ID   RUVC_DEIRA              Reviewed;         179 AA.
AC   Q9RX75;
DT   15-MAY-2002, integrated into UniProtKB/Swiss-Prot.
DT   01-MAY-2000, sequence version 1.
DT   27-MAR-2024, entry version 121.
DE   RecName: Full=Crossover junction endodeoxyribonuclease RuvC {ECO:0000255|HAMAP-Rule:MF_00034};
DE            EC=3.1.21.10 {ECO:0000255|HAMAP-Rule:MF_00034, ECO:0000269|PubMed:35744678, ECO:0000269|PubMed:36000732};
DE   AltName: Full=Holliday junction nuclease RuvC {ECO:0000255|HAMAP-Rule:MF_00034};
DE   AltName: Full=Holliday junction resolvase RuvC {ECO:0000255|HAMAP-Rule:MF_00034, ECO:0000303|PubMed:10567266};
GN   Name=ruvC {ECO:0000255|HAMAP-Rule:MF_00034,
GN   ECO:0000303|PubMed:10567266}; OrderedLocusNames=DR_0440;
OS   Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG
OS   27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1).
OC   Bacteria; Deinococcota; Deinococci; Deinococcales; Deinococcaceae;
OC   Deinococcus.
OX   NCBI_TaxID=243230;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 /
RC   NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1;
RX   PubMed=10567266; DOI=10.1126/science.286.5444.1571;
RA   White O., Eisen J.A., Heidelberg J.F., Hickey E.K., Peterson J.D.,
RA   Dodson R.J., Haft D.H., Gwinn M.L., Nelson W.C., Richardson D.L.,
RA   Moffat K.S., Qin H., Jiang L., Pamphile W., Crosby M., Shen M.,
RA   Vamathevan J.J., Lam P., McDonald L.A., Utterback T.R., Zalewski C.,
RA   Makarova K.S., Aravind L., Daly M.J., Minton K.W., Fleischmann R.D.,
RA   Ketchum K.A., Nelson K.E., Salzberg S.L., Smith H.O., Venter J.C.,
RA   Fraser C.M.;
RT   "Genome sequence of the radioresistant bacterium Deinococcus radiodurans
RT   R1.";
RL   Science 286:1571-1577(1999).
RN   [2] {ECO:0000312|PDB:7XHJ}
RP   X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS), FUNCTION, PROBABLE ACTIVE SITES,
RP   CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, DNA-BINDING, MOTIF, AND MUTAGENESIS
RP   OF ASP-7; GLU-67; HIS-139 AND ASP-142.
RC   STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 /
RC   NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1;
RX   PubMed=35744678; DOI=10.3390/microorganisms10061160;
RA   Qin C., Han W., Xu Y., Zhao Y., Xu H., Tian B., Wang L., Hua Y.;
RT   "Structural and Functional Characterization of the Holliday Junction
RT   Resolvase RuvC from Deinococcus radiodurans.";
RL   Microorganisms 10:0-0(2022).
RN   [3] {ECO:0000312|PDB:7W8D}
RP   X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS) IN COMPLEX WITH MG(2+), PROBABLE
RP   ACTIVE SITES, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, DISRUPTION PHENOTYPE,
RP   DNA-BINDING, AND MUTAGENESIS OF ASP-7; GLU-67; HIS-139 AND ASP-142.
RC   STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 /
RC   NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1;
RX   PubMed=36000732; DOI=10.1128/mbio.01834-22;
RA   Sun Y., Yang J., Xu G., Cheng K.;
RT   "Biochemical and Structural Study of RuvC and YqgF from Deinococcus
RT   radiodurans.";
RL   MBio 13:e0183422-e0183422(2022).
CC   -!- FUNCTION: The RuvA-RuvB-RuvC complex processes Holliday junction (HJ)
CC       DNA during genetic recombination and DNA repair (PubMed:36000732).
CC       Endonuclease that resolves HJ intermediates (PubMed:35744678,
CC       PubMed:36000732). Cleaves cruciform DNA by making single-stranded nicks
CC       across the HJ at symmetrical positions within the homologous arms,
CC       probably yielding a 5'-phosphate and a 3'-hydroxyl group; requires a
CC       central core of homology in the junction (PubMed:35744678,
CC       PubMed:36000732). The consensus cleavage sequence is 5'-(G/C)TC(C/G)-3'
CC       (a different site than E.coli); cleavage occurs on the 3'-side of the
CC       TC dinucleotide at the point of strand exchange (PubMed:36000732). Also
CC       resolves nicked HJ intermediates, replication forks and Y-junction DNA
CC       in vitro (PubMed:36000732). HJ branch migration catalyzed by RuvA-RuvB
CC       allows RuvC to scan DNA until it finds its consensus sequence, where it
CC       cleaves and resolves the cruciform DNA (By similarity).
