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ATP-dependent RNA helicase DOB1 (EC 3.6.4.13) (mRNA transport regulator MTR4)

 MTR4_YEAST              Reviewed;        1073 AA.
P47047; D6VWD3;
01-FEB-1996, integrated into UniProtKB/Swiss-Prot.
01-FEB-1996, sequence version 1.
27-SEP-2017, entry version 160.
RecName: Full=ATP-dependent RNA helicase DOB1;
EC=3.6.4.13;
AltName: Full=mRNA transport regulator MTR4;
Name=MTR4; Synonyms=DOB1; OrderedLocusNames=YJL050W; ORFNames=J1158;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=8641269;
Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N.,
Chuat J.-C., Coster F., Cziepluch C., de Haan M., Domdey H.,
Durand P., Entian K.-D., Gatius M., Goffeau A., Grivell L.A.,
Hennemann A., Herbert C.J., Heumann K., Hilger F., Hollenberg C.P.,
Huang M.-E., Jacq C., Jauniaux J.-C., Katsoulou C., Kirchrath L.,
Kleine K., Kordes E., Koetter P., Liebl S., Louis E.J., Manus V.,
Mewes H.-W., Miosga T., Obermaier B., Perea J., Pohl T.M.,
Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rasmussen S.W.,
Rose M., Rossau R., Schaaff-Gerstenschlaeger I., Smits P.H.M.,
Scarcez T., Soriano N., To Van D., Tzermia M., Van Broekhoven A.,
Vandenbol M., Wedler H., von Wettstein D., Wambutt R., Zagulski M.,
Zollner A., Karpfinger-Hartl L.;
"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome
X.";
EMBO J. 15:2031-2049(1996).
[2]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[3]
CHARACTERIZATION.
PubMed=8756671; DOI=10.1128/MCB.16.9.5139;
Liang S., Hitomi M., Hu Y.-H., Liu Y., Tartakoff A.M.;
"A DEAD-box-family protein is required for nucleocytoplasmic transport
of yeast mRNA.";
Mol. Cell. Biol. 16:5139-5146(1996).
[4]
CHARACTERIZATION.
PubMed=9463390; DOI=10.1093/emboj/17.4.1128;
de la Cruz J., Kressler D., Tollervey D., Linder P.;
"Dob1p (Mtr4p) is a putative ATP-dependent RNA helicase required for
the 3' end formation of 5.8S rRNA in Saccharomyces cerevisiae.";
EMBO J. 17:1128-1140(1998).
[5]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[6]
IDENTIFICATION IN THE TRF4 COMPLEX, IDENTIFICATION BY MASS
SPECTROMETRY, AND FUNCTION OF THE TRF4 COMPLEX.
PubMed=15828860; DOI=10.1371/journal.pbio.0030189;
Vanacova S., Wolf J., Martin G., Blank D., Dettwiler S., Friedlein A.,
Langen H., Keith G., Keller W.;
"A new yeast poly(A) polymerase complex involved in RNA quality
control.";
PLoS Biol. 3:986-997(2005).
[7]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-34, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=17287358; DOI=10.1073/pnas.0607084104;
Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L.,
Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.;
"Analysis of phosphorylation sites on proteins from Saccharomyces
cerevisiae by electron transfer dissociation (ETD) mass
spectrometry.";
Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
[8]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-84 AND SER-843, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=18407956; DOI=10.1074/mcp.M700468-MCP200;
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
"A multidimensional chromatography technology for in-depth
phosphoproteome analysis.";
Mol. Cell. Proteomics 7:1389-1396(2008).
[9]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-84, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19779198; DOI=10.1126/science.1172867;
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
"Global analysis of Cdk1 substrate phosphorylation sites provides
insights into evolution.";
Science 325:1682-1686(2009).
-!- FUNCTION: ATP-dependent RNA helicase required for the 3'-end
formation of 5.8S RNA. Cofactor for the exosome complex that
unwinds secondary structure in pre-rRNA. Required for
nucleocytoplasmic transport of mRNA. May serve as a chaperone
which translocates or normalizes the structure of mRNAs in
preparation for export. Component of the TRAMP complex which has a
poly(A) RNA polymerase activity and is involved in a post-
transcriptional quality control mechanism limiting inappropriate
expression of genetic information. Polyadenylation is required for
the degradative activity of the exosome on several of its nuclear
RNA substrates. {ECO:0000269|PubMed:15828860}.
