RNH_SULTO
ID RNH_SULTO Reviewed; 149 AA.
AC F9VN79;
DT 06-FEB-2013, integrated into UniProtKB/Swiss-Prot.
DT 19-OCT-2011, sequence version 1.
DT 03-AUG-2022, entry version 52.
DE RecName: Full=Ribonuclease HI;
DE Short=RNase HI;
DE Short=Sto-RNase HI;
DE EC=3.1.26.4;
GN Name=rnhA; OrderedLocusNames=STK_07530;
OS Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)
OS (Sulfolobus tokodaii).
OC Archaea; Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae;
OC Sulfurisphaera.
OX NCBI_TaxID=273063;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 16993 / JCM 10545 / NBRC 100140 / 7;
RX PubMed=11572479; DOI=10.1093/dnares/8.4.123;
RA Kawarabayasi Y., Hino Y., Horikawa H., Jin-no K., Takahashi M., Sekine M.,
RA Baba S., Ankai A., Kosugi H., Hosoyama A., Fukui S., Nagai Y.,
RA Nishijima K., Otsuka R., Nakazawa H., Takamiya M., Kato Y., Yoshizawa T.,
RA Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K.,
RA Masuda S., Yanagii M., Nishimura M., Yamagishi A., Oshima T., Kikuchi H.;
RT "Complete genome sequence of an aerobic thermoacidophilic Crenarchaeon,
RT Sulfolobus tokodaii strain7.";
RL DNA Res. 8:123-140(2001).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, AND MUTAGENESIS OF ASP-7;
RP GLU-52; ASP-76 AND ASP-125.
RC STRAIN=DSM 16993 / JCM 10545 / NBRC 100140 / 7;
RX PubMed=15520465; DOI=10.1093/nar/gkh917;
RA Ohtani N., Yanagawa H., Tomita M., Itaya M.;
RT "Cleavage of double-stranded RNA by RNase HI from a thermoacidophilic
RT archaeon, Sulfolobus tokodaii 7.";
RL Nucleic Acids Res. 32:5809-5819(2004).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS), PROTEIN STABILITY, SUBUNIT,
RP DISULFIDE BOND, NUCLEIC ACID-BINDING, AND MUTAGENESIS OF CYS-58; LYS-91;
RP ARG-118; 144-GLY--THR-149 AND CYS-145.
RC STRAIN=DSM 16993 / JCM 10545 / NBRC 100140 / 7;
RX PubMed=17892305; DOI=10.1021/bi700830f;
RA You D.J., Chon H., Koga Y., Takano K., Kanaya S.;
RT "Crystal structure of type 1 ribonuclease H from hyperthermophilic archaeon
RT Sulfolobus tokodaii: role of arginine 118 and C-terminal anchoring.";
RL Biochemistry 46:11494-11503(2007).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.66 ANGSTROMS) OF 1-143, AND PROTEIN STABILITY.
RC STRAIN=DSM 16993 / JCM 10545 / NBRC 100140 / 7;
RX PubMed=21283826; DOI=10.1371/journal.pone.0016226;
RA Takano K., Okamoto T., Okada J., Tanaka S., Angkawidjaja C., Koga Y.,
RA Kanaya S.;
RT "Stabilization by fusion to the C-terminus of hyperthermophile Sulfolobus
RT tokodaii RNase HI: a possibility of protein stabilization tag.";
RL PLoS ONE 6:E16226-E16226(2011).
CC -!- FUNCTION: Nuclease that specifically degrades the RNA of RNA-DNA
CC hybrids. Endonucleolytically removes RNA primers from the Okazaki
CC fragments of lagging strand synthesis on its own. In the presence of
CC Mn(2+) or Co(2+) can also cleave an RNA-RNA hybrid; the dsRNase
CC activity is 10- 100-fold lower than RNase H activity. Complements the
CC temperature-sensitive phenotype of an E.coli double rnhA/rnhB (RNase H)
CC disruption mutant. {ECO:0000269|PubMed:15520465}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endonucleolytic cleavage to 5'-phosphomonoester.; EC=3.1.26.4;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00408,
CC ECO:0000269|PubMed:15520465};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:15520465};
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:15520465};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:15520465};
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Evidence={ECO:0000269|PubMed:15520465};
CC Note=Divalent metal cations; Mn(2+) and Mg(2+) are preferred over
CC Co(2+) or Ni(2+). {ECO:0000269|PubMed:15520465};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:15520465,
CC ECO:0000269|PubMed:17892305}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- PTM: The disulfide bond confers considerable stability to the protein.
CC -!- MISCELLANEOUS: The protein is hyperthermostable, melting temperature
CC (TM) for wild-type is 102 degrees Celsius, for the double Cys mutant is
CC 93 degrees Celsius and for a C-terminal deletion of 6 residues is 77
CC degrees Celsius.
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DR EMBL; BA000023; BAK54376.1; -; Genomic_DNA.
DR RefSeq; WP_010978745.1; NC_003106.2.
DR PDB; 2EHG; X-ray; 1.60 A; A=1-149.
DR PDB; 3ALY; X-ray; 1.66 A; A/B=1-143.
