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Helicase SEN1 (EC 3.6.4.-) (tRNA-splicing endonuclease positive effector)

 SEN1_YEAST              Reviewed;        2231 AA.
Q00416; D6VZ65; E9P9Z4; Q06448;
01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
15-JUL-1998, sequence version 2.
18-JUL-2018, entry version 161.
RecName: Full=Helicase SEN1;
EC=3.6.4.-;
AltName: Full=tRNA-splicing endonuclease positive effector;
Name=SEN1; OrderedLocusNames=YLR430W; ORFNames=L9576.1;
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=9169871;
Johnston M., Hillier L.W., Riles L., Albermann K., Andre B.,
Ansorge W., Benes V., Brueckner M., Delius H., Dubois E.,
Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U.,
Heumann K., Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K.,
Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T.,
Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E.,
Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M.,
Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C.,
Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M.,
Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H.,
Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A.,
Hani J., Hoheisel J.D.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
Nature 387:87-90(1997).
[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]
NUCLEOTIDE SEQUENCE [MRNA] OF 31-2231, AND MUTAGENESIS OF GLY-1747.
PubMed=1569945; DOI=10.1128/MCB.12.5.2154;
Demarini D.J., Winey M., Ursic D., Webb F., Culbertson M.R.;
"SEN1, a positive effector of tRNA-splicing endonuclease in
Saccharomyces cerevisiae.";
Mol. Cell. Biol. 12:2154-2164(1992).
[4]
SUBCELLULAR LOCATION.
PubMed=8544822; DOI=10.1007/BF00418026;
Ursic D., DeMarini D.J., Culbertson M.R.;
"Inactivation of the yeast Sen1 protein affects the localization of
nucleolar proteins.";
Mol. Gen. Genet. 249:571-584(1995).
[5]
FUNCTION.
PubMed=8943355; DOI=10.1128/MCB.16.12.6993;
Steinmetz E.J., Brow D.A.;
"Repression of gene expression by an exogenous sequence element acting
in concert with a heterogeneous nuclear ribonucleoprotein-like
protein, Nrd1, and the putative helicase Sen1.";
Mol. Cell. Biol. 16:6993-7003(1996).
[6]
FUNCTION.
PubMed=9365256; DOI=10.1093/nar/25.23.4778;
Ursic D., Himmel K.L., Gurley K.A., Webb F., Culbertson M.R.;
"The yeast SEN1 gene is required for the processing of diverse RNA
classes.";
Nucleic Acids Res. 25:4778-4785(1997).
[7]
FUNCTION.
PubMed=9819377; DOI=10.1128/MCB.18.12.6885;
Rasmussen T.P., Culbertson M.R.;
"The putative nucleic acid helicase Sen1p is required for formation
and stability of termini and for maximal rates of synthesis and levels
of accumulation of small nucleolar RNAs in Saccharomyces cerevisiae.";
Mol. Cell. Biol. 18:6885-6896(1998).
[8]
FUNCTION.
PubMed=11565036; DOI=10.1038/35095090;
Steinmetz E.J., Conrad N.K., Brow D.A., Corden J.L.;
"RNA-binding protein Nrd1 directs poly(A)-independent 3'-end formation
of RNA polymerase II transcripts.";
Nature 413:327-331(2001).
[9]
SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
PubMed=14562095; DOI=10.1038/nature02026;
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
Weissman J.S., O'Shea E.K.;
"Global analysis of protein localization in budding yeast.";
Nature 425:686-691(2003).
[10]
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).
[11]
FUNCTION, AND INTERACTION WITH RAD2; RNT1 AND RPB1.
PubMed=15121901; DOI=10.1093/nar/gkh561;
Ursic D., Chinchilla K., Finkel J.S., Culbertson M.R.;
"Multiple protein/protein and protein/RNA interactions suggest roles
for yeast DNA/RNA helicase Sen1p in transcription, transcription-
coupled DNA repair and RNA processing.";
Nucleic Acids Res. 32:2441-2452(2004).
[12]
FUNCTION, AND MUTAGENESIS OF GLU-1597.
PubMed=17157256; DOI=10.1016/j.molcel.2006.10.023;
Steinmetz E.J., Warren C.L., Kuehner J.N., Panbehi B., Ansari A.Z.,
Brow D.A.;
"Genome-wide distribution of yeast RNA polymerase II and its control
by Sen1 helicase.";
Mol. Cell 24:735-746(2006).
