)-RuvB(12)-Holliday junction (HJ)
CC complex. HJ DNA is sandwiched between 2 RuvA tetramers; dsDNA enters
CC through RuvA and exits via RuvB. An RuvB hexamer assembles on each DNA
CC strand where it exits the tetramer. Each RuvB hexamer is contacted by
CC two RuvA subunits (via domain III) on 2 adjacent RuvB subunits; this
CC complex drives branch migration. In the full resolvosome a probable
CC DNA-RuvA(4)-RuvB(12)-RuvC(2) complex forms which resolves the HJ.
CC {ECO:0000256|HAMAP-Rule:MF_00016}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00016}.
CC -!- DOMAIN: Has 3 domains, the large (RuvB-L) and small ATPase (RuvB-S)
CC domains and the C-terminal head (RuvB-H) domain. The head domain binds
CC DNA, while the ATPase domains jointly bind ATP, ADP or are empty
CC depending on the state of the subunit in the translocation cycle.
CC During a single DNA translocation step the structure of each domain
CC remains the same, but their relative positions change.
CC {ECO:0000256|HAMAP-Rule:MF_00016}.
CC -!- SIMILARITY: Belongs to the RuvB family. {ECO:0000256|HAMAP-
CC Rule:MF_00016}.
CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_00016}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:RQH00656.1}.
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DR EMBL; RQIS01000025; RQH00656.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A3N6PNF5; -.
DR OrthoDB; 9804478at2; -.
DR Proteomes; UP000272778; Unassembled WGS sequence.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0048476; C:Holliday junction resolvase complex; IEA:UniProtKB-UniRule.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:InterPro.
DR GO; GO:0000400; F:four-way junction DNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009378; F:four-way junction helicase activity; IEA:InterPro.
DR GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-UniRule.
DR GO; GO:0006281; P:DNA repair; IEA:UniProtKB-UniRule.
DR CDD; cd00009; AAA; 1.
DR Gene3D; 1.10.8.60; -; 1.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 1.
DR Gene3D; 1.10.10.10; Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain; 1.
DR HAMAP; MF_00016; DNA_HJ_migration_RuvB; 1.
DR InterPro; IPR003593; AAA+_ATPase.
DR InterPro; IPR041445; AAA_lid_4.
DR InterPro; IPR004605; DNA_helicase_Holl-junc_RuvB.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR008824; RuvB-like_N.
DR InterPro; IPR008823; RuvB_C.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR InterPro; IPR036390; WH_DNA-bd_sf.
DR NCBIfam; TIGR00635; ruvB; 1.
DR PANTHER; PTHR42848; -; 1.
DR PANTHER; PTHR42848:SF1; HOLLIDAY JUNCTION ATP-DEPENDENT DNA HELICASE RUVB; 1.
DR Pfam; PF17864; AAA_lid_4; 1.
DR Pfam; PF05491; RuvB_C; 1.
DR Pfam; PF05496; RuvB_N; 1.
DR SMART; SM00382; AAA; 1.
DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 1.
DR SUPFAM; SSF46785; Winged helix' DNA-binding domain; 1.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|HAMAP-
KW Rule:MF_00016};
KW Cytoplasm {ECO:0000256|ARBA:ARBA00022490, ECO:0000256|HAMAP-Rule:MF_00016};
KW DNA damage {ECO:0000256|ARBA:ARBA00022763, ECO:0000256|HAMAP-
KW Rule:MF_00016};
KW DNA recombination {ECO:0000256|ARBA:ARBA00023172, ECO:0000256|HAMAP-
KW Rule:MF_00016};
KW DNA repair {ECO:0000256|ARBA:ARBA00023204, ECO:0000256|HAMAP-
KW Rule:MF_00016};
KW DNA-binding {ECO:0000256|ARBA:ARBA00023125, ECO:0000256|HAMAP-
KW Rule:MF_00016}; Helicase {ECO:0000313|EMBL:RQH00656.1};
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801, ECO:0000256|HAMAP-Rule:MF_00016};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW Rule:MF_00016}; Reference proteome {ECO:0000313|Proteomes:UP000272778}.
FT DOMAIN 65..193
FT /note="AAA+ ATPase"
FT /evidence="ECO:0000259|SMART:SM00382"
FT REGION 196..266
FT /note="Small ATPAse domain (RuvB-S)"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00016"
FT REGION 269..358
FT /note="Head domain (RuvB-H)"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00016"
FT BINDING 34
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00016"
FT BINDING 35
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00016"
FT BINDING 76
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00016"
FT BINDING 79
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00016"
FT BINDING 80
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00016"
FT BINDING 80
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00016"
FT BINDING 81
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00016"
FT BINDING 142..144
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00016"
FT BINDING 185
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00016"
FT BINDING 195
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00016"
FT BINDING 232
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00016"
FT BINDING 305
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00016"
FT BINDING 324
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00016"
FT BINDING 329
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00016"
SQ SEQUENCE 358 AA; 39287 MW; D4F3F62E60044DB4 CRC64;
MIETDKLAAN RASTERVIDA APTSPNEEAF ERALRPRHLD EYVGQEKIRG QLEIFIEAAK
RRSEPLDHVL LFGPPGLGKT TLAHIIAREM GVNLRQTSGP VLERAGDLAA LLTNLEANDV
LFIDEIHRLS PVVEEILYPA LEDYQIDIMI GEGPAARSVK LDLQPFTLVG ATTRAGMLTN
PLRDRFGIVS RLEFYNASEL SRIVQRSASL LGAHIHPDGA LEIARRARGT PRIANRLLRR
VRDYAEVKAD GSITATVADA ALKMLDVDPV GFDLMDRKLL EAILHKFDGG PVGIDNLAAA
IGEERDTIED VLEPYLIQQG YLQRTPRGRV ATLLTYRHFG LAAPDSAASG GLWDPNAS
//