ID RUVC_THET8 Reviewed; 166 AA. AC Q5SJC4; DT 07-MAR-2006, integrated into UniProtKB/Swiss-Prot. DT 21-DEC-2004, sequence version 1. DT 27-MAR-2024, entry version 103. 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:23118486, ECO:0000269|PubMed:23980027}; 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}; GN Name=ruvC {ECO:0000255|HAMAP-Rule:MF_00034, ECO:0000303|Ref.1}; GN OrderedLocusNames=TTHA1090; OS Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8). OC Bacteria; Deinococcota; Deinococci; Thermales; Thermaceae; Thermus. OX NCBI_TaxID=300852; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 27634 / DSM 579 / HB8; RA Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T., RA Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.; RT "Complete genome sequence of Thermus thermophilus HB8."; RL Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases. RN [2] {ECO:0007744|PDB:4EP4, ECO:0007744|PDB:4EP5} RP X-RAY CRYSTALLOGRAPHY (1.28 ANGSTROMS) IN COMPLEX WITH MG(2+), FUNCTION, RP CATALYTIC ACTIVITY, PROBABLE ACTIVE SITE, COFACTOR, BIOPHYSICOCHEMICAL RP PROPERTIES, SUBUNIT, AND MUTAGENESIS OF PHE-73; PHE-74; TYR-75 AND ASP-146. RC STRAIN=ATCC 27634 / DSM 579 / HB8; RX PubMed=23118486; DOI=10.1093/nar/gks1015; RA Chen L., Shi K., Yin Z., Aihara H.; RT "Structural asymmetry in the Thermus thermophilus RuvC dimer suggests a RT basis for sequential strand cleavages during Holliday junction RT resolution."; RL Nucleic Acids Res. 41:648-656(2013). RN [3] {ECO:0007744|PDB:4LD0} RP X-RAY CRYSTALLOGRAPHY (3.75 ANGSTROMS) IN COMPLEX WITH DNA, FUNCTION, RP CATALYTIC ACTIVITY, PROBABLE ACTIVE SITE, SUBUNIT, DNA-BINDING, AND RP MUTAGENESIS OF GLU-70; TYR-75; ARG-76 AND HIS-143. RX PubMed=23980027; DOI=10.1093/nar/gkt769; RA Gorecka K.M., Komorowska W., Nowotny M.; RT "Crystal structure of RuvC resolvase in complex with Holliday junction RT substrate."; RL Nucleic Acids Res. 41:9945-9955(2013). RN [4] {ECO:0007744|PDB:6S16} RP X-RAY CRYSTALLOGRAPHY (3.41 ANGSTROMS) IN COMPLEX WITH DNA, FUNCTION, DNA RP CLEAVAGE SITE, CATALYTIC ACTIVITY, PROBABLE ACTIVE SITE, WEDGE MOTIF, AND RP MUTAGENESIS OF ARG-76. RX PubMed=31506434; DOI=10.1038/s41467-019-11900-8; RA Gorecka K.M., Krepl M., Szlachcic A., Poznanski J., Sponer J., Nowotny M.; RT "RuvC uses dynamic probing of the Holliday junction to achieve sequence RT specificity and efficient resolution."; RL Nat. Commun. 10:4102-4102(2019). CC -!- FUNCTION: The RuvA-RuvB-RuvC complex processes Holliday junction (HJ) CC DNA during genetic recombination and DNA repair (Probable). CC Endonuclease that resolves Holliday junction (HJ) intermediates. CC Cleaves cruciform DNA by making single-stranded nicks across the HJ at CC symmetrical positions within the homologous arms, yielding a 5'- CC phosphate and a 3'-hydroxyl group; requires a central core of homology CC in the junction. The cleavage reactions can be uncoupled; the presence CC of a 5'-phosphate in a half-cut site is required for second strand CC cleavage (PubMed:23118486, PubMed:23980027, PubMed:31506434). The CC consensus cleavage sequence is 5'-(A/T)TT(C/G)-3'. Cleavage occurs on CC the 3'-side of the TT dinucleotide at the point of strand exchange CC (PubMed:31506434). {ECO:0000255|HAMAP-Rule:MF_00034, CC ECO:0000269|PubMed:23118486, ECO:0000269|PubMed:23980027, CC ECO:0000269|PubMed:31506434}. 