RNH2_THEKO
ID RNH2_THEKO Reviewed; 228 AA.
AC O74035;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1998, sequence version 1.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=Ribonuclease HII;
DE Short=RNase HII;
DE EC=3.1.26.4;
GN Name=rnhB; OrderedLocusNames=TK0805;
OS Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
OS (Pyrococcus kodakaraensis (strain KOD1)).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Thermococcus.
OX NCBI_TaxID=69014;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND CHARACTERIZATION.
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=9829929; DOI=10.1128/jb.180.23.6207-6214.1998;
RA Haruki M., Hayashi K., Kochi T., Muroya A., Koga Y., Morikawa M.,
RA Imanaka T., Kanaya S.;
RT "Gene cloning and characterization of recombinant RNase HII from a
RT hyperthermophilic archaeon.";
RL J. Bacteriol. 180:6207-6214(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=15710748; DOI=10.1101/gr.3003105;
RA Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.;
RT "Complete genome sequence of the hyperthermophilic archaeon Thermococcus
RT kodakaraensis KOD1 and comparison with Pyrococcus genomes.";
RL Genome Res. 15:352-363(2005).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 1-213, AND MUTAGENESIS OF ASP-7;
RP GLU-8; ASP-105; HIS-132 AND ASP-135.
RC STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX PubMed=11274461; DOI=10.1110/ps.48001;
RA Muroya A., Tsuchiya D., Ishikawa M., Haruki M., Morikawa M., Kanaya S.,
RA Morikawa K.;
RT "Catalytic center of an archaeal type 2 ribonuclease H as revealed by X-ray
RT crystallographic and mutational analyses.";
RL Protein Sci. 10:707-714(2001).
CC -!- FUNCTION: Endonuclease that specifically degrades the RNA of RNA-DNA
CC hybrids. {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endonucleolytic cleavage to 5'-phosphomonoester.; EC=3.1.26.4;
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Note=Manganese or magnesium. Binds 1 divalent metal ion per monomer in
CC the absence of substrate. May bind a second metal ion after substrate
CC binding. {ECO:0000250};
CC -!- SUBUNIT: Monomer.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the RNase HII family. {ECO:0000305}.
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DR EMBL; AB012613; BAA32803.1; -; Genomic_DNA.
DR EMBL; AP006878; BAD84994.1; -; Genomic_DNA.
DR PIR; T43891; T43891.
DR RefSeq; WP_011249756.1; NC_006624.1.
DR PDB; 1IO2; X-ray; 2.00 A; A=1-213.
DR PDB; 1X1P; X-ray; 2.80 A; A=1-197.
DR PDB; 2DFE; X-ray; 2.40 A; A=1-200.
DR PDB; 2DFF; X-ray; 2.70 A; A=1-204.
DR PDB; 2DFH; X-ray; 2.27 A; A=1-212.
DR PDBsum; 1IO2; -.
DR PDBsum; 1X1P; -.
DR PDBsum; 2DFE; -.
DR PDBsum; 2DFF; -.
DR PDBsum; 2DFH; -.
DR AlphaFoldDB; O74035; -.
DR SMR; O74035; -.
DR STRING; 69014.TK0805; -.
DR EnsemblBacteria; BAD84994; BAD84994; TK0805.
DR GeneID; 3233981; -.
DR KEGG; tko:TK0805; -.
DR PATRIC; fig|69014.16.peg.785; -.
DR eggNOG; arCOG04121; Archaea.
DR HOGENOM; CLU_036532_0_4_2; -.
DR InParanoid; O74035; -.
DR OMA; REECRFF; -.
DR OrthoDB; 105421at2157; -.
DR PhylomeDB; O74035; -.
DR BRENDA; 3.1.26.4; 5246.
DR EvolutionaryTrace; O74035; -.
DR Proteomes; UP000000536; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0032299; C:ribonuclease H2 complex; IBA:GO_Central.
DR GO; GO:0030145; F:manganese ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR GO; GO:0004523; F:RNA-DNA hybrid ribonuclease activity; IBA:GO_Central.
DR GO; GO:0043137; P:DNA replication, removal of RNA primer; IBA:GO_Central.
DR GO; GO:0006298; P:mismatch repair; IBA:GO_Central.
