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Ribonuclease H1 (RNase H1) (EC 3.1.26.4) (Ribonuclease H type II)

 RNH1_HUMAN              Reviewed;         286 AA.
O60930; B3KQU4; O60523; O60857; Q57Z93; Q5U0C1; Q6FHD4;
27-APR-2001, integrated into UniProtKB/Swiss-Prot.
27-APR-2001, sequence version 2.
28-MAR-2018, entry version 168.
RecName: Full=Ribonuclease H1;
Short=RNase H1;
EC=3.1.26.4;
AltName: Full=Ribonuclease H type II;
Name=RNASEH1; Synonyms=RNH1;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [MRNA], AND VARIANT PHE-4.
PubMed=9799596; DOI=10.1006/geno.1998.5497;
Cerritelli S.M., Crouch R.J.;
"Cloning, expression, and mapping of ribonucleases H of human and
mouse related to bacterial RNase HI.";
Genomics 53:300-307(1998).
[2]
NUCLEOTIDE SEQUENCE [MRNA].
PubMed=9512096; DOI=10.1089/oli.1.1998.8.53;
Wu H., Lima W.F., Crooke S.T.;
"Molecular cloning and expression of cDNA for human RNase H.";
Antisense Nucleic Acid Drug Dev. 8:53-61(1998).
[3]
NUCLEOTIDE SEQUENCE [MRNA].
PubMed=9894807; DOI=10.1515/bchm.1998.379.12.1407;
Frank P., Braunshofer-Reiter C., Poltl A., Holzmann K.;
"Cloning, subcellular localization and functional expression of human
RNase HII.";
Biol. Chem. 379:1407-1412(1998).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Halleck A., Ebert L., Mkoundinya M., Schick M., Eisenstein S.,
Neubert P., Kstrang K., Schatten R., Shen B., Henze S., Mar W.,
Korn B., Zuo D., Hu Y., LaBaer J.;
"Cloning of human full open reading frames in Gateway(TM) system entry
vector (pDONR201).";
Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases.
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], AND VARIANT PHE-4.
Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S.,
Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y.,
Phelan M., Farmer A.;
"Cloning of human full-length CDSs in BD Creator(TM) system donor
vector.";
Submitted (OCT-2004) to the EMBL/GenBank/DDBJ databases.
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
TISSUE=Ovary;
PubMed=16303743; DOI=10.1093/dnares/12.2.117;
Otsuki T., Ota T., Nishikawa T., Hayashi K., Suzuki Y., Yamamoto J.,
Wakamatsu A., Kimura K., Sakamoto K., Hatano N., Kawai Y., Ishii S.,
Saito K., Kojima S., Sugiyama T., Ono T., Okano K., Yoshikawa Y.,
Aotsuka S., Sasaki N., Hattori A., Okumura K., Nagai K., Sugano S.,
Isogai T.;
"Signal sequence and keyword trap in silico for selection of full-
length human cDNAs encoding secretion or membrane proteins from oligo-
capped cDNA libraries.";
DNA Res. 12:117-126(2005).
[7]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=15815621; DOI=10.1038/nature03466;
Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H.,
Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M.,
Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E.,
Kremitzki C., Oddy L., Du H., Sun H., Bradshaw-Cordum H., Ali J.,
Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C.,
Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J.,
Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A.,
Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K.,
Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M.,
Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K.,
McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C.,
Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N.,
Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M.,
Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E.,
Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P.,
Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A.,
Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A.,
Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T.,
Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D.,
Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X.,
McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C.,
Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S.,
Miller W., Eichler E.E., Bork P., Suyama M., Torrents D.,
Waterston R.H., Wilson R.K.;
"Generation and annotation of the DNA sequences of human chromosomes 2
and 4.";
Nature 434:724-731(2005).
[8]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L.,
Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R.,
Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V.,
Hannenhalli S., Turner R., Yooseph S., Lu F., Nusskern D.R.,
Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H.,
Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G.,
Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W.,
Venter J.C.;
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
[9]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
TISSUE=Lung;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[10]
CHARACTERIZATION.
PubMed=10497183; DOI=10.1074/jbc.274.40.28270;
Wu H., Lima W.F., Crooke S.T.;
"Properties of cloned and expressed human RNase H1.";
J. Biol. Chem. 274:28270-28278(1999).
[11]
FUNCTION.
