SLN13_RAT
ID SLN13_RAT Reviewed; 907 AA.
AC Q5U311; A0A096MJD4; A0A096MKD0;
DT 20-JUN-2018, integrated into UniProtKB/Swiss-Prot.
DT 07-DEC-2004, sequence version 1.
DT 03-AUG-2022, entry version 120.
DE RecName: Full=Schlafen family member 13 {ECO:0000305};
DE EC=3.1.-.- {ECO:0000269|PubMed:29563550};
DE AltName: Full=Ribonuclease S13 {ECO:0000303|PubMed:29563550};
DE Short=RNase S13 {ECO:0000303|PubMed:29563550};
DE AltName: Full=Schlafen-13 {ECO:0000305};
DE Short=Schlafen13 {ECO:0000303|PubMed:29563550};
DE Short=rSLFN13 {ECO:0000303|PubMed:29563550};
GN Name=Slfn13 {ECO:0000312|RGD:1359139};
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Brown Norway;
RX PubMed=15057822; DOI=10.1038/nature02426;
RA Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J.,
RA Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G.,
RA Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G.,
RA Morgan M., Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G.,
RA Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S.,
RA Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T.,
RA Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D.,
RA Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L.,
RA Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D.,
RA Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M.,
RA Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C.,
RA Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J.,
RA Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H.,
RA Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X.,
RA Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q.,
RA Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P.,
RA Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A.,
RA Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C.,
RA Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J.,
RA Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J.,
RA Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F.,
RA Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A.,
RA Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A.,
RA Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J.,
RA Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E.,
RA Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M.,
RA Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C.,
RA Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L.,
RA Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W.,
RA Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y.,
RA Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V.,
RA Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M.,
RA Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S.,
RA Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B.,
RA Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R.,
RA Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J.,
RA Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D.,
RA Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S.,
RA Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S.,
RA Mockrin S., Collins F.S.;
RT "Genome sequence of the Brown Norway rat yields insights into mammalian
RT evolution.";
RL Nature 428:493-521(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Kidney;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (3.18 ANGSTROMS) OF 14-353 IN COMPLEX WITH ZINC,
RP FUNCTION, COFACTOR, DOMAIN, ACTIVE SITE, AND MUTAGENESIS OF ASP-34; LYS-38;
RP ARG-39; LYS-42; GLU-47; GLU-84; GLU-96; GLU-146; GLU-193; GLU-205; GLU-210;
RP ARG-217; GLU-221; LYS-224; GLU-229; GLU-249; ASP-259; LYS-276; HIS-281;
RP CYS-283; CYS-318 AND GLU-323.
RX PubMed=29563550; DOI=10.1038/s41467-018-03544-x;
RA Yang J.Y., Deng X.Y., Li Y.S., Ma X.C., Feng J.X., Yu B., Chen Y.,
RA Luo Y.L., Wang X., Chen M.L., Fang Z.X., Zheng F.X., Li Y.P., Zhong Q.,
RA Kang T.B., Song L.B., Xu R.H., Zeng M.S., Chen W., Zhang H., Xie W.,
RA Gao S.;
RT "Structure of Schlafen13 reveals a new class of tRNA/rRNA- targeting RNase
RT engaged in translational control.";
RL Nat. Commun. 9:1165-1165(2018).
CC -!- FUNCTION: Endoribonuclease that cleaves tRNAs and rRNAs
CC (PubMed:29563550). Cleaves tRNAs 11 nucleotides from the 3'-terminus at
CC the acceptor stem (PubMed:29563550). Does not act on tRNA(Sec)
CC (PubMed:29563550). {ECO:0000269|PubMed:29563550}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:29563550};
CC Note=Can also use Mn(2+). {ECO:0000269|PubMed:29563550};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q68D06}.
CC -!- DOMAIN: Shows a pseudo-dimeric U-pillow-shaped architecture of the
CC SLFN13 N'-domain that may clamp base-paired RNAs.
CC {ECO:0000269|PubMed:29563550}.
CC -!- SIMILARITY: Belongs to the Schlafen family. Subgroup III subfamily.
CC {ECO:0000305}.
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DR EMBL; AC128859; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC085777; AAH85777.1; -; mRNA.
DR RefSeq; NP_001013992.1; NM_001013970.1.
DR RefSeq; XP_006247061.1; XM_006246999.3.
DR RefSeq; XP_008766251.1; XM_008768029.2.
DR RefSeq; XP_008766252.1; XM_008768030.1.
DR RefSeq; XP_008766253.1; XM_008768031.2.
DR RefSeq; XP_008766254.1; XM_008768032.2.
DR PDB; 5YD0; X-ray; 3.18 A; A/B/C/D=14-353.
DR PDBsum; 5YD0; -.
DR AlphaFoldDB; Q5U311; -.
DR SMR; Q5U311; -.
DR STRING; 10116.ENSRNOP00000067903; -.
DR jPOST; Q5U311; -.
DR PaxDb; Q5U311; -.
DR PRIDE; Q5U311; -.
DR Ensembl; ENSRNOT00000076618; ENSRNOP00000067903; ENSRNOG00000021412.