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:23118486, CC ECO:0000269|PubMed:23980027, ECO:0000269|PubMed:31506434}; CC -!- COFACTOR: CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000255|HAMAP- CC Rule:MF_00034, ECO:0000269|PubMed:23118486}; CC Note=Binds 2 Mg(2+) ion per subunit. {ECO:0000255|HAMAP-Rule:MF_00034, CC ECO:0000305|PubMed:23118486, ECO:0000305|PubMed:31506434}; CC -!- BIOPHYSICOCHEMICAL PROPERTIES: CC Temperature dependence: CC Optimum temperature is 58 degrees Celsius. CC {ECO:0000269|PubMed:23118486}; CC -!- SUBUNIT: Homodimer which binds Holliday junction (HJ) DNA. The HJ CC becomes 2-fold symmetrical on binding to RuvC with unstacked arms; it CC has a different conformation from HJ DNA in complex with RuvA. In the CC full resolvosome a probable DNA-RuvA(4)-RuvB(12)-RuvC(2) complex forms CC which resolves the HJ. {ECO:0000255|HAMAP-Rule:MF_00034, CC ECO:0000269|PubMed:23118486, ECO:0000269|PubMed:23980027}. CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00034}. CC -!- DOMAIN: The wedge motif stacks with DNA close to the Holliday junction CC point; Arg-76 interacts with and eventually disrupts the T:A base pair CC cleavage site, and subsequent to cleavage may prevent their CC reannealment. {ECO:0000269|PubMed:31506434}. CC -!- SIMILARITY: Belongs to the RuvC family. {ECO:0000255|HAMAP- CC Rule:MF_00034}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; AP008226; BAD70913.1; -; Genomic_DNA. DR RefSeq; WP_011173164.1; NC_006461.1. DR RefSeq; YP_144356.1; NC_006461.1. DR PDB; 4EP4; X-ray; 1.28 A; A/B=1-166. DR PDB; 4EP5; X-ray; 2.08 A; A=1-166. DR PDB; 4LD0; X-ray; 3.75 A; A/B=1-166. DR PDB; 6S16; X-ray; 3.41 A; A/B=1-166. DR PDBsum; 4EP4; -. DR PDBsum; 4EP5; -. DR PDBsum; 4LD0; -. DR PDBsum; 6S16; -. DR AlphaFoldDB; Q5SJC4; -. DR SMR; Q5SJC4; -. DR EnsemblBacteria; BAD70913; BAD70913; BAD70913. DR GeneID; 3168165; -. DR KEGG; ttj:TTHA1090; -. DR PATRIC; fig|300852.9.peg.1070; -. DR eggNOG; COG0817; Bacteria. DR HOGENOM; CLU_091257_3_1_0; -. DR PhylomeDB; Q5SJC4; -. DR BRENDA; 3.1.21.10; 2305. DR Proteomes; UP000000532; Chromosome. 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..166 FT /note="Crossover junction endodeoxyribonuclease RuvC" FT /id="PRO_0000225184" FT MOTIF 74..76 FT /note="Wedge" FT /evidence="ECO:0000269|PubMed:31506434" FT ACT_SITE 7 FT /evidence="ECO:0000255|HAMAP-Rule:MF_00034, FT ECO:0000305|PubMed:23118486, ECO:0000305|PubMed:23980027, FT ECO:0000305|PubMed:31506434" FT ACT_SITE 70 FT /evidence="ECO:0000255|HAMAP-Rule:MF_00034, FT ECO:0000305|PubMed:23118486, ECO:0000305|PubMed:23980027, FT ECO:0000305|PubMed:31506434" FT ACT_SITE 143 FT /evidence="ECO:0000255|HAMAP-Rule:MF_00034, FT ECO:0000305|PubMed:23118486, ECO:0000305|PubMed:23980027, FT ECO:0000305|PubMed:31506434" FT ACT_SITE 146 FT /evidence="ECO:0000305|PubMed:23118486" FT BINDING 7 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00034, FT ECO:0000269|PubMed:23118486, ECO:0000312|PDB:4EP4" FT BINDING 10..11 FT /ligand="DNA" FT /ligand_id="ChEBI:CHEBI:16991" FT /evidence="ECO:0000269|PubMed:23980027, FT ECO:0000269|PubMed:31506434, ECO:0000312|PDB:4LD0, FT ECO:0000312|PDB:6S16" FT BINDING 40 FT /ligand="DNA" FT /ligand_id="ChEBI:CHEBI:16991" FT /evidence="ECO:0000269|PubMed:23980027, FT ECO:0000269|PubMed:31506434, ECO:0000312|PDB:4LD0, FT ECO:0000312|PDB:6S16" FT