-!- CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
-!- SUBUNIT: Component of the TRAMP complex (also called TRF4 complex)
composed of at least HUL4, MTR4, PAP2/TRF4 and either AIR1 or
AIR2. {ECO:0000269|PubMed:15828860}.
-!- INTERACTION:
Self; NbExp=2; IntAct=EBI-11592, EBI-11592;
P40507:AIR1; NbExp=7; IntAct=EBI-11592, EBI-25083;
Q12476:AIR2; NbExp=23; IntAct=EBI-11592, EBI-31475;
Q03532:HAS1; NbExp=3; IntAct=EBI-11592, EBI-8170;
P38074:HMT1; NbExp=2; IntAct=EBI-11592, EBI-8394;
Q12080:NOP53; NbExp=5; IntAct=EBI-11592, EBI-29395;
P53632:PAP2; NbExp=26; IntAct=EBI-11592, EBI-19517;
P53131:PRP43; NbExp=7; IntAct=EBI-11592, EBI-505;
P36160:RPF2; NbExp=2; IntAct=EBI-11592, EBI-15881;
P25359:RRP43; NbExp=5; IntAct=EBI-11592, EBI-1773;
Q12149:RRP6; NbExp=2; IntAct=EBI-11592, EBI-1782;
P32585:SRB5; NbExp=3; IntAct=EBI-11592, EBI-18032;
P18851:STE4; NbExp=4; IntAct=EBI-11592, EBI-7390;
P48561:TRF5; NbExp=10; IntAct=EBI-11592, EBI-19525;
Q12159:YRA1; NbExp=17; IntAct=EBI-11592, EBI-29516;
-!- SUBCELLULAR LOCATION: Nucleus.
-!- MISCELLANEOUS: Present with 12500 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the helicase family. SKI2 subfamily.
{ECO:0000305}.
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EMBL; Z49325; CAA89341.1; -; Genomic_DNA.
EMBL; BK006943; DAA08749.1; -; Genomic_DNA.
PIR; S56822; S56822.
RefSeq; NP_012485.1; NM_001181483.1.
PDB; 2XGJ; X-ray; 2.90 A; A/B=81-1073.
PDB; 4QU4; X-ray; 3.39 A; A=1-1073.
PDB; 4U4C; X-ray; 2.40 A; A=81-1073.
PDB; 4WFD; X-ray; 2.40 A; C/F/I=1-19.
PDBsum; 2XGJ; -.
PDBsum; 4QU4; -.
PDBsum; 4U4C; -.
PDBsum; 4WFD; -.
ProteinModelPortal; P47047; -.
SMR; P47047; -.
BioGrid; 33705; 250.
DIP; DIP-6394N; -.
ELM; P47047; -.
IntAct; P47047; 62.
MINT; MINT-620894; -.
STRING; 4932.YJL050W; -.
iPTMnet; P47047; -.
MaxQB; P47047; -.
PRIDE; P47047; -.
EnsemblFungi; YJL050W; YJL050W; YJL050W.
GeneID; 853397; -.
KEGG; sce:YJL050W; -.
EuPathDB; FungiDB:YJL050W; -.
SGD; S000003586; MTR4.
GeneTree; ENSGT00820000127042; -.
HOGENOM; HOG000163047; -.
InParanoid; P47047; -.
KO; K12598; -.
OMA; NMLYRGS; -.
OrthoDB; EOG092C0MRM; -.
BioCyc; YEAST:G3O-31514-MONOMER; -.
BRENDA; 3.6.4.13; 984.
Reactome; R-SCE-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
EvolutionaryTrace; P47047; -.
PRO; PR:P47047; -.
Proteomes; UP000002311; Chromosome X.
GO; GO:0005730; C:nucleolus; IDA:SGD.
GO; GO:0005654; C:nucleoplasm; IEA:EnsemblPlants.
GO; GO:0005634; C:nucleus; IDA:SGD.
GO; GO:0031499; C:TRAMP complex; IDA:SGD.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0034459; F:ATP-dependent 3'-5' RNA helicase activity; IDA:SGD.
GO; GO:0016491; F:oxidoreductase activity; IEA:InterPro.
GO; GO:0008143; F:poly(A) binding; IDA:SGD.
