RNH2_ARCFU
ID RNH2_ARCFU Reviewed; 205 AA.
AC O29634;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 133.
DE RecName: Full=Ribonuclease HII;
DE Short=RNase HII;
DE EC=3.1.26.4;
GN Name=rnhB; OrderedLocusNames=AF_0621;
OS Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC
OS 100126 / VC-16).
OC Archaea; Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae;
OC Archaeoglobus.
OX NCBI_TaxID=224325;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16;
RX PubMed=9389475; DOI=10.1038/37052;
RA Klenk H.-P., Clayton R.A., Tomb J.-F., White O., Nelson K.E., Ketchum K.A.,
RA Dodson R.J., Gwinn M.L., Hickey E.K., Peterson J.D., Richardson D.L.,
RA Kerlavage A.R., Graham D.E., Kyrpides N.C., Fleischmann R.D.,
RA Quackenbush J., Lee N.H., Sutton G.G., Gill S.R., Kirkness E.F.,
RA Dougherty B.A., McKenney K., Adams M.D., Loftus B.J., Peterson S.N.,
RA Reich C.I., McNeil L.K., Badger J.H., Glodek A., Zhou L., Overbeek R.,
RA Gocayne J.D., Weidman J.F., McDonald L.A., Utterback T.R., Cotton M.D.,
RA Spriggs T., Artiach P., Kaine B.P., Sykes S.M., Sadow P.W., D'Andrea K.P.,
RA Bowman C., Fujii C., Garland S.A., Mason T.M., Olsen G.J., Fraser C.M.,
RA Smith H.O., Woese C.R., Venter J.C.;
RT "The complete genome sequence of the hyperthermophilic, sulphate-reducing
RT archaeon Archaeoglobus fulgidus.";
RL Nature 390:364-370(1997).
RN [2]
RP COFACTOR, AND MUTAGENESIS.
RX PubMed=11527410; DOI=10.1006/bbrc.2001.5523;
RA Chai Q., Qiu J., Chapados B.R., Shen B.;
RT "Archaeoglobus fulgidus RNase HII in DNA replication: enzymological
RT functions and activity regulation via metal cofactors.";
RL Biochem. Biophys. Res. Commun. 286:1073-1081(2001).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH DIVALENT METAL IONS,
RP AND MUTAGENESIS OF ASP-6; GLU-7; ARG-46; ASP-101; ASP-129; LYS-143; ARG-146
RP AND TYR-164.
RX PubMed=11254381; DOI=10.1006/jmbi.2001.4494;
RA Chapados B.R., Chai Q., Hosfield D.J., Qiu J., Shen B., Tainer J.A.;
RT "Structural biochemistry of a type 2 RNase H: RNA primer recognition and
RT removal during DNA replication.";
RL J. Mol. Biol. 307:541-556(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;
CC Evidence={ECO:0000269|PubMed:11527410};
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:11527410};
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:0000269|PubMed:11527410};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the RNase HII family. {ECO:0000305}.
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DR EMBL; AE000782; AAB90620.1; -; Genomic_DNA.
DR PIR; E69327; E69327.
DR RefSeq; WP_010878125.1; NC_000917.1.
DR PDB; 1I39; X-ray; 1.95 A; A=1-205.
DR PDB; 1I3A; X-ray; 2.15 A; A=1-205.
DR PDB; 3P83; X-ray; 3.05 A; D/E/F=1-205.
DR PDBsum; 1I39; -.
DR PDBsum; 1I3A; -.
DR PDBsum; 3P83; -.
DR AlphaFoldDB; O29634; -.
DR SMR; O29634; -.
DR STRING; 224325.AF_0621; -.
DR EnsemblBacteria; AAB90620; AAB90620; AF_0621.
DR GeneID; 24794224; -.
DR KEGG; afu:AF_0621; -.
DR eggNOG; arCOG04121; Archaea.
DR HOGENOM; CLU_036532_0_4_2; -.
DR OMA; REECRFF; -.
DR OrthoDB; 105421at2157; -.
DR PhylomeDB; O29634; -.
DR BRENDA; 3.1.26.4; 414.
DR EvolutionaryTrace; O29634; -.
DR Proteomes; UP000002199; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
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; IEA:UniProtKB-UniRule.
DR GO; GO:0006401; P:RNA catabolic process; IEA:UniProtKB-UniRule.
DR Gene3D; 1.10.10.460; -; 1.
