RNH_HALSA
ID RNH_HALSA Reviewed; 199 AA.
AC Q9HSF6;
DT 06-FEB-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 112.
DE RecName: Full=Ribonuclease HI;
DE Short=Halo-RNase HI;
DE Short=RNase HI;
DE EC=3.1.26.4;
GN Name=rnhA; OrderedLocusNames=VNG_0255C;
OS Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)
OS (Halobacterium halobium).
OC Archaea; Euryarchaeota; Stenosarchaea group; Halobacteria; Halobacteriales;
OC Halobacteriaceae; Halobacterium.
OX NCBI_TaxID=64091;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700922 / JCM 11081 / NRC-1;
RX PubMed=11016950; DOI=10.1073/pnas.190337797;
RA Ng W.V., Kennedy S.P., Mahairas G.G., Berquist B., Pan M., Shukla H.D.,
RA Lasky S.R., Baliga N.S., Thorsson V., Sbrogna J., Swartzell S., Weir D.,
RA Hall J., Dahl T.A., Welti R., Goo Y.A., Leithauser B., Keller K., Cruz R.,
RA Danson M.J., Hough D.W., Maddocks D.G., Jablonski P.E., Krebs M.P.,
RA Angevine C.M., Dale H., Isenbarger T.A., Peck R.F., Pohlschroder M.,
RA Spudich J.L., Jung K.-H., Alam M., Freitas T., Hou S., Daniels C.J.,
RA Dennis P.P., Omer A.D., Ebhardt H., Lowe T.M., Liang P., Riley M., Hood L.,
RA DasSarma S.;
RT "Genome sequence of Halobacterium species NRC-1.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:12176-12181(2000).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND MUTAGENESIS OF HIS-29; HIS-33;
RP HIS-40 AND HIS-179.
RC STRAIN=ATCC 700922 / JCM 11081 / NRC-1;
RX PubMed=15115438; DOI=10.1042/bj20040153;
RA Ohtani N., Yanagawa H., Tomita M., Itaya M.;
RT "Identification of the first archaeal Type 1 RNase H gene from
RT Halobacterium sp. NRC-1: archaeal RNase HI can cleave an RNA-DNA
RT junction.";
RL Biochem. J. 381:795-802(2004).
RN [3]
RP COFACTOR, AND NUCLEIC ACID-BINDING.
RC STRAIN=ATCC 700922 / JCM 11081 / NRC-1;
RX DOI=10.1016/j.fob.2012.10.003;
RA Tannous E., Yokoyama K., You D.J., Koga Y., Kanaya S.;
RT "A dual role of divalent metal ions in catalysis and folding of RNase H1
RT from extreme halophilic archaeon Halobacterium sp. NRC-1.";
RL FEBS Open Bio 2:345-352(2012).
CC -!- FUNCTION: Nuclease that specifically degrades the RNA of RNA-DNA
CC hybrids; seems to act exonucleolytically on RNA/DNA hybrids.
CC Endonucleolytically removes RNA primers from the Okazaki fragments of
CC lagging strand synthesis on its own. Complements the temperature-
CC sensitive phenotype of an E.coli double rnhA/rnhB (RNase H) disruption
CC mutant. {ECO:0000269|PubMed:15115438}.
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:15115438};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:15115438, ECO:0000269|Ref.3};
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:15115438, ECO:0000269|Ref.3};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:15115438, ECO:0000269|Ref.3};
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Evidence={ECO:0000269|PubMed:15115438, ECO:0000269|Ref.3};
CC Note=Divalent cations; Mn(2+) and Mg(2+) are preferred over Co(2+) or
CC Ni(2+). Divalent cations are required for folding and substrate-
CC binding, while divalent cations and NaCl are required for maximal
CC protein stability. {ECO:0000269|PubMed:15115438, ECO:0000269|Ref.3};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the RNase H family. {ECO:0000305}.
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DR EMBL; AE004437; AAG18851.1; -; Genomic_DNA.
DR PIR; G84185; G84185.
DR RefSeq; WP_010902145.1; NC_002607.1.