GO; GO:0000467; P:exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
GO; GO:0043629; P:ncRNA polyadenylation; IDA:SGD.
GO; GO:0071031; P:nuclear mRNA surveillance of mRNA 3'-end processing; IMP:SGD.
GO; GO:0071042; P:nuclear polyadenylation-dependent mRNA catabolic process; IMP:SGD.
GO; GO:0071035; P:nuclear polyadenylation-dependent rRNA catabolic process; IMP:SGD.
GO; GO:0071038; P:nuclear polyadenylation-dependent tRNA catabolic process; IDA:SGD.
GO; GO:0071049; P:nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription; IGI:SGD.
GO; GO:0016973; P:poly(A)+ mRNA export from nucleus; IMP:SGD.
GO; GO:0071051; P:polyadenylation-dependent snoRNA 3'-end processing; IMP:SGD.
GO; GO:0016075; P:rRNA catabolic process; IMP:SGD.
GO; GO:0034475; P:U4 snRNA 3'-end processing; IMP:SGD.
GO; GO:0034476; P:U5 snRNA 3'-end processing; IMP:SGD.
InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
InterPro; IPR014001; Helicase_ATP-bd.
InterPro; IPR001650; Helicase_C.
InterPro; IPR027417; P-loop_NTPase.
InterPro; IPR011254; Prismane-like.
InterPro; IPR025696; rRNA_proc-arch_dom.
InterPro; IPR016438; Ski2.
InterPro; IPR012961; Ski2_C.
Pfam; PF00270; DEAD; 1.
Pfam; PF08148; DSHCT; 1.
Pfam; PF00271; Helicase_C; 1.
Pfam; PF13234; rRNA_proc-arch; 1.
PIRSF; PIRSF005198; Antiviral_helicase_SKI2; 1.
SMART; SM00487; DEXDc; 1.
SMART; SM01142; DSHCT; 1.
SMART; SM00490; HELICc; 1.
SUPFAM; SSF52540; SSF52540; 3.
SUPFAM; SSF56821; SSF56821; 1.
PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
PROSITE; PS51194; HELICASE_CTER; 1.
1: Evidence at protein level;
3D-structure; ATP-binding; Complete proteome; Helicase; Hydrolase;
Nucleotide-binding; Nucleus; Phosphoprotein; Reference proteome;
rRNA processing.
CHAIN 1 1073 ATP-dependent RNA helicase DOB1.
/FTId=PRO_0000102092.
DOMAIN 158 314 Helicase ATP-binding.
{ECO:0000255|PROSITE-ProRule:PRU00541}.
DOMAIN 393 597 Helicase C-terminal.
{ECO:0000255|PROSITE-ProRule:PRU00542}.
NP_BIND 171 178 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00541}.
MOTIF 262 265 DEVH box.
MOD_RES 34 34 Phosphothreonine.
{ECO:0000244|PubMed:17287358}.
MOD_RES 84 84 Phosphoserine.
{ECO:0000244|PubMed:18407956,
ECO:0000244|PubMed:19779198}.
MOD_RES 843 843 Phosphoserine.
{ECO:0000244|PubMed:18407956}.
HELIX 8 11 {ECO:0000244|PDB:4WFD}.
STRAND 81 94 {ECO:0000244|PDB:2XGJ}.
STRAND 100 102 {ECO:0000244|PDB:2XGJ}.
STRAND 119 124 {ECO:0000244|PDB:4U4C}.
HELIX 134 136 {ECO:0000244|PDB:4U4C}.
HELIX 152 162 {ECO:0000244|PDB:4U4C}.
STRAND 166 170 {ECO:0000244|PDB:4U4C}.
HELIX 173 175 {ECO:0000244|PDB:4U4C}.
HELIX 177 190 {ECO:0000244|PDB:4U4C}.
STRAND 194 201 {ECO:0000244|PDB:4U4C}.
HELIX 202 216 {ECO:0000244|PDB:4U4C}.
STRAND 219 222 {ECO:0000244|PDB:4U4C}.
STRAND 233 238 {ECO:0000244|PDB:4U4C}.
HELIX 239 247 {ECO:0000244|PDB:4U4C}.
HELIX 252 255 {ECO:0000244|PDB:4U4C}.