DR PDBsum; 2EHG; -.
DR PDBsum; 3ALY; -.
DR AlphaFoldDB; F9VN79; -.
DR SMR; F9VN79; -.
DR STRING; 273063.STK_07530; -.
DR EnsemblBacteria; BAK54376; BAK54376; STK_07530.
DR GeneID; 1458712; -.
DR KEGG; sto:STK_07530; -.
DR PATRIC; fig|273063.9.peg.846; -.
DR eggNOG; arCOG02942; Archaea.
DR OMA; CEPVNPG; -.
DR OrthoDB; 104728at2157; -.
DR BRENDA; 3.1.13.2; 15396.
DR BRENDA; 3.1.26.4; 15396.
DR Proteomes; UP000001015; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0004523; F:RNA-DNA hybrid ribonuclease activity; IEA:UniProtKB-EC.
DR Gene3D; 3.30.420.10; -; 1.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR002156; RNaseH_domain.
DR InterPro; IPR036397; RNaseH_sf.
DR Pfam; PF13456; RVT_3; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
DR PROSITE; PS50879; RNASE_H_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Disulfide bond; DNA-binding; Endonuclease;
KW Hydrolase; Magnesium; Manganese; Metal-binding; Nuclease;
KW Reference proteome; RNA-binding.
FT CHAIN 1..149
FT /note="Ribonuclease HI"
FT /id="PRO_0000420870"
FT DOMAIN 1..140
FT /note="RNase H type-1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT BINDING 7
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT BINDING 7
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT BINDING 7
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT BINDING 7
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT BINDING 52
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT BINDING 52
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT BINDING 76
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT BINDING 76
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT BINDING 125
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT BINDING 125
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT DISULFID 58..145
FT /evidence="ECO:0000269|PubMed:17892305"
FT MUTAGEN 7
FT /note="D->N: Loss of RNase H activity, loss of dsRNase
FT activity. Does not complement E.coli double deletion
FT mutant."
FT /evidence="ECO:0000269|PubMed:15520465"
FT MUTAGEN 52
FT /note="E->Q: Loss of RNase H activity, loss of dsRNase
FT activity. Does not complement E.coli double deletion
FT mutant."
FT /evidence="ECO:0000269|PubMed:15520465"
FT MUTAGEN 58
FT /note="C->A: RNase H and dsRNase activity increase
FT slightly, decreased thermostability; when associated with
FT A-145."
FT /evidence="ECO:0000269|PubMed:17892305"
FT MUTAGEN 76
FT /note="D->N: Loss of RNase H activity, loss of dsRNase
FT activity. Does not complement E.coli double deletion
FT mutant."
FT /evidence="ECO:0000269|PubMed:15520465"
FT MUTAGEN 91
FT /note="K->A: Retains RNase H activity, considerable loss of
FT dsRNase activity."
FT /evidence="ECO:0000269|PubMed:17892305"
FT MUTAGEN 118
FT /note="R->A: 10-fold reduction in both RNase H and dsRNase
FT activity."
FT /evidence="ECO:0000269|PubMed:17892305"
FT MUTAGEN 125
FT /note="D->N: Retains RNase H activity, loss of dsRNase
FT activity. Complements E.coli double deletion mutant."
FT /evidence="ECO:0000269|PubMed:15520465"
FT MUTAGEN 144..149
FT /note="Missing: 20% reduction in RNase H activity, 40%
FT reduction in dsRNase activity, partial loss of
FT thermostability."
FT /evidence="ECO:0000269|PubMed:17892305"
FT MUTAGEN 145
FT /note="C->A: RNase H and dsRNase activity increase
FT slightly, decreased thermostability; when associated with
FT A-58."
FT /evidence="ECO:0000269|PubMed:17892305"
FT STRAND 3..26
FT /evidence="ECO:0007829|PDB:2EHG"
FT STRAND 31..37
FT /evidence="ECO:0007829|PDB:2EHG"
FT HELIX 48..66
FT /evidence="ECO:0007829|PDB:2EHG"
FT STRAND 72..76
FT /evidence="ECO:0007829|PDB:2EHG"
FT HELIX 78..84
FT /evidence="ECO:0007829|PDB:2EHG"
FT HELIX 95..109
FT /evidence="ECO:0007829|PDB:2EHG"
FT STRAND 112..115
FT /evidence="ECO:0007829|PDB:2EHG"
FT HELIX 118..120
FT /evidence="ECO:0007829|PDB:2EHG"
FT HELIX 122..136
FT /evidence="ECO:0007829|PDB:2EHG"
FT STRAND 142..147
FT /evidence="ECO:0007829|PDB:2EHG"
SQ SEQUENCE 149 AA; 16813 MW; 195DB9BAA869A571 CRC64;
MIIGYFDGLC EPKNPGGIAT FGFVIYLDNR KIEGYGLAEK PFSINSTNNV AEYSGLICLM
ETMLRLGISS PIIKGDSQLV IKQMNGEYKV KAKRIIPLYE KAIELKKKLN ATLIWVPREE
NKEADRLSRV AYELVRRGKL RDIGCIILT
