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Protein

Helicase SEN1

Gene

SEN1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.6 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei1339 – 13391ATPBy similarity
Binding sitei1619 – 16191ATPBy similarity
Binding sitei1655 – 16551ATPBy similarity
Binding sitei1787 – 17871ATPBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi1360 – 13645ATPBy similarity

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • ATP-dependent 5'-3' RNA helicase activity Source: SGD
  • DNA-dependent ATPase activity Source: SGD
  • protein domain specific binding Source: SGD
  • RNA-dependent ATPase activity Source: SGD
  • single-stranded DNA-dependent ATP-dependent DNA helicase activity Source: SGD

GO - Biological processi

  • DNA-dependent DNA replication maintenance of fidelity Source: SGD
  • DNA duplex unwinding Source: GOC
  • DNA-templated transcription, termination Source: SGD
  • mRNA 3'-end processing Source: SGD
  • mRNA polyadenylation Source: SGD
  • regulation of transcription from RNA polymerase II promoter in response to DNA damage Source: SGD
  • rRNA processing Source: SGD
  • snoRNA 3'-end processing Source: SGD
  • snRNA processing Source: SGD
  • termination of RNA polymerase II transcription Source: SGD
  • tRNA processing Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

mRNA processing, rRNA processing, tRNA processing

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-32489-MONOMER.
ReactomeiR-SCE-6781823. Formation of TC-NER Pre-Incision Complex.
R-SCE-6782135. Dual incision in TC-NER.
R-SCE-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.

Names & Taxonomyi

Protein namesi
Recommended name:
Helicase SEN1 (EC:3.6.4.-)
Alternative name(s):
tRNA-splicing endonuclease positive effector
Gene namesi
Name:SEN1
Ordered Locus Names:YLR430W
ORF Names:L9576.1
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XII

Organism-specific databases

EuPathDBiFungiDB:YLR430W.
SGDiS000004422. SEN1.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: SGD
  • Nrd1 complex Source: SGD
  • nucleus Source: SGD
  • replication fork Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi1597 – 15971E → K: Causes read-through of both a snoRNA gene terminator and the poly(A) site of a protein-coding gene. 1 Publication
Mutagenesisi1747 – 17471G → A in SEN1-1; gives rise to a temperature-sensitive mutant. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 22312231Helicase SEN1PRO_0000080722Add
BLAST

Proteomic databases

MaxQBiQ00416.
PeptideAtlasiQ00416.
TopDownProteomicsiQ00416.

PTM databases

iPTMnetiQ00416.

Interactioni

Subunit structurei

Interacts with RAD2, RNT1 and RPB1. Binds to multiple snoRNAs.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
RAD2P072763EBI-16945,EBI-14757
RNT1Q025552EBI-16945,EBI-15673
RPO21P040503EBI-16945,EBI-15760

GO - Molecular functioni

  • protein domain specific binding Source: SGD

Protein-protein interaction databases

BioGridi31689. 85 interactions.
DIPiDIP-881N.
IntActiQ00416. 22 interactions.
MINTiMINT-427565.

Structurei

3D structure databases

ProteinModelPortaliQ00416.
SMRiQ00416. Positions 1250-1873.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi1909 – 192719Nuclear localization signalSequence analysisAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi1908 – 196154Lys-rich (basic)Add
BLAST

Sequence similaritiesi

Belongs to the DNA2/NAM7 helicase family.Curated

Phylogenomic databases

GeneTreeiENSGT00830000128421.
HOGENOMiHOG000246755.
InParanoidiQ00416.
KOiK10706.
OMAiEIIIMSC.
OrthoDBiEOG70PC5T.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR024481. Helicase_Sen1_N.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF12726. SEN1_N. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.

Sequencei

Sequence statusi: Complete.