PubMed=21700224; DOI=10.1016/j.molcel.2011.04.026;
Skourti-Stathaki K., Proudfoot N.J., Gromak N.;
"Human senataxin resolves RNA/DNA hybrids formed at transcriptional
pause sites to promote Xrn2-dependent termination.";
Mol. Cell 42:794-805(2011).
[12]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=21406692; DOI=10.1126/scisignal.2001570;
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J.,
Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V.,
Blagoev B.;
"System-wide temporal characterization of the proteome and
phosphoproteome of human embryonic stem cell differentiation.";
Sci. Signal. 4:RS3-RS3(2011).
[13]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Erythroleukemia;
PubMed=23186163; DOI=10.1021/pr300630k;
Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J.,
Mohammed S.;
"Toward a comprehensive characterization of a human cancer cell
phosphoproteome.";
J. Proteome Res. 12:260-271(2013).
[14]
INVOLVEMENT IN PEOB2, VARIANTS PEOB2 ILE-142 AND VAL-185, AND
CHARACTERIZATION OF VARIANTS PEOB2 ILE-142 AND VAL-185.
PubMed=26094573; DOI=10.1016/j.ajhg.2015.05.013;
Reyes A., Melchionda L., Nasca A., Carrara F., Lamantea E.,
Zanolini A., Lamperti C., Fang M., Zhang J., Ronchi D., Bonato S.,
Fagiolari G., Moggio M., Ghezzi D., Zeviani M.;
"RNASEH1 mutations impair mtDNA replication and cause adult-onset
mitochondrial encephalomyopathy.";
Am. J. Hum. Genet. 97:186-193(2015).
-!- FUNCTION: Endonuclease that specifically degrades the RNA of RNA-
DNA hybrids (PubMed:10497183). Plays a role in RNA polymerase II
(RNAp II) transcription termination by degrading R-loop RNA-DNA
hybrid formation at G-rich pause sites located downstream of the
poly(A) site and behind the elongating RNAp II (PubMed:21700224).
{ECO:0000269|PubMed:10497183, ECO:0000269|PubMed:21700224}.
-!- CATALYTIC ACTIVITY: Endonucleolytic cleavage to 5'-
phosphomonoester. {ECO:0000255|PROSITE-ProRule:PRU00408}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Note=Binds 1 Mg(2+) ion per subunit. May bind a second metal ion
at a regulatory site, or after substrate binding.;
-!- ENZYME REGULATION: In the presence of magnesium, manganese is
inhibitory.
-!- SUBUNIT: Monomer. {ECO:0000305}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
-!- TISSUE SPECIFICITY: Ubiquitous.
-!- DISEASE: Progressive external ophthalmoplegia with mitochondrial
DNA deletions, autosomal recessive 2 (PEOB2) [MIM:616479]: A form
of progressive external ophthalmoplegia, a mitochondrial myopathy
characterized by progressive paralysis of the levator palpebrae,
orbicularis oculi, and extraocular muscles. PEOB2 patients
manifest exercise intolerance, muscle weakness, and signs and
symptoms of spinocerebellar ataxia, such as impaired gait and
dysarthria. Some patients may have respiratory insufficiency.
{ECO:0000269|PubMed:26094573}. Note=The disease is caused by
mutations affecting the gene represented in this entry.
-!- SIMILARITY: Belongs to the RNase H family. {ECO:0000305}.
-!- WEB RESOURCE: Name=Wikipedia; Note=RNase H entry;
URL="https://en.wikipedia.org/wiki/RNase_H";
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EMBL; AF048995; AAC78564.1; -; mRNA.
EMBL; AF048994; AAC78563.1; -; mRNA.
EMBL; AF039652; AAC09261.1; -; mRNA.
EMBL; AJ224117; CAA11835.1; -; mRNA.
EMBL; CR541820; CAG46619.1; -; mRNA.
EMBL; BT019670; AAV38476.1; -; mRNA.
EMBL; AK075490; BAG52156.1; -; mRNA.
EMBL; AC108488; AAX82026.1; -; Genomic_DNA.
EMBL; CH471053; EAX01061.1; -; Genomic_DNA.
EMBL; BC002973; AAH02973.1; -; mRNA.
CCDS; CCDS1647.1; -.
RefSeq; NP_002927.2; NM_002936.4.
UniGene; Hs.568006; -.
PDB; 2QK9; X-ray; 2.55 A; A=136-286.