DR PDB; 4E19; X-ray; 1.41 A; A/B=1-199.
DR PDB; 4NYN; X-ray; 1.41 A; A/B=1-199.
DR PDBsum; 4E19; -.
DR PDBsum; 4NYN; -.
DR AlphaFoldDB; Q9HSF6; -.
DR SMR; Q9HSF6; -.
DR STRING; 64091.VNG_0255C; -.
DR PaxDb; Q9HSF6; -.
DR DNASU; 1447160; -.
DR EnsemblBacteria; AAG18851; AAG18851; VNG_0255C.
DR GeneID; 5954339; -.
DR KEGG; hal:VNG_0255C; -.
DR PATRIC; fig|64091.14.peg.187; -.
DR HOGENOM; CLU_1375506_0_0_2; -.
DR InParanoid; Q9HSF6; -.
DR OMA; NTDHERW; -.
DR OrthoDB; 81085at2157; -.
DR PhylomeDB; Q9HSF6; -.
DR BRENDA; 3.1.13.2; 2559.
DR BRENDA; 3.1.26.4; 2552.
DR Proteomes; UP000000554; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0004527; F:exonuclease activity; 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; DNA-binding; Endonuclease; Exonuclease; Hydrolase;
KW Magnesium; Manganese; Metal-binding; Nuclease; Reference proteome;
KW RNA-binding.
FT CHAIN 1..199
FT /note="Ribonuclease HI"
FT /id="PRO_0000420869"
FT DOMAIN 66..197
FT /note="RNase H type-1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT REGION 1..68
FT /note="Not required for RNase H activity"
FT REGION 69..199
FT /note="As active as intact RNase H"
FT BINDING 75
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT BINDING 75
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT BINDING 75
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT BINDING 75
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT BINDING 115
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT BINDING 115
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT BINDING 139
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT BINDING 139
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT BINDING 189
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT BINDING 189
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00408"
FT MUTAGEN 29
FT /note="H->A: No loss of RNase H activity."
FT /evidence="ECO:0000269|PubMed:15115438"
FT MUTAGEN 33
FT /note="H->A: No loss of RNase H activity."
FT /evidence="ECO:0000269|PubMed:15115438"
FT MUTAGEN 40
FT /note="H->A: No loss of RNase H activity."
FT /evidence="ECO:0000269|PubMed:15115438"
FT MUTAGEN 71
FT /note="H->A: No loss of RNase H activity."
FT MUTAGEN 179
FT /note="H->A,W: No loss of RNase H activity."
FT /evidence="ECO:0000269|PubMed:15115438"
FT STRAND 69..80
FT /evidence="ECO:0007829|PDB:4E19"
FT STRAND 83..92
FT /evidence="ECO:0007829|PDB:4E19"
FT STRAND 98..109
FT /evidence="ECO:0007829|PDB:4E19"
FT HELIX 111..128
FT /evidence="ECO:0007829|PDB:4E19"
FT STRAND 132..139
FT /evidence="ECO:0007829|PDB:4E19"
FT HELIX 141..147
FT /evidence="ECO:0007829|PDB:4E19"
FT HELIX 156..170
FT /evidence="ECO:0007829|PDB:4E19"
FT STRAND 172..179
FT /evidence="ECO:0007829|PDB:4E19"
FT TURN 182..185
FT /evidence="ECO:0007829|PDB:4E19"
FT HELIX 186..197
FT /evidence="ECO:0007829|PDB:4E19"
SQ SEQUENCE 199 AA; 20981 MW; C29CB636384B8E97 CRC64;
MPVVECDIQT ARAALADAGA SFSDGNSEHE LWHADLGDAH AVAYADKLVV QGGSPTDITA
VVQPDRGGRV HAYFDGASRG NPGPAAVGWV LVSGDGGIVA EGGDTIGRAT NNQAEYDALI
AALEAAADFG FDDIELRGDS QLVEKQLTGA WDTNDPDLRR KRVRARELLT GFDDWSITHV
PRATNERADA LANEALDDA