CC       {ECO:0000250|UniProtKB:P0A814, ECO:0000269|PubMed:35744678,
CC       ECO:0000269|PubMed:36000732}.
CC   -!- FUNCTION: Binds HJ DNA independently of homologous core or consensus
CC       sequence; Mn(2+) is not essential for binding but improves it, while
CC       >1.0 mM Mg(2+) inhibit binding. Also binds Y-junction DNA less well.
CC       Requires a homologous core to cleave DNA (PubMed:35744678). Another
CC       study shows divalent cations (Mn(2+), Mg(2+) and Ca(2+), tested up to
CC       5.0 mM) improve DNA binding considerably over binding in their absence
CC       (PubMed:36000732). {ECO:0000269|PubMed:35744678,
CC       ECO:0000269|PubMed:36000732}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Endonucleolytic cleavage at a junction such as a reciprocal
CC         single-stranded crossover between two homologous DNA duplexes
CC         (Holliday junction).; EC=3.1.21.10; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_00034, ECO:0000269|PubMed:35744678,
CC         ECO:0000269|PubMed:36000732};
CC   -!- COFACTOR:
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000269|PubMed:35744678};
CC       Note=In vitro only Mn(2+) supports endonuclease activity; Mg(2+)
CC       inhibits binding to HJ DNA (PubMed:35744678). Another study shows
CC       Mn(2+) is the preferred cofactor but Mg(2+) does support cleavage
CC       (PubMed:36000732). Binds 2 Mn(2+) ion per subunit (By similarity).
CC       {ECO:0000250|UniProtKB:Q5SJC4, ECO:0000269|PubMed:35744678,
CC       ECO:0000269|PubMed:36000732};
CC   -!- SUBUNIT: Homodimer which binds Holliday junction (HJ) DNA
CC       (PubMed:35744678). The HJ becomes 2-fold symmetrical on binding to RuvC
CC       with unstacked arms; it has a different conformation from HJ DNA in
CC       complex with RuvA. In the full resolvosome a probable DNA-RuvA(4)-
CC       RuvB(12)-RuvC(2) complex forms which resolves the HJ.
CC       {ECO:0000255|HAMAP-Rule:MF_00034, ECO:0000269|PubMed:35744678}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00034}.
CC   -!- DISRUPTION PHENOTYPE: Only heterozygous strains can be obtained,
CC       suggesting this gene is essential. {ECO:0000269|PubMed:36000732}.
CC   -!- MISCELLANEOUS: D.radiodurans metalloenzymes exhibit a strong preference
CC       for Mn(2+) rather than Mg(2+). {ECO:0000305|PubMed:35744678}.
CC   -!- SIMILARITY: Belongs to the RuvC family. {ECO:0000255|HAMAP-
CC       Rule:MF_00034}.
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DR   EMBL; AE000513; AAF10018.1; -; Genomic_DNA.
DR   PIR; F75519; F75519.
DR   RefSeq; NP_294163.1; NC_001263.1.
DR   RefSeq; WP_010887085.1; NZ_JMLF01000001.1.
DR   PDB; 7W8D; X-ray; 2.75 A; A/B=1-179.
DR   PDB; 7XHJ; X-ray; 1.60 A; A/B=1-179.
DR   PDBsum; 7W8D; -.
DR   PDBsum; 7XHJ; -.
DR   AlphaFoldDB; Q9RX75; -.
DR   SMR; Q9RX75; -.
DR   STRING; 243230.DR_0440; -.
DR   PaxDb; 243230-DR_0440; -.
DR   EnsemblBacteria; AAF10018; AAF10018; DR_0440.
DR   GeneID; 69516673; -.
DR   KEGG; dra:DR_0440; -.
DR   PATRIC; fig|243230.17.peg.615; -.
DR   eggNOG; COG0817; Bacteria.
DR   HOGENOM; CLU_091257_3_1_0; -.
DR   InParanoid; Q9RX75; -.
DR   OrthoDB; 9805499at2; -.
DR   Proteomes; UP000002524; Chromosome I.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0048476; C:Holliday junction resolvase complex; IEA:UniProtKB-UniRule.
DR   GO; GO:0008821; F:crossover junction DNA endonuclease activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-UniRule.
DR   GO; GO:0006281; P:DNA repair; IEA:UniProtKB-UniRule.
DR   CDD; cd16962; RuvC; 1.
DR   Gene3D; 3.30.420.10; Ribonuclease H-like superfamily/Ribonuclease H; 1.
DR   HAMAP; MF_00034; RuvC; 1.