-!- FUNCTION: ATP-dependent 5'->3' DNA/RNA helicase required for the
expression and maturation of diverse classes of non-protein-coding
RNAs like precursor tRNAs, rRNAs and small nuclear (snRNA) and
nucleolar (snoRNA) RNAs. Directs RNA polymerase II transcription
termination on snoRNAs as well as on several short protein-coding
genes. May also play a role in transcription-coupled nucleotide
excision repair. {ECO:0000269|PubMed:11565036,
ECO:0000269|PubMed:15121901, ECO:0000269|PubMed:17157256,
ECO:0000269|PubMed:8943355, ECO:0000269|PubMed:9365256,
ECO:0000269|PubMed:9819377}.
-!- SUBUNIT: Interacts with RAD2, RNT1 and RPB1. Binds to multiple
snoRNAs. {ECO:0000269|PubMed:15121901}.
-!- INTERACTION:
P32598:GLC7; NbExp=8; IntAct=EBI-16945, EBI-13715;
P38996:NAB3; NbExp=5; IntAct=EBI-16945, EBI-11776;
P38351:PAF1; NbExp=5; IntAct=EBI-16945, EBI-12855;
P07276:RAD2; NbExp=3; IntAct=EBI-16945, EBI-14757;
Q02555:RNT1; NbExp=2; IntAct=EBI-16945, EBI-15673;
P04050:RPO21; NbExp=4; IntAct=EBI-16945, EBI-15760;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14562095,
ECO:0000269|PubMed:8544822}.
-!- MISCELLANEOUS: Present with 125 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the DNA2/NAM7 helicase family.
{ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=AAB63976.1; Type=Frameshift; Positions=130; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; U20939; AAB67502.1; -; Genomic_DNA.
EMBL; U21094; AAB67523.1; -; Genomic_DNA.
EMBL; M74589; AAB63976.1; ALT_FRAME; mRNA.
EMBL; BK006945; DAA09731.1; -; Genomic_DNA.
PIR; S53416; S53416.
RefSeq; NP_013534.3; NM_001182318.3.
PDB; 5MZN; X-ray; 1.79 A; A=1095-1470, A=1525-1902.
PDBsum; 5MZN; -.
ProteinModelPortal; Q00416; -.
SMR; Q00416; -.
BioGrid; 31689; 442.
ComplexPortal; CPX-1316; NRD1 snoRNA termination complex.
ComplexPortal; CPX-1604; Small ribosomal subunit processome, variant 1.
ComplexPortal; CPX-1607; Small ribosomal subunit processome, variant 2.
ComplexPortal; CPX-1608; Small ribosomal subunit processome, variant 3.
DIP; DIP-881N; -.
IntAct; Q00416; 125.
MINT; Q00416; -.
STRING; 4932.YLR430W; -.
iPTMnet; Q00416; -.
MaxQB; Q00416; -.
PaxDb; Q00416; -.
PRIDE; Q00416; -.
TopDownProteomics; Q00416; -.
EnsemblFungi; YLR430W; YLR430W; YLR430W.
GeneID; 851150; -.
KEGG; sce:YLR430W; -.
EuPathDB; FungiDB:YLR430W; -.
SGD; S000004422; SEN1.
GeneTree; ENSGT00810000125415; -.
HOGENOM; HOG000246755; -.
InParanoid; Q00416; -.
KO; K10706; -.
OMA; WANQFHL; -.
OrthoDB; EOG092C0D29; -.
BioCyc; YEAST:G3O-32489-MONOMER; -.
Reactome; R-SCE-6781823; Formation of TC-NER Pre-Incision Complex.
Reactome; R-SCE-6782135; Dual incision in TC-NER.
Reactome; R-SCE-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
PRO; PR:Q00416; -.
Proteomes; UP000002311; Chromosome XII.
GO; GO:0005737; C:cytoplasm; IDA:SGD.
GO; GO:0035649; C:Nrd1 complex; IDA:SGD.
GO; GO:0005634; C:nucleus; IDA:SGD.
GO; GO:0005657; C:replication fork; IDA:SGD.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0043141; F:ATP-dependent 5'-3' DNA helicase activity; IDA:SGD.
GO; GO:0033682; F:ATP-dependent 5'-3' DNA/RNA helicase activity; IDA:SGD.