STRAND 256 261 {ECO:0000244|PDB:4U4C}.
HELIX 264 268 {ECO:0000244|PDB:4U4C}.
TURN 270 272 {ECO:0000244|PDB:4U4C}.
HELIX 273 282 {ECO:0000244|PDB:4U4C}.
STRAND 288 293 {ECO:0000244|PDB:4U4C}.
HELIX 299 310 {ECO:0000244|PDB:4U4C}.
STRAND 314 319 {ECO:0000244|PDB:4U4C}.
STRAND 326 332 {ECO:0000244|PDB:4U4C}.
STRAND 336 342 {ECO:0000244|PDB:4U4C}.
HELIX 350 361 {ECO:0000244|PDB:4U4C}.
HELIX 393 403 {ECO:0000244|PDB:4U4C}.
STRAND 408 412 {ECO:0000244|PDB:4U4C}.
STRAND 413 415 {ECO:0000244|PDB:4QU4}.
HELIX 416 426 {ECO:0000244|PDB:4U4C}.
STRAND 427 429 {ECO:0000244|PDB:4QU4}.
HELIX 434 448 {ECO:0000244|PDB:4U4C}.
HELIX 453 456 {ECO:0000244|PDB:4U4C}.
HELIX 459 462 {ECO:0000244|PDB:4U4C}.
HELIX 465 469 {ECO:0000244|PDB:4U4C}.
STRAND 472 475 {ECO:0000244|PDB:4U4C}.
STRAND 477 479 {ECO:0000244|PDB:4QU4}.
HELIX 481 492 {ECO:0000244|PDB:4U4C}.
STRAND 497 501 {ECO:0000244|PDB:4U4C}.
HELIX 503 507 {ECO:0000244|PDB:4U4C}.
STRAND 513 519 {ECO:0000244|PDB:4U4C}.
STRAND 521 524 {ECO:0000244|PDB:4U4C}.
STRAND 526 531 {ECO:0000244|PDB:4U4C}.
HELIX 534 541 {ECO:0000244|PDB:4U4C}.
TURN 547 549 {ECO:0000244|PDB:4U4C}.
STRAND 553 559 {ECO:0000244|PDB:4U4C}.
HELIX 565 572 {ECO:0000244|PDB:4U4C}.
HELIX 587 595 {ECO:0000244|PDB:4U4C}.
STRAND 596 598 {ECO:0000244|PDB:2XGJ}.
HELIX 601 607 {ECO:0000244|PDB:4U4C}.
HELIX 609 635 {ECO:0000244|PDB:4U4C}.
HELIX 642 664 {ECO:0000244|PDB:4U4C}.
HELIX 667 670 {ECO:0000244|PDB:4U4C}.
HELIX 671 673 {ECO:0000244|PDB:4U4C}.
STRAND 678 684 {ECO:0000244|PDB:4U4C}.
TURN 685 687 {ECO:0000244|PDB:4U4C}.
STRAND 688 700 {ECO:0000244|PDB:4U4C}.
HELIX 713 715 {ECO:0000244|PDB:4U4C}.
STRAND 716 727 {ECO:0000244|PDB:4U4C}.
HELIX 732 734 {ECO:0000244|PDB:4U4C}.
STRAND 755 763 {ECO:0000244|PDB:4U4C}.
HELIX 764 766 {ECO:0000244|PDB:4U4C}.
STRAND 767 774 {ECO:0000244|PDB:4U4C}.
HELIX 786 800 {ECO:0000244|PDB:4U4C}.
STRAND 801 803 {ECO:0000244|PDB:2XGJ}.
TURN 810 814 {ECO:0000244|PDB:4U4C}.
HELIX 819 837 {ECO:0000244|PDB:4U4C}.
HELIX 839 841 {ECO:0000244|PDB:4U4C}.
STRAND 843 845 {ECO:0000244|PDB:2XGJ}.
HELIX 847 871 {ECO:0000244|PDB:4U4C}.
HELIX 876 891 {ECO:0000244|PDB:4U4C}.
HELIX 903 909 {ECO:0000244|PDB:4U4C}.
HELIX 916 925 {ECO:0000244|PDB:4U4C}.
TURN 926 930 {ECO:0000244|PDB:4U4C}.
HELIX 933 944 {ECO:0000244|PDB:4U4C}.