DR   InterPro; IPR012337; RNaseH-like_sf.
DR   InterPro; IPR036397; RNaseH_sf.
DR   InterPro; IPR002176; X-over_junc_endoDNase_RuvC.
DR   NCBIfam; TIGR00228; ruvC; 1.
DR   PANTHER; PTHR30194; CROSSOVER JUNCTION ENDODEOXYRIBONUCLEASE RUVC; 1.
DR   PANTHER; PTHR30194:SF3; CROSSOVER JUNCTION ENDODEOXYRIBONUCLEASE RUVC; 1.
DR   Pfam; PF02075; RuvC; 1.
DR   PRINTS; PR00696; RSOLVASERUVC.
DR   SUPFAM; SSF53098; Ribonuclease H-like; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Cytoplasm; DNA damage; DNA recombination; DNA repair;
KW   DNA-binding; Endonuclease; Hydrolase; Magnesium; Metal-binding; Nuclease;
KW   Reference proteome.
FT   CHAIN           1..179
FT                   /note="Crossover junction endodeoxyribonuclease RuvC"
FT                   /id="PRO_0000183095"
FT   MOTIF           68..74
FT                   /note="DNA-binding loop"
FT                   /evidence="ECO:0000305|PubMed:35744678"
FT   ACT_SITE        7
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00034,
FT                   ECO:0000305|PubMed:35744678, ECO:0000305|PubMed:36000732"
FT   ACT_SITE        67
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00034,
FT                   ECO:0000305|PubMed:35744678, ECO:0000305|PubMed:36000732"
FT   ACT_SITE        139
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00034,
FT                   ECO:0000305|PubMed:35744678, ECO:0000305|PubMed:36000732"
FT   ACT_SITE        142
FT                   /evidence="ECO:0000305|PubMed:35744678,
FT                   ECO:0000305|PubMed:36000732"
FT   BINDING         7
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000269|PubMed:36000732"
FT   BINDING         67
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000269|PubMed:36000732"
FT   BINDING         139
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000305|PubMed:36000732"
FT   MUTAGEN         7
FT                   /note="D->A,N: Loss of Holliday junction (HJ) cleavage."
FT                   /evidence="ECO:0000269|PubMed:36000732"
FT   MUTAGEN         67
FT                   /note="E->A,Q: Loss of HJ cleavage."
FT                   /evidence="ECO:0000269|PubMed:35744678,
FT                   ECO:0000269|PubMed:36000732"
FT   MUTAGEN         139
FT                   /note="H->A: Loss of HJ cleavage."
FT                   /evidence="ECO:0000269|PubMed:35744678,
FT                   ECO:0000269|PubMed:36000732"
FT   MUTAGEN         139
FT                   /note="H->D: Slightly decreased activity with Mn(2+),
FT                   slighlty increased activity with Mg(2+)."
FT                   /evidence="ECO:0000269|PubMed:36000732"
FT   MUTAGEN         142
FT                   /note="D->A,N: Loss of HJ cleavage."
FT                   /evidence="ECO:0000269|PubMed:35744678,
FT                   ECO:0000269|PubMed:36000732"
FT   STRAND          2..7
FT                   /evidence="ECO:0007829|PDB:7XHJ"
FT   STRAND          10..20
FT                   /evidence="ECO:0007829|PDB:7XHJ"
FT   STRAND          25..34
FT                   /evidence="ECO:0007829|PDB:7XHJ"
FT   HELIX           41..59
FT                   /evidence="ECO:0007829|PDB:7XHJ"
FT   STRAND          62..67
FT                   /evidence="ECO:0007829|PDB:7XHJ"
FT   HELIX           75..94
FT                   /evidence="ECO:0007829|PDB:7XHJ"
FT   STRAND          99..102
FT                   /evidence="ECO:0007829|PDB:7XHJ"
FT   HELIX           104..112
FT                   /evidence="ECO:0007829|PDB:7XHJ"
FT   HELIX           119..130
FT                   /evidence="ECO:0007829|PDB:7XHJ"
FT   HELIX           138..153
FT                   /evidence="ECO:0007829|PDB:7XHJ"
SQ   SEQUENCE   179 AA;  19652 MW;  3D0C4FFE232B9970 CRC64;
     MRVLGIDPGL ANLGLGLVEG DVRRAKHLYH VCLTTESAWL MPRRLQYLHE ELTRLLTEYR
     PDAVAIEDQI LRRQADVAFK VGQAFGVVQL ACAQAGVPIH AYGPMQVKKS LVGTGRADKE
     QVIYMVKASL GIRELFNNHA ADALALALTH LAHAPMQERS ERLAAAGRAA RTGDAPLRR
//