DR GeneID; 303378; -.
DR KEGG; rno:303378; -.
DR CTD; 146857; -.
DR RGD; 1359139; Slfn13.
DR eggNOG; ENOG502QWKG; Eukaryota.
DR GeneTree; ENSGT00410000025651; -.
DR HOGENOM; CLU_1536072_0_0_1; -.
DR InParanoid; Q5U311; -.
DR OMA; TKQQGSC; -.
DR OrthoDB; 211385at2759; -.
DR PhylomeDB; Q5U311; -.
DR TreeFam; TF337168; -.
DR PRO; PR:Q5U311; -.
DR Proteomes; UP000002494; Chromosome 10.
DR Bgee; ENSRNOG00000021412; Expressed in spleen and 18 other tissues.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0005634; C:nucleus; ISO:RGD.
DR GO; GO:0090734; C:site of DNA damage; ISO:RGD.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; ISO:RGD.
DR GO; GO:0004521; F:endoribonuclease activity; IDA:UniProtKB.
DR GO; GO:0000049; F:tRNA binding; ISO:RGD.
DR GO; GO:0008270; F:zinc ion binding; IDA:UniProtKB.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; ISO:RGD.
DR GO; GO:0051607; P:defense response to virus; ISO:RGD.
DR GO; GO:0008156; P:negative regulation of DNA replication; ISO:RGD.
DR GO; GO:2000134; P:negative regulation of G1/S transition of mitotic cell cycle; ISO:RGD.
DR GO; GO:0010942; P:positive regulation of cell death; ISO:RGD.
DR GO; GO:0043111; P:replication fork arrest; ISO:RGD.
DR GO; GO:0016075; P:rRNA catabolic process; IDA:UniProtKB.
DR GO; GO:0016078; P:tRNA catabolic process; IDA:UniProtKB.
DR Gene3D; 3.30.950.30; -; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR029684; Schlafen.
DR InterPro; IPR007421; Schlafen_AlbA_2_dom.
DR InterPro; IPR038461; Schlafen_AlbA_2_dom_sf.
DR InterPro; IPR018647; SLFN_3-like_DNA/RNA_helicase.
DR PANTHER; PTHR12155; PTHR12155; 1.
DR Pfam; PF04326; AlbA_2; 1.
DR Pfam; PF09848; DUF2075; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cytoplasm; Endonuclease; Hydrolase; Magnesium;
KW Metal-binding; Nuclease; Nucleotide-binding; Reference proteome; Zinc.
FT CHAIN 1..907
FT /note="Schlafen family member 13"
FT /id="PRO_0000444606"
FT REGION 1..353
FT /note="N'-domain region"
FT /evidence="ECO:0000303|PubMed:29563550"
FT ACT_SITE 205
FT /evidence="ECO:0000269|PubMed:29563550"
FT ACT_SITE 210
FT /evidence="ECO:0000269|PubMed:29563550"
FT BINDING 281
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:29563550"
FT BINDING 283
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:29563550"
FT BINDING 318
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:29563550"
FT BINDING 604..611
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255"
FT MUTAGEN 34
FT /note="D->A: Reduced endoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:29563550"
FT MUTAGEN 38
FT /note="K->A: Reduced endoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:29563550"
FT MUTAGEN 39
FT /note="R->A: Reduced endoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:29563550"
FT MUTAGEN 42
FT /note="K->A: Reduced endoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:29563550"
FT MUTAGEN 47
FT /note="E->A: Reduced endoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:29563550"
FT MUTAGEN 84
FT /note="E->A: Reduced endoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:29563550"
FT MUTAGEN 96
FT /note="E->A: Reduced endoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:29563550"
FT MUTAGEN 146
FT /note="E->A: Reduced endoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:29563550"
FT MUTAGEN 193
FT /note="E->A: Reduced endoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:29563550"
FT MUTAGEN 205
FT /note="E->A: Abolished endoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:29563550"
FT MUTAGEN 210
FT /note="E->A: Abolished endoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:29563550"
FT MUTAGEN 217
FT /note="R->A: Reduced endoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:29563550"
FT MUTAGEN 221
FT /note="E->A: Reduced endoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:29563550"
FT MUTAGEN 224
FT /note="K->A: Reduced endoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:29563550"
FT MUTAGEN 229
FT /note="E->A: Reduced endoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:29563550"
FT MUTAGEN 249
FT /note="E->A: Reduced endoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:29563550"
FT MUTAGEN 259
FT /note="D->A: Reduced endoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:29563550"
FT MUTAGEN 276
FT /note="K->A: Reduced endoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:29563550"
FT MUTAGEN 281
FT /note="H->A: Renders the protein insoluble."
FT /evidence="ECO:0000269|PubMed:29563550"
FT MUTAGEN 283
FT /note="C->A: Renders the protein insoluble."
FT /evidence="ECO:0000269|PubMed:29563550"
FT MUTAGEN 318
FT /note="C->A: Renders the protein insoluble."