GO; GO:0032575; F:ATP-dependent 5'-3' RNA helicase activity; ISS:SGD.
GO; GO:0008094; F:DNA-dependent ATPase activity; ISS:SGD.
GO; GO:0019904; F:protein domain specific binding; IDA:SGD.
GO; GO:0008186; F:RNA-dependent ATPase activity; ISS:SGD.
GO; GO:0045454; P:cell redox homeostasis; IMP:SGD.
GO; GO:0045005; P:DNA-dependent DNA replication maintenance of fidelity; IMP:SGD.
GO; GO:0006353; P:DNA-templated transcription, termination; IMP:SGD.
GO; GO:0031124; P:mRNA 3'-end processing; IMP:SGD.
GO; GO:0006378; P:mRNA polyadenylation; IMP:SGD.
GO; GO:1990248; P:regulation of transcription from RNA polymerase II promoter in response to DNA damage; IMP:SGD.
GO; GO:0006364; P:rRNA processing; IMP:SGD.
GO; GO:0031126; P:snoRNA 3'-end processing; IMP:SGD.
GO; GO:0016180; P:snRNA processing; IMP:SGD.
GO; GO:0006369; P:termination of RNA polymerase II transcription; IMP:SGD.
GO; GO:0006283; P:transcription-coupled nucleotide-excision repair; IGI:SGD.
GO; GO:0008033; P:tRNA processing; IMP:SGD.
InterPro; IPR024481; Helicase_Sen1_N.
InterPro; IPR027417; P-loop_NTPase.
Pfam; PF12726; SEN1_N; 1.
SUPFAM; SSF52540; SSF52540; 2.
1: Evidence at protein level;
3D-structure; ATP-binding; Complete proteome; Helicase; Hydrolase;
mRNA processing; Nucleotide-binding; Nucleus; Reference proteome;
rRNA processing; tRNA processing.
CHAIN 1 2231 Helicase SEN1.
/FTId=PRO_0000080722.
NP_BIND 1360 1364 ATP. {ECO:0000250}.
MOTIF 1909 1927 Nuclear localization signal.
{ECO:0000255}.
COMPBIAS 1908 1961 Lys-rich (basic).
BINDING 1339 1339 ATP. {ECO:0000250}.
BINDING 1619 1619 ATP. {ECO:0000250}.
BINDING 1655 1655 ATP. {ECO:0000250}.
BINDING 1787 1787 ATP. {ECO:0000250}.
MUTAGEN 1597 1597 E->K: Causes read-through of both a
snoRNA gene terminator and the poly(A)
site of a protein-coding gene.
{ECO:0000269|PubMed:17157256}.
MUTAGEN 1747 1747 G->A: In SEN1-1; gives rise to a
temperature-sensitive mutant.
{ECO:0000269|PubMed:1569945}.
HELIX 1100 1109 {ECO:0000244|PDB:5MZN}.
HELIX 1114 1120 {ECO:0000244|PDB:5MZN}.
STRAND 1129 1133 {ECO:0000244|PDB:5MZN}.
HELIX 1137 1139 {ECO:0000244|PDB:5MZN}.
HELIX 1150 1174 {ECO:0000244|PDB:5MZN}.
STRAND 1181 1191 {ECO:0000244|PDB:5MZN}.
STRAND 1194 1202 {ECO:0000244|PDB:5MZN}.
HELIX 1203 1208 {ECO:0000244|PDB:5MZN}.
STRAND 1215 1220 {ECO:0000244|PDB:5MZN}.
HELIX 1233 1237 {ECO:0000244|PDB:5MZN}.
STRAND 1240 1252 {ECO:0000244|PDB:5MZN}.
STRAND 1256 1265 {ECO:0000244|PDB:5MZN}.
HELIX 1269 1273 {ECO:0000244|PDB:5MZN}.
STRAND 1279 1287 {ECO:0000244|PDB:5MZN}.
HELIX 1289 1300 {ECO:0000244|PDB:5MZN}.
HELIX 1301 1303 {ECO:0000244|PDB:5MZN}.
HELIX 1307 1312 {ECO:0000244|PDB:5MZN}.
HELIX 1323 1333 {ECO:0000244|PDB:5MZN}.
HELIX 1337 1348 {ECO:0000244|PDB:5MZN}.