DR Gene3D; 1.10.10.460; -; 1.
DR Gene3D; 3.30.420.10; -; 1.
DR HAMAP; MF_00052_A; RNase_HII_A; 1.
DR InterPro; IPR004649; RNase_H2_suA.
DR InterPro; IPR001352; RNase_HII/HIII.
DR InterPro; IPR024567; RNase_HII/HIII_dom.
DR InterPro; IPR020787; RNase_HII_arc.
DR InterPro; IPR023160; RNase_HII_hlx-loop-hlx_cap_dom.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR PANTHER; PTHR10954; PTHR10954; 1.
DR Pfam; PF01351; RNase_HII; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
DR TIGRFAMs; TIGR00729; TIGR00729; 1.
DR PROSITE; PS51975; RNASE_H_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cobalt; Cytoplasm; Endonuclease; Hydrolase; Magnesium;
KW Metal-binding; Nuclease; Reference proteome.
FT CHAIN 1..228
FT /note="Ribonuclease HII"
FT /id="PRO_0000111671"
FT DOMAIN 1..210
FT /note="RNase H type-2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01319"
FT BINDING 7
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250"
FT BINDING 8
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250"
FT BINDING 105
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250"
FT MUTAGEN 7
FT /note="D->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11274461"
FT MUTAGEN 8
FT /note="E->A: Reduces activity by 99%."
FT /evidence="ECO:0000269|PubMed:11274461"
FT MUTAGEN 105
FT /note="D->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11274461"
FT MUTAGEN 132
FT /note="H->A: Reduces activity by 75%."
FT /evidence="ECO:0000269|PubMed:11274461"
FT MUTAGEN 135
FT /note="D->A: Reduces activity by 98%."
FT /evidence="ECO:0000269|PubMed:11274461"
FT STRAND 2..9
FT /evidence="ECO:0007829|PDB:1IO2"
FT STRAND 14..16
FT /evidence="ECO:0007829|PDB:1IO2"
FT STRAND 18..26
FT /evidence="ECO:0007829|PDB:1IO2"
FT HELIX 27..29
FT /evidence="ECO:0007829|PDB:1IO2"
FT HELIX 30..35
FT /evidence="ECO:0007829|PDB:1IO2"
FT HELIX 38..40
FT /evidence="ECO:0007829|PDB:1IO2"
FT STRAND 42..44
FT /evidence="ECO:0007829|PDB:2DFF"
FT HELIX 46..57
FT /evidence="ECO:0007829|PDB:1IO2"
FT STRAND 61..68
FT /evidence="ECO:0007829|PDB:1IO2"
FT HELIX 70..74
FT /evidence="ECO:0007829|PDB:1IO2"
FT STRAND 76..79
FT /evidence="ECO:0007829|PDB:2DFE"
FT HELIX 80..94
FT /evidence="ECO:0007829|PDB:1IO2"
FT STRAND 100..105
FT /evidence="ECO:0007829|PDB:1IO2"
FT HELIX 111..120
FT /evidence="ECO:0007829|PDB:1IO2"
FT STRAND 122..124
FT /evidence="ECO:0007829|PDB:1X1P"
FT STRAND 127..131
FT /evidence="ECO:0007829|PDB:1IO2"
FT HELIX 134..137
FT /evidence="ECO:0007829|PDB:1IO2"
FT HELIX 139..163
FT /evidence="ECO:0007829|PDB:1IO2"
FT HELIX 174..187
FT /evidence="ECO:0007829|PDB:1IO2"
FT HELIX 199..211
FT /evidence="ECO:0007829|PDB:1IO2"
SQ SEQUENCE 228 AA; 25801 MW; 6578C937BBB60F2C CRC64;
MKIAGIDEAG RGPVIGPMVI AAVVVDENSL PKLEELKVRD SKKLTPKRRE KLFNEILGVL
DDYVILELPP DVIGSREGTL NEFEVENFAK ALNSLKVKPD VIYADAADVD EERFARELGE
RLNFEAEVVA KHKADDIFPV VSAASILAKV TRDRAVEKLK EEYGEIGSGY PSDPRTRAFL
ENYYREHGEF PPIVRKGWKT LKKIAEKVES EKKAEERQAT LDRYFRKV