BINDING 47 FT /ligand="DNA" FT /ligand_id="ChEBI:CHEBI:16991" FT /evidence="ECO:0000269|PubMed:23980027, FT ECO:0000269|PubMed:31506434, ECO:0000312|PDB:4LD0, FT ECO:0000312|PDB:6S16" FT BINDING 70 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="2" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00034" FT BINDING 73..74 FT /ligand="DNA" FT /ligand_id="ChEBI:CHEBI:16991" FT /evidence="ECO:0000269|PubMed:23980027, FT ECO:0000269|PubMed:31506434, ECO:0000305|PubMed:23118486, FT ECO:0000312|PDB:4LD0" FT BINDING 76..77 FT /ligand="DNA" FT /ligand_id="ChEBI:CHEBI:16991" FT /evidence="ECO:0000269|PubMed:23980027, FT ECO:0000269|PubMed:31506434, ECO:0000312|PDB:4LD0" FT BINDING 80 FT /ligand="DNA" FT /ligand_id="ChEBI:CHEBI:16991" FT /evidence="ECO:0000269|PubMed:31506434, FT ECO:0000305|PubMed:23980027, ECO:0000312|PDB:6S16" FT BINDING 83 FT /ligand="DNA" FT /ligand_id="ChEBI:CHEBI:16991" FT /evidence="ECO:0000269|PubMed:23980027, FT ECO:0000269|PubMed:31506434, ECO:0000312|PDB:4LD0, FT ECO:0000312|PDB:6S16" FT BINDING 108 FT /ligand="DNA" FT /ligand_id="ChEBI:CHEBI:16991" FT /evidence="ECO:0000269|PubMed:23980027, FT ECO:0000312|PDB:4LD0" FT BINDING 140 FT /ligand="DNA" FT /ligand_id="ChEBI:CHEBI:16991" FT /evidence="ECO:0000269|PubMed:23980027, FT ECO:0000312|PDB:4LD0" FT BINDING 143 FT /ligand="Mg(2+)" FT /ligand_id="ChEBI:CHEBI:18420" FT /ligand_label="1" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00034, FT ECO:0000269|PubMed:23118486, ECO:0000312|PDB:4EP4" FT MUTAGEN 70 FT /note="E->Q: Loss of HJ resolution." FT /evidence="ECO:0000269|PubMed:23980027" FT MUTAGEN 73 FT /note="F->A: About 50% HJ resolution activity." FT /evidence="ECO:0000269|PubMed:23118486" FT MUTAGEN 74 FT /note="F->A: Slightly reduced HJ resolution activity, FT altered sequence specificity." FT /evidence="ECO:0000269|PubMed:23118486" FT MUTAGEN 75 FT /note="Y->A: Improved HJ resolution." FT /evidence="ECO:0000269|PubMed:23118486, FT ECO:0000269|PubMed:23980027" FT MUTAGEN 76 FT /note="R->A: Reduced HJ resolution." FT /evidence="ECO:0000269|PubMed:23980027, FT ECO:0000269|PubMed:31506434" FT MUTAGEN 143 FT /note="H->A: About wild-type HJ resolution." FT /evidence="ECO:0000269|PubMed:23980027" FT MUTAGEN 143 FT /note="H->D: Improved HJ resolution." FT /evidence="ECO:0000269|PubMed:23980027" FT MUTAGEN 146 FT /note="D->N: Loss of HJ resolution." FT /evidence="ECO:0000269|PubMed:23118486" FT STRAND 2..7 FT /evidence="ECO:0007829|PDB:4EP4" FT STRAND 10..20 FT /evidence="ECO:0007829|PDB:4EP4" FT STRAND 22..26 FT /evidence="ECO:0007829|PDB:4EP4" FT STRAND 28..37 FT /evidence="ECO:0007829|PDB:4EP4" FT STRAND 40..42 FT /evidence="ECO:0007829|PDB:4EP5" FT HELIX 44..62 FT /evidence="ECO:0007829|PDB:4EP4" FT STRAND 65..70 FT /evidence="ECO:0007829|PDB:4EP4" FT HELIX 79..98 FT /evidence="ECO:0007829|PDB:4EP4" FT STRAND 102..105 FT /evidence="ECO:0007829|PDB:4EP4" FT HELIX 107..115 FT /evidence="ECO:0007829|PDB:4EP4" FT STRAND 117..119 FT /evidence="ECO:0007829|PDB:6S16" FT HELIX 122..132 FT /evidence="ECO:0007829|PDB:4EP4" FT HELIX 142..159 FT /evidence="ECO:0007829|PDB:4EP4" SQ SEQUENCE 166 AA; 17755 MW; 214FBE6E1D4A91C3 CRC64; MVVAGIDPGI THLGLGVVAV EGKGALKARL LHGEVVKTSP QEPAKERVGR IHARVLEVLH RFRPEAVAVE EQFFYRQNEL AYKVGWALGA VLVAAFEAGV PVYAYGPMQV KQALAGHGHA AKEEVALMVR GILGLKEAPR PSHLADALAI ALTHAFYARM GTAKPL //