PDB; 2QKB; X-ray; 2.40 A; A/B=136-286.
PDB; 2QKK; X-ray; 3.20 A; A/B/E/F/I/J/M/N/R/S/W=136-286.
PDB; 3BSU; X-ray; 2.10 A; A/B/C/F/G/H=27-76.
PDBsum; 2QK9; -.
PDBsum; 2QKB; -.
PDBsum; 2QKK; -.
PDBsum; 3BSU; -.
ProteinModelPortal; O60930; -.
SMR; O60930; -.
BioGrid; 128882; 13.
IntAct; O60930; 4.
MINT; O60930; -.
STRING; 9606.ENSP00000313350; -.
BindingDB; O60930; -.
ChEMBL; CHEMBL5893; -.
iPTMnet; O60930; -.
PhosphoSitePlus; O60930; -.
EPD; O60930; -.
MaxQB; O60930; -.
PaxDb; O60930; -.
PeptideAtlas; O60930; -.
PRIDE; O60930; -.
DNASU; 246243; -.
Ensembl; ENST00000315212; ENSP00000313350; ENSG00000171865.
GeneID; 246243; -.
KEGG; hsa:246243; -.
UCSC; uc002qxt.5; human.
CTD; 246243; -.
DisGeNET; 246243; -.
EuPathDB; HostDB:ENSG00000171865.9; -.
GeneCards; RNASEH1; -.
H-InvDB; HIX0039191; -.
HGNC; HGNC:18466; RNASEH1.
HPA; HPA043037; -.
MalaCards; RNASEH1; -.
MIM; 604123; gene.
MIM; 616479; phenotype.
neXtProt; NX_O60930; -.
OpenTargets; ENSG00000171865; -.
PharmGKB; PA38543; -.
eggNOG; KOG3752; Eukaryota.
eggNOG; COG0328; LUCA.
GeneTree; ENSGT00390000003466; -.
HOGENOM; HOG000040465; -.
HOVERGEN; HBG002135; -.
InParanoid; O60930; -.
KO; K03469; -.
OMA; ELWYGLY; -.
OrthoDB; EOG091G0RCI; -.
PhylomeDB; O60930; -.
TreeFam; TF313356; -.
ChiTaRS; RNASEH1; human.
EvolutionaryTrace; O60930; -.
GeneWiki; RNASEH1; -.
GenomeRNAi; 246243; -.
PRO; PR:O60930; -.
Proteomes; UP000005640; Chromosome 2.
Bgee; ENSG00000171865; -.
CleanEx; HS_RNASEH1; -.
CleanEx; HS_RNH1; -.
ExpressionAtlas; O60930; baseline and differential.
Genevisible; O60930; HS.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0005634; C:nucleus; IBA:GO_Central.
GO; GO:0000287; F:magnesium ion binding; IEA:InterPro.
GO; GO:0003676; F:nucleic acid binding; TAS:ProtInc.
GO; GO:0004540; F:ribonuclease activity; TAS:ProtInc.
GO; GO:0003723; F:RNA binding; TAS:ProtInc.
GO; GO:0004523; F:RNA-DNA hybrid ribonuclease activity; IDA:UniProtKB.
GO; GO:0043137; P:DNA replication, removal of RNA primer; IBA:GO_Central.
GO; GO:0006401; P:RNA catabolic process; TAS:ProtInc.
Gene3D; 3.30.420.10; -; 1.
Gene3D; 3.40.970.10; -; 1.
InterPro; IPR009027; Ribosomal_L9/RNase_H1_N.
InterPro; IPR017067; RNase_H1_euk.
InterPro; IPR011320; RNase_H1_N.
InterPro; IPR037056; RNase_H1_N_sf.
InterPro; IPR012337; RNaseH-like_sf.
InterPro; IPR002156; RNaseH_domain.
InterPro; IPR036397; RNaseH_sf.
Pfam; PF01693; Cauli_VI; 1.
Pfam; PF00075; RNase_H; 1.
PIRSF; PIRSF036852; Ribonuclease_H1_euk; 1.
SUPFAM; SSF53098; SSF53098; 1.
SUPFAM; SSF55658; SSF55658; 1.
PROSITE; PS50879; RNASE_H; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; Disease mutation;
Endonuclease; Hydrolase; Magnesium; Metal-binding; Nuclease;
Polymorphism; Primary mitochondrial disease;
Progressive external ophthalmoplegia; Reference proteome.