DR Gene3D; 3.30.420.10; -; 1.
DR HAMAP; MF_00052_A; RNase_HII_A; 1.
DR IDEAL; IID90025; -.
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; Cytoplasm; Endonuclease; Hydrolase; Magnesium; Manganese;
KW Metal-binding; Nuclease; Reference proteome.
FT CHAIN 1..205
FT /note="Ribonuclease HII"
FT /id="PRO_0000111661"
FT DOMAIN 1..203
FT /note="RNase H type-2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01319"
FT BINDING 6
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT BINDING 7
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT BINDING 46
FT /ligand="substrate"
FT /evidence="ECO:0000305"
FT BINDING 101
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT BINDING 143
FT /ligand="substrate"
FT /evidence="ECO:0000305"
FT BINDING 146
FT /ligand="substrate"
FT /evidence="ECO:0000305"
FT BINDING 164
FT /ligand="substrate"
FT /evidence="ECO:0000305"
FT MUTAGEN 6
FT /note="D->N: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11254381"
FT MUTAGEN 7
FT /note="E->N: Slight decrease of activity."
FT /evidence="ECO:0000269|PubMed:11254381"
FT MUTAGEN 7
FT /note="E->Q: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11254381"
FT MUTAGEN 46
FT /note="R->A: Increases Km for RNA 60-fold."
FT /evidence="ECO:0000269|PubMed:11254381"
FT MUTAGEN 101
FT /note="D->N: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11254381"
FT MUTAGEN 129
FT /note="D->N: Lowers activity by 50%."
FT /evidence="ECO:0000269|PubMed:11254381"
FT MUTAGEN 143
FT /note="K->A: Decrease of activity. Increases Km for RNA 30-
FT fold."
FT /evidence="ECO:0000269|PubMed:11254381"
FT MUTAGEN 146
FT /note="R->A: Decrease of activity. Increases Km for RNA 26-
FT fold."
FT /evidence="ECO:0000269|PubMed:11254381"
FT MUTAGEN 164
FT /note="Y->A: Loss of activity. Increases Km for RNA 44-
FT fold."
FT /evidence="ECO:0000269|PubMed:11254381"
FT STRAND 2..8
FT /evidence="ECO:0007829|PDB:1I39"
FT STRAND 13..15
FT /evidence="ECO:0007829|PDB:1I39"
FT STRAND 17..25
FT /evidence="ECO:0007829|PDB:1I39"
FT HELIX 27..32
FT /evidence="ECO:0007829|PDB:1I39"
FT HELIX 35..40
FT /evidence="ECO:0007829|PDB:1I3A"
FT HELIX 43..56
FT /evidence="ECO:0007829|PDB:1I39"
FT STRAND 57..64
FT /evidence="ECO:0007829|PDB:1I39"
FT HELIX 66..72
FT /evidence="ECO:0007829|PDB:1I39"
FT TURN 73..75
FT /evidence="ECO:0007829|PDB:1I39"
FT HELIX 78..93
FT /evidence="ECO:0007829|PDB:1I39"
FT STRAND 96..105
FT /evidence="ECO:0007829|PDB:1I39"
FT HELIX 108..118
FT /evidence="ECO:0007829|PDB:1I39"
FT STRAND 120..127
FT /evidence="ECO:0007829|PDB:1I39"
FT HELIX 128..130
FT /evidence="ECO:0007829|PDB:1I39"
FT HELIX 133..157
FT /evidence="ECO:0007829|PDB:1I39"
FT STRAND 162..164
FT /evidence="ECO:0007829|PDB:1I39"
FT HELIX 168..180
FT /evidence="ECO:0007829|PDB:1I39"
FT HELIX 192..198
FT /evidence="ECO:0007829|PDB:1I39"
FT HELIX 202..204
FT /evidence="ECO:0007829|PDB:3P83"
SQ SEQUENCE 205 AA; 23182 MW; E7B07EC5BD34F7A3 CRC64;
MKAGIDEAGK GCVIGPLVVA GVACSDEDRL RKLGVKDSKK LSQGRREELA EEIRKICRTE
VLKVSPENLD ERMAAKTINE ILKECYAEII LRLKPEIAYV DSPDVIPERL SRELEEITGL
RVVAEHKADE KYPLVAAASI IAKVEREREI ERLKEKFGDF GSGYASDPRT REVLKEWIAS
GRIPSCVRMR WKTVSNLRQK TLDDF