Q00416-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNSNNPDNNN SNNINNNNKD KDIAPNSDVQ LATVYTKAKS YIPQIEQVYQ
60 70 80 90 100
GTNPNIQEAK LLGELLQVLA EVPKGTHLFC DPILEPISIF SLTIFSFNEE
110 120 130 140 150
ATATWLKNHF NPILSVCDKC ILNFARGKCK MLQHFAIQRH VPHEHVAKFN
160 170 180 190 200
DIVCQWRVEA VFPILRNISV NDNTGINITN EIETAMYECL CNPHMLRLNK
210 220 230 240 250
QLKATFEAIF KFFYDTKHRL LDVTNPLSIK TFISGVIFCW CEGSKEENEW
260 270 280 290 300
SRAFLKDLYS RNFHINLSNL TPDIIEEVYI HILFLQNPAN WTEIVVSQFW
310 320 330 340 350
SRLLPVFNLF DKDVFIEYFQ VPKNVESLKK TFKFPLEPIF KMWYNHLSKS
360 370 380 390 400
YHDKPLDFLL RGLTMFLNKF GSEFWSKIEP FTFHSILDII FNRDSFPIKL
410 420 430 440 450
IKIQDNPIVE HQTEVYFQLT GSVTDLLSWT LPFYHALSPS KRIQMVRKVS
460 470 480 490 500
MAFLRIIANY PSLKSIPKAC LMNSATALLR AVLTIKENER AMLYKNDEFE
510 520 530 540 550
TVLLTKTDSR ALLNNPLIQD IIIRSASNPN DFYPGLGAAS ASVATSTMMV
560 570 580 590 600
LAECIDFDIL LLCHRTFKLY SGKPISEIPI STNVLENVTN KIDLRSFHDG
610 620 630 640 650
PLLAKQLLVS LKNINGLLIV PSNTAVAEAH NALNQKFLLL STRLMEKFAD
660 670 680 690 700
ILPGQLSKIL ADEDASQGFW SCIFSSDKHL YQAATNILYN TFDVEGRLEG
710 720 730 740 750
ILAILNSNLT VNLKNINVML QRLINCEFYE PCPRAVRVLM DVVSAFVDPI
760 770 780 790 800
SGVFANFQTL KSQNTEKEFL KFWESCWLFL DTIYKFTLKW ASKYDYSELE
810 820 830 840 850
NFTKDTLDLS RSLVDSFREF SDILHDQTKN LLLNVLETFK NMLYWLRLSD
860 870 880 890 900
EVLLESCVRL IISTSDLAHE KHVKVDDSLV EMMAKYASKA KRFSNKLTEQ
910 920 930 940 950
QASEILQKAK IFNKALTEEV ATEAENYRKE KELSRLGKVI DLTDSVPASP
960 970 980 990 1000
SLSPSLSSTI ASSSAESRAD YLQRKALSSS ITGRPRVAQP KITSFGTFQS
1010 1020 1030 1040 1050
SANAKLHRTK PVKPLSKMEL ARMQLLNNRV VHPPSAPAFH TKSRGLSNKN
1060 1070 1080 1090 1100
DDSSSEESDN DIESARELFA IAKAKGKGIQ TVDINGKVVK RQTAAELAKQ
1110 1120 1130 1140 1150
ELEHMRKRLN VDMNPLYEII LQWDYTRNSE YPDDEPIGNY SDVKDFFNSP
1160 1170 1180 1190 1200
ADYQKVMKPL LLLESWQGLC SSRDREDYKP FSIIVGNRTA VSDFYDVYAS
1210 1220 1230 1240 1250
VAKQVIQDCG ISESDLIVMA YLPDFRPDKR LSSDDFKKAQ HTCLAKVRTL
1260 1270 1280 1290 1300
KNTKGGNVDV TLRIHRNHSF SKFLTLRSEI YCVKVMQMTT IEREYSTLEG
1310 1320 1330 1340 1350
LEYYDLVGQI LQAKPSPPVN VDAAEIETVK KSYKLNTSQA EAIVNSVSKE
1360 1370 1380 1390 1400
GFSLIQGPPG TGKTKTILGI IGYFLSTKNA SSSNVIKVPL EKNSSNTEQL
1410 1420 1430 1440 1450
LKKQKILICA PSNAAVDEIC LRLKSGVYDK QGHQFKPQLV RVGRSDVVNV
1460 1470 1480 1490 1500
AIKDLTLEEL VDKRIGERNY EIRTDPELER KFNNAVTKRR ELRGKLDSES
1510 1520 1530 1540 1550
GNPESPMSTE DISKLQLKIR ELSKIINELG RDRDEMREKN SVNYRNRDLD
1560 1570 1580 1590 1600
RRNAQAHILA VSDIICSTLS GSAHDVLATM GIKFDTVIID EACQCTELSS
1610 1620 1630 1640 1650
IIPLRYGGKR CIMVGDPNQL PPTVLSGAAS NFKYNQSLFV RMEKNSSPYL
1660 1670 1680 1690 1700
LDVQYRMHPS ISKFPSSEFY QGRLKDGPGM DILNKRPWHQ LEPLAPYKFF
1710 1720 1730 1740 1750
DIISGRQEQN AKTMSYTNME EIRVAIELVD YLFRKFDNKI DFTGKIGIIS
1760 1770 1780 1790 1800
PYREQMQKMR KEFARYFGGM INKSIDFNTI DGFQGQEKEI ILISCVRADD
1810 1820 1830 1840 1850
TKSSVGFLKD FRRMNVALTR AKTSIWVLGH QRSLAKSKLW RDLIEDAKDR
1860 1870 1880 1890 1900
SCLAYACSGF LDPRNNRAQS ILRKFNVPVP SEQEDDYKLP MEYITQGPDE
1910 1920 1930 1940 1950
VKSNKDTKKR RVVDEGEEAD KAVKKKKKEK KKEKKKSKAD DKKKNNKKAE
1960 1970 1980 1990 2000
SPSTSSGTKK KSSIFGGMSV PSAVVPKTFP DVDSNKKAAA VVGKKKNNKH
2010 2020 2030 2040 2050
VCFSDDVSFI PRNDEPEIKV TRSLSSVLKE KQLGLKETRT ISPPEISNNE
2060 2070 2080 2090 2100
DDDDEDDYTP SISDSSLMKS EANGRNNRVA SHNQNFSASI YDDPQVSQAK
2110 2120 2130 2140 2150
QTQVPAAITK HRSSNSVLSG GSSRILTASD YGEPNQNGQN GANRTLSQHV
2160 2170 2180 2190 2200
GNANQYSTAP VGTGELHETL PAHPQDSYPA EAEDPYDLNP HPQPQSSAFK
2210 2220 2230
GPGSGPTGTR NSSRRNASSS PFIPKKRKPR S
Length:2,231
Mass (Da):252,497
Last modified:July 15, 1998 - v2
Checksum:i88F0FF95B3A8BD89
GO