CHAIN 1 286 Ribonuclease H1.
/FTId=PRO_0000195433.
DOMAIN 136 282 RNase H. {ECO:0000255|PROSITE-
ProRule:PRU00408}.
METAL 145 145 Magnesium 1. {ECO:0000255|PROSITE-
ProRule:PRU00408}.
METAL 145 145 Magnesium 2. {ECO:0000255|PROSITE-
ProRule:PRU00408}.
METAL 186 186 Magnesium 1. {ECO:0000255|PROSITE-
ProRule:PRU00408}.
METAL 210 210 Magnesium 1. {ECO:0000255|PROSITE-
ProRule:PRU00408}.
METAL 274 274 Magnesium 2. {ECO:0000255|PROSITE-
ProRule:PRU00408}.
VARIANT 4 4 L -> F (in dbSNP:rs1136545).
{ECO:0000269|PubMed:9799596,
ECO:0000269|Ref.5}.
/FTId=VAR_023469.
VARIANT 142 142 V -> I (in PEOB2; has partial residual
endonuclease activity;
dbSNP:rs766294940).
{ECO:0000269|PubMed:26094573}.
/FTId=VAR_074561.
VARIANT 185 185 A -> V (in PEOB2; has partial residual
endonuclease activity;
dbSNP:rs1057517675).
{ECO:0000269|PubMed:26094573}.
/FTId=VAR_074562.
CONFLICT 24 24 G -> R (in Ref. 5; AAV38476).
{ECO:0000305}.
CONFLICT 33 33 R -> K (in Ref. 4; CAG46619).
{ECO:0000305}.
CONFLICT 68 68 W -> R (in Ref. 5; AAV38476).
{ECO:0000305}.
CONFLICT 89 89 Q -> R (in Ref. 3; CAA11835).
{ECO:0000305}.
CONFLICT 136 136 M -> I (in Ref. 4; CAG46619).
{ECO:0000305}.
CONFLICT 223 223 Q -> R (in Ref. 3; CAA11835).
{ECO:0000305}.
STRAND 28 36 {ECO:0000244|PDB:3BSU}.
STRAND 38 42 {ECO:0000244|PDB:3BSU}.
HELIX 43 50 {ECO:0000244|PDB:3BSU}.
STRAND 57 63 {ECO:0000244|PDB:3BSU}.
HELIX 64 72 {ECO:0000244|PDB:3BSU}.
STRAND 139 149 {ECO:0000244|PDB:2QKB}.
TURN 150 152 {ECO:0000244|PDB:2QKB}.
STRAND 153 155 {ECO:0000244|PDB:2QKB}.
STRAND 157 163 {ECO:0000244|PDB:2QKB}.
STRAND 172 175 {ECO:0000244|PDB:2QKB}.
HELIX 182 199 {ECO:0000244|PDB:2QKB}.
STRAND 204 210 {ECO:0000244|PDB:2QKB}.
HELIX 212 219 {ECO:0000244|PDB:2QKB}.
HELIX 221 226 {ECO:0000244|PDB:2QKB}.
TURN 227 229 {ECO:0000244|PDB:2QKB}.
STRAND 235 237 {ECO:0000244|PDB:2QKB}.
HELIX 241 251 {ECO:0000244|PDB:2QKB}.
STRAND 255 260 {ECO:0000244|PDB:2QKB}.
STRAND 263 265 {ECO:0000244|PDB:2QKK}.
HELIX 268 281 {ECO:0000244|PDB:2QKB}.
SEQUENCE 286 AA; 32064 MW; 400FE04E7E85CA6A CRC64;
MSWLLFLAHR VALAALPCRR GSRGFGMFYA VRRGRKTGVF LTWNECRAQV DRFPAARFKK
FATEDEAWAF VRKSASPEVS EGHENQHGQE SEAKASKRLR EPLDGDGHES AEPYAKHMKP
SVEPAPPVSR DTFSYMGDFV VVYTDGCCSS NGRRRPRAGI GVYWGPGHPL NVGIRLPGRQ
TNQRAEIHAA CKAIEQAKTQ NINKLVLYTD SMFTINGITN WVQGWKKNGW KTSAGKEVIN
KEDFVALERL TQGMDIQWMH VPGHSGFIGN EEADRLAREG AKQSED


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