STRAND 950 952 {ECO:0000244|PDB:4U4C}.
HELIX 957 979 {ECO:0000244|PDB:4U4C}.
HELIX 986 992 {ECO:0000244|PDB:4U4C}.
HELIX 998 1006 {ECO:0000244|PDB:4U4C}.
HELIX 1010 1015 {ECO:0000244|PDB:4U4C}.
HELIX 1021 1043 {ECO:0000244|PDB:4U4C}.
TURN 1044 1046 {ECO:0000244|PDB:4U4C}.
HELIX 1048 1061 {ECO:0000244|PDB:4U4C}.
HELIX 1064 1067 {ECO:0000244|PDB:4U4C}.
SEQUENCE 1073 AA; 122055 MW; 1FA9EAADC546F669 CRC64;
MDSTDLFDVF EETPVELPTD SNGEKNADTN VGDTPDHTQD KKHGLEEEKE EHEENNSENK
KIKSNKSKTE DKNKKVVVPV LADSFEQEAS REVDASKGLT NSETLQVEQD GKVRLSHQVR
HQVALPPNYD YTPIAEHKRV NEARTYPFTL DPFQDTAISC IDRGESVLVS AHTSAGKTVV
AEYAIAQSLK NKQRVIYTSP IKALSNQKYR ELLAEFGDVG LMTGDITINP DAGCLVMTTE
ILRSMLYRGS EVMREVAWVI FDEVHYMRDK ERGVVWEETI ILLPDKVRYV FLSATIPNAM
EFAEWICKIH SQPCHIVYTN FRPTPLQHYL FPAHGDGIYL VVDEKSTFRE ENFQKAMASI
SNQIGDDPNS TDSRGKKGQT YKGGSAKGDA KGDIYKIVKM IWKKKYNPVI VFSFSKRDCE
ELALKMSKLD FNSDDEKEAL TKIFNNAIAL LPETDRELPQ IKHILPLLRR GIGIHHSGLL
PILKEVIEIL FQEGFLKVLF ATETFSIGLN MPAKTVVFTS VRKWDGQQFR WVSGGEYIQM
SGRAGRRGLD DRGIVIMMID EKMEPQVAKG MVKGQADRLD SAFHLGYNMI LNLMRVEGIS
PEFMLEHSFF QFQNVISVPV MEKKLAELKK DFDGIEVEDE ENVKEYHEIE QAIKGYREDV
RQVVTHPANA LSFLQPGRLV EISVNGKDNY GWGAVVDFAK RINKRNPSAV YTDHESYIVN
VVVNTMYIDS PVNLLKPFNP TLPEGIRPAE EGEKSICAVI PITLDSIKSI GNLRLYMPKD
IRASGQKETV GKSLREVNRR FPDGIPVLDP VKNMKIEDED FLKLMKKIDV LNTKLSSNPL
TNSMRLEELY GKYSRKHDLH EDMKQLKRKI SESQAVIQLD DLRRRKRVLR RLGFCTPNDI
IELKGRVACE ISSGDELLLT ELIFNGNFNE LKPEQAAALL SCFAFQERCK EAPRLKPELA
EPLKAMREIA AKIAKIMKDS KIEVVEKDYV ESFRHELMEV VYEWCRGATF TQICKMTDVY
EGSLIRMFKR LEELVKELVD VANTIGNSSL KEKMEAVLKL IHRDIVSAGS LYL


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CSB-EL006880BO Bovine Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16(DHX38) ELISA kit SpeciesBovine 96T
CSB-EL006880HU Human Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16(DHX38) ELISA kit SpeciesHuman 96T
18-272-195642 SMARCA2 - Rabbit polyclonal to SMARCA2; EC 3.6.1.-; ATP-dependent helicase SMARCA2; SNF2-alpha; SWI_SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2; hBRM Poly 0.1 ml
18-272-195641 SMARCA2 - Rabbit polyclonal to SMARCA2; EC 3.6.1.-; ATP-dependent helicase SMARCA2; SNF2-alpha; SWI_SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2; hBRM Poly 0.1 ml
18-003-42773 Probable ATP-dependent RNA helicase DDX6 - EC 3.6.1.-; DEAD box protein 6; ATP-dependent RNA helicase p54; Oncogene RCK Polyclonal 0.1 mg Protein A


 

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