STRAND 1351 1356 {ECO:0000244|PDB:5MZN}.
HELIX 1363 1379 {ECO:0000244|PDB:5MZN}.
STRAND 1406 1412 {ECO:0000244|PDB:5MZN}.
HELIX 1413 1423 {ECO:0000244|PDB:5MZN}.
STRAND 1439 1441 {ECO:0000244|PDB:5MZN}.
HELIX 1450 1453 {ECO:0000244|PDB:5MZN}.
HELIX 1457 1465 {ECO:0000244|PDB:5MZN}.
TURN 1466 1469 {ECO:0000244|PDB:5MZN}.
HELIX 1544 1561 {ECO:0000244|PDB:5MZN}.
STRAND 1563 1568 {ECO:0000244|PDB:5MZN}.
HELIX 1570 1573 {ECO:0000244|PDB:5MZN}.
HELIX 1575 1578 {ECO:0000244|PDB:5MZN}.
STRAND 1586 1591 {ECO:0000244|PDB:5MZN}.
HELIX 1597 1601 {ECO:0000244|PDB:5MZN}.
HELIX 1602 1606 {ECO:0000244|PDB:5MZN}.
STRAND 1610 1615 {ECO:0000244|PDB:5MZN}.
STRAND 1617 1619 {ECO:0000244|PDB:5MZN}.
HELIX 1627 1631 {ECO:0000244|PDB:5MZN}.
TURN 1632 1635 {ECO:0000244|PDB:5MZN}.
HELIX 1638 1643 {ECO:0000244|PDB:5MZN}.
HELIX 1659 1669 {ECO:0000244|PDB:5MZN}.
HELIX 1680 1683 {ECO:0000244|PDB:5MZN}.
HELIX 1687 1690 {ECO:0000244|PDB:5MZN}.
STRAND 1696 1702 {ECO:0000244|PDB:5MZN}.
HELIX 1719 1736 {ECO:0000244|PDB:5MZN}.
TURN 1737 1739 {ECO:0000244|PDB:5MZN}.
STRAND 1746 1751 {ECO:0000244|PDB:5MZN}.
HELIX 1753 1767 {ECO:0000244|PDB:5MZN}.
HELIX 1768 1771 {ECO:0000244|PDB:5MZN}.
TURN 1772 1774 {ECO:0000244|PDB:5MZN}.
STRAND 1775 1779 {ECO:0000244|PDB:5MZN}.
TURN 1780 1785 {ECO:0000244|PDB:5MZN}.
STRAND 1788 1794 {ECO:0000244|PDB:5MZN}.
HELIX 1804 1817 {ECO:0000244|PDB:5MZN}.
STRAND 1820 1829 {ECO:0000244|PDB:5MZN}.
HELIX 1831 1834 {ECO:0000244|PDB:5MZN}.
HELIX 1838 1849 {ECO:0000244|PDB:5MZN}.
STRAND 1853 1856 {ECO:0000244|PDB:5MZN}.
TURN 1858 1861 {ECO:0000244|PDB:5MZN}.
HELIX 1866 1873 {ECO:0000244|PDB:5MZN}.