FT /evidence="ECO:0000269|PubMed:29563550"
FT MUTAGEN 323
FT /note="E->A: Reduced endoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:29563550"
FT STRAND 17..23
FT /evidence="ECO:0007829|PDB:5YD0"
FT HELIX 27..31
FT /evidence="ECO:0007829|PDB:5YD0"
FT HELIX 35..53
FT /evidence="ECO:0007829|PDB:5YD0"
FT TURN 54..56
FT /evidence="ECO:0007829|PDB:5YD0"
FT STRAND 58..66
FT /evidence="ECO:0007829|PDB:5YD0"
FT HELIX 67..69
FT /evidence="ECO:0007829|PDB:5YD0"
FT HELIX 76..85
FT /evidence="ECO:0007829|PDB:5YD0"
FT HELIX 91..93
FT /evidence="ECO:0007829|PDB:5YD0"
FT STRAND 95..100
FT /evidence="ECO:0007829|PDB:5YD0"
FT STRAND 103..108
FT /evidence="ECO:0007829|PDB:5YD0"
FT HELIX 144..158
FT /evidence="ECO:0007829|PDB:5YD0"
FT HELIX 180..183
FT /evidence="ECO:0007829|PDB:5YD0"
FT HELIX 187..190
FT /evidence="ECO:0007829|PDB:5YD0"
FT STRAND 193..196
FT /evidence="ECO:0007829|PDB:5YD0"
FT STRAND 207..212
FT /evidence="ECO:0007829|PDB:5YD0"
FT HELIX 219..236
FT /evidence="ECO:0007829|PDB:5YD0"
FT STRAND 240..246
FT /evidence="ECO:0007829|PDB:5YD0"
FT STRAND 248..250
FT /evidence="ECO:0007829|PDB:5YD0"
FT STRAND 256..258
FT /evidence="ECO:0007829|PDB:5YD0"
FT HELIX 263..275
FT /evidence="ECO:0007829|PDB:5YD0"
FT STRAND 282..284
FT /evidence="ECO:0007829|PDB:5YD0"
FT STRAND 291..313
FT /evidence="ECO:0007829|PDB:5YD0"
FT STRAND 317..320
FT /evidence="ECO:0007829|PDB:5YD0"
FT STRAND 322..324
FT /evidence="ECO:0007829|PDB:5YD0"
FT STRAND 328..331
FT /evidence="ECO:0007829|PDB:5YD0"
FT TURN 332..334
FT /evidence="ECO:0007829|PDB:5YD0"
FT STRAND 335..338
FT /evidence="ECO:0007829|PDB:5YD0"
FT HELIX 341..348
FT /evidence="ECO:0007829|PDB:5YD0"
SQ SEQUENCE 907 AA; 103655 MW; 6D5D6D7714F488AB CRC64;
MEIHPSLVVE PSYPDLIIHA GEVTLGEKDR NKMDSKKKRL EKARITEAAC ALLNSGGGVI
VMQMSNKSEH PVEMGLDLET SLRELIPSSD LQAFIETKQQ GDLFYIFVKS WSCSPKDGST
KPRICSLSSS LYCRSLTSKL PLDSKETFEF LERKKTCVKG SLTDGKGPPA KIPRLMYQND
LESNPAFEIF QSERLEYGQR LPFSESASIE FKQFSTRRAH EYIKSVIPEY ISAFANTQGG
YLLFGVDDES KRVLGCPKDN VDRDSLKAVV NEAISKLPVF HFCSSKEKVS YKTRVIDVFK
EGNLYGYLCV IKVERFCCAV FSEAPISWMA DKENGVYSLN TEKWVRMMVD IGPEAASSKQ
SSLDDLSKDF ECQLSLSNSP PHCRPVYSKK GLEHKGDLQK RLFQVSADCF KYTPESLWRE
LCSQHERLEN LISQQMCSFS CGLLILSRSW AVDLNLEGKQ GVICDALLIA ENSPPTLYTI
LEEQDELGQD YCTRTAFTLK QKLVNTGGYT GRVCVMTKVL CLSSQNNIET NGNSVSLIDY
PRSYNLANIQ EMEDLLQALV IVLLNFSSFL SDQLGCEILN LLTVQQYEIL SKSLHKTRKL
FVHGMPGSGK TIIAMKIMEK IKNTFHCERD SILYICENQL LRDFIRAKNV CRAVTRKTFM
TPNFEVEKIQ HIIVDEAQNF RTENGDWYMK AKRITQRMKT CPQIFWIFLD YFQTSHQKES
GLPDFLHQYP KEELTKVVRN ADKIAEFLQK ISEKIRSNPP PIIPRESLNM VCEFNWSQGV
SGTCKLLTSL GLEQMARYVA ERCYFFLKNG YSAQDIAVLF STEDEKDNNE DMFLREIRNR
TSQIDDAYHL YMFDSIRRFS GLERSIVFGI DPRTAEKSIF HNLMLCLASR ARKHLYILSK
VPNPFNF