Sequence cautioni

The sequence AAB63976.1 differs from that shown. Reason: Frameshift at position 130. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U20939 Genomic DNA. Translation: AAB67502.1.
U21094 Genomic DNA. Translation: AAB67523.1.
M74589 mRNA. Translation: AAB63976.1. Frameshift.
BK006945 Genomic DNA. Translation: DAA09731.1.
PIRiS53416.
RefSeqiNP_013534.3. NM_001182318.3.

Genome annotation databases

EnsemblFungiiYLR430W; YLR430W; YLR430W.
GeneIDi851150.
KEGGisce:YLR430W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U20939 Genomic DNA. Translation: AAB67502.1.
U21094 Genomic DNA. Translation: AAB67523.1.
M74589 mRNA. Translation: AAB63976.1. Frameshift.
BK006945 Genomic DNA. Translation: DAA09731.1.
PIRiS53416.
RefSeqiNP_013534.3. NM_001182318.3.

3D structure databases

ProteinModelPortaliQ00416.
SMRiQ00416. Positions 1250-1873.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31689. 85 interactions.
DIPiDIP-881N.
IntActiQ00416. 22 interactions.
MINTiMINT-427565.

PTM databases

iPTMnetiQ00416.

Proteomic databases

MaxQBiQ00416.
PeptideAtlasiQ00416.
TopDownProteomicsiQ00416.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYLR430W; YLR430W; YLR430W.
GeneIDi851150.
KEGGisce:YLR430W.

Organism-specific databases

EuPathDBiFungiDB:YLR430W.
SGDiS000004422. SEN1.

Phylogenomic databases

GeneTreeiENSGT00830000128421.
HOGENOMiHOG000246755.
InParanoidiQ00416.
KOiK10706.
OMAiEIIIMSC.
OrthoDBiEOG70PC5T.

Enzyme and pathway databases

BioCyciYEAST:G3O-32489-MONOMER.
ReactomeiR-SCE-6781823. Formation of TC-NER Pre-Incision Complex.
R-SCE-6782135. Dual incision in TC-NER.
R-SCE-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.

Miscellaneous databases

NextBioi967924.
PROiQ00416.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR024481. Helicase_Sen1_N.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF12726. SEN1_N. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII."
    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.
    Nature 387:87-90(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. "SEN1, a positive effector of tRNA-splicing endonuclease in Saccharomyces cerevisiae."
    Demarini D.J., Winey M., Ursic D., Webb F., Culbertson M.R.
    Mol. Cell. Biol. 12:2154-2164(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 31-2231, MUTAGENESIS OF GLY-1747.
  4. "Inactivation of the yeast Sen1 protein affects the localization of nucleolar proteins."
    Ursic D., DeMarini D.J., Culbertson M.R.
    Mol. Gen. Genet. 249:571-584(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.
  5. "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."
    Steinmetz E.J., Brow D.A.
    Mol. Cell. Biol. 16:6993-7003(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  6. "The yeast SEN1 gene is required for the processing of diverse RNA classes."
    Ursic D., Himmel K.L., Gurley K.A., Webb F., Culbertson M.R.
    Nucleic Acids Res. 25:4778-4785(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  7. "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."
    Rasmussen T.P., Culbertson M.R.
    Mol. Cell. Biol. 18:6885-6896(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  8. "RNA-binding protein Nrd1 directs poly(A)-independent 3'-end formation of RNA polymerase II transcripts."
    Steinmetz E.J., Conrad N.K., Brow D.A., Corden J.L.
    Nature 413:327-331(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  9. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  10. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  11. "Multiple protein/protein and protein/RNA interactions suggest roles for yeast DNA/RNA helicase Sen1p in transcription, transcription-coupled DNA repair and RNA processing."
    Ursic D., Chinchilla K., Finkel J.S., Culbertson M.R.
    Nucleic Acids Res. 32:2441-2452(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH RAD2; RNT1 AND RPB1.
  12. "Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase."
    Steinmetz E.J., Warren C.L., Kuehner J.N., Panbehi B., Ansari A.Z., Brow D.A.
    Mol. Cell 24:735-746(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, MUTAGENESIS OF GLU-1597.

Entry informationi

Entry nameiSEN1_YEAST
AccessioniPrimary (citable) accession number: Q00416
Secondary accession number(s): D6VZ65, E9P9Z4, Q06448
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: July 15, 1998
Last modified: May 11, 2016
This is version 139 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 125 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome XII
    Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.