SEQUENCE 2231 AA; 252497 MW; 88F0FF95B3A8BD89 CRC64;
MNSNNPDNNN SNNINNNNKD KDIAPNSDVQ LATVYTKAKS YIPQIEQVYQ GTNPNIQEAK
LLGELLQVLA EVPKGTHLFC DPILEPISIF SLTIFSFNEE ATATWLKNHF NPILSVCDKC
ILNFARGKCK MLQHFAIQRH VPHEHVAKFN DIVCQWRVEA VFPILRNISV NDNTGINITN
EIETAMYECL CNPHMLRLNK QLKATFEAIF KFFYDTKHRL LDVTNPLSIK TFISGVIFCW
CEGSKEENEW SRAFLKDLYS RNFHINLSNL TPDIIEEVYI HILFLQNPAN WTEIVVSQFW
SRLLPVFNLF DKDVFIEYFQ VPKNVESLKK TFKFPLEPIF KMWYNHLSKS YHDKPLDFLL
RGLTMFLNKF GSEFWSKIEP FTFHSILDII FNRDSFPIKL IKIQDNPIVE HQTEVYFQLT
GSVTDLLSWT LPFYHALSPS KRIQMVRKVS MAFLRIIANY PSLKSIPKAC LMNSATALLR
AVLTIKENER AMLYKNDEFE TVLLTKTDSR ALLNNPLIQD IIIRSASNPN DFYPGLGAAS
ASVATSTMMV LAECIDFDIL LLCHRTFKLY SGKPISEIPI STNVLENVTN KIDLRSFHDG
PLLAKQLLVS LKNINGLLIV PSNTAVAEAH NALNQKFLLL STRLMEKFAD ILPGQLSKIL
ADEDASQGFW SCIFSSDKHL YQAATNILYN TFDVEGRLEG ILAILNSNLT VNLKNINVML
QRLINCEFYE PCPRAVRVLM DVVSAFVDPI SGVFANFQTL KSQNTEKEFL KFWESCWLFL
DTIYKFTLKW ASKYDYSELE NFTKDTLDLS RSLVDSFREF SDILHDQTKN LLLNVLETFK
NMLYWLRLSD EVLLESCVRL IISTSDLAHE KHVKVDDSLV EMMAKYASKA KRFSNKLTEQ
QASEILQKAK IFNKALTEEV ATEAENYRKE KELSRLGKVI DLTDSVPASP SLSPSLSSTI
ASSSAESRAD YLQRKALSSS ITGRPRVAQP KITSFGTFQS SANAKLHRTK PVKPLSKMEL
ARMQLLNNRV VHPPSAPAFH TKSRGLSNKN DDSSSEESDN DIESARELFA IAKAKGKGIQ
TVDINGKVVK RQTAAELAKQ ELEHMRKRLN VDMNPLYEII LQWDYTRNSE YPDDEPIGNY
SDVKDFFNSP ADYQKVMKPL LLLESWQGLC SSRDREDYKP FSIIVGNRTA VSDFYDVYAS
VAKQVIQDCG ISESDLIVMA YLPDFRPDKR LSSDDFKKAQ HTCLAKVRTL KNTKGGNVDV
TLRIHRNHSF SKFLTLRSEI YCVKVMQMTT IEREYSTLEG LEYYDLVGQI LQAKPSPPVN
VDAAEIETVK KSYKLNTSQA EAIVNSVSKE GFSLIQGPPG TGKTKTILGI IGYFLSTKNA
SSSNVIKVPL EKNSSNTEQL LKKQKILICA PSNAAVDEIC LRLKSGVYDK QGHQFKPQLV
RVGRSDVVNV AIKDLTLEEL VDKRIGERNY EIRTDPELER KFNNAVTKRR ELRGKLDSES
GNPESPMSTE DISKLQLKIR ELSKIINELG RDRDEMREKN SVNYRNRDLD RRNAQAHILA
VSDIICSTLS GSAHDVLATM GIKFDTVIID EACQCTELSS IIPLRYGGKR CIMVGDPNQL
PPTVLSGAAS NFKYNQSLFV RMEKNSSPYL LDVQYRMHPS ISKFPSSEFY QGRLKDGPGM
DILNKRPWHQ LEPLAPYKFF DIISGRQEQN AKTMSYTNME EIRVAIELVD YLFRKFDNKI
DFTGKIGIIS PYREQMQKMR KEFARYFGGM INKSIDFNTI DGFQGQEKEI ILISCVRADD
TKSSVGFLKD FRRMNVALTR AKTSIWVLGH QRSLAKSKLW RDLIEDAKDR SCLAYACSGF
LDPRNNRAQS ILRKFNVPVP SEQEDDYKLP MEYITQGPDE VKSNKDTKKR RVVDEGEEAD
KAVKKKKKEK KKEKKKSKAD DKKKNNKKAE SPSTSSGTKK KSSIFGGMSV PSAVVPKTFP
DVDSNKKAAA VVGKKKNNKH VCFSDDVSFI PRNDEPEIKV TRSLSSVLKE KQLGLKETRT
ISPPEISNNE DDDDEDDYTP SISDSSLMKS EANGRNNRVA SHNQNFSASI YDDPQVSQAK
QTQVPAAITK HRSSNSVLSG GSSRILTASD YGEPNQNGQN GANRTLSQHV GNANQYSTAP
VGTGELHETL PAHPQDSYPA EAEDPYDLNP HPQPQSSAFK GPGSGPTGTR NSSRRNASSS
PFIPKKRKPR S


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