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Protein

E3 ubiquitin-protein ligase TOM1

Gene

TOM1

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

Probable ubiquitin ligase protein involved in many cellular processes, such as transcription regulation, maintenance of nuclear structure, cell cycle, mRNA export and rRNA maturation. E3 ubiquitin ligase proteins mediate ubiquitination and subsequent proteasomal degradation of target proteins. Involved in transcription regulation by interacting, and probably mediating, ubiquitination of some subunit of the SAGA complex. Required for SPT7 ubiquitination. Participates in mRNA export from the nucleus by regulating the transport of hnRNP proteins. Required for the shuttling of hnRNP protein NAB2, probably by mediating ubiquitination of a protein associated with NAB2. Also required for full induction of the general stress and heat-shock responses. Involved in 18S rRNA maturation by affecting several early steps in the rRNA processing pathway.5 Publications

Miscellaneous

Present with 350 molecules/cell in log phase SD medium.1 Publication

Catalytic activityi

S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N6-ubiquitinyl-[acceptor protein]-L-lysine.

Pathwayi: protein ubiquitination

This protein is involved in the pathway protein ubiquitination, which is part of Protein modification.
View all proteins of this organism that are known to be involved in the pathway protein ubiquitination and in Protein modification.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei3235Glycyl thioester intermediatePROSITE-ProRule annotation1

GO - Molecular functioni

  • ubiquitin protein ligase activity Source: GO_Central
  • ubiquitin-protein transferase activity Source: SGD

GO - Biological processi

  • cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
  • endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
  • endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
  • endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
  • mitotic cell cycle Source: SGD
  • mRNA transport Source: UniProtKB-KW
  • nucleocytoplasmic transport Source: SGD
  • nucleus organization Source: SGD
  • protein ubiquitination Source: SGD
  • protein ubiquitination involved in ubiquitin-dependent protein catabolic process Source: SGD
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • transcription, DNA-templated Source: UniProtKB-KW

Keywordsi

Molecular functionTransferase
Biological processCell cycle, mRNA transport, rRNA processing, Transcription, Transcription regulation, Transport, Ubl conjugation pathway

Enzyme and pathway databases

BioCyciYEAST:G3O-29985-MONOMER.
ReactomeiR-SCE-6798695. Neutrophil degranulation.
R-SCE-983168. Antigen processing: Ubiquitination & Proteasome degradation.
UniPathwayiUPA00143.

Names & Taxonomyi

Protein namesi
Recommended name:
E3 ubiquitin-protein ligase TOM1 (EC:2.3.2.26)
Alternative name(s):
HECT-type E3 ubiquitin transferase TOM1
Suppressor of snRNA protein 2
Temperature-dependent organization in mitotic nucleus protein 1
Gene namesi
Name:TOM1
Synonyms:SSR2
Ordered Locus Names:YDR457W
ORF Names:D8035.1
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IV

Organism-specific databases

EuPathDBiFungiDB:YDR457W.
SGDiS000002865. TOM1.

Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi3235C → A: Loss of function. Induces a decrease in transcription activation. 3 Publications1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001203481 – 3268E3 ubiquitin-protein ligase TOM1Add BLAST3268

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1890PhosphoserineCombined sources1
Modified residuei2096PhosphothreonineCombined sources1
Modified residuei2119PhosphoserineCombined sources1
Modified residuei2376PhosphoserineCombined sources1
Modified residuei2406PhosphoserineCombined sources1
Modified residuei2418PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ03280.
PRIDEiQ03280.

PTM databases

iPTMnetiQ03280.

Interactioni

Subunit structurei

Interacts with the ADA3/NGG1 subunit of the SAGA complex. Interacts with KRR1.2 Publications

Protein-protein interaction databases

BioGridi32511. 700 interactors.
DIPiDIP-5927N.
IntActiQ03280. 5 interactors.
MINTiMINT-696504.
STRINGi4932.YDR457W.

Structurei

3D structure databases

ProteinModelPortaliQ03280.
SMRiQ03280.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini2932 – 3268HECTPROSITE-ProRule annotationAdd BLAST337

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi1879 – 2054Asp-richAdd BLAST176

Sequence similaritiesi

Belongs to the UPL family. TOM1/PTR1 subfamily.Curated

Phylogenomic databases

GeneTreeiENSGT00850000132302.
HOGENOMiHOG000093627.
InParanoidiQ03280.
KOiK10592.
OMAiLLNCPNF.
OrthoDBiEOG092C016J.

Family and domain databases

CDDicd00078. HECTc. 1 hit.
Gene3Di1.25.10.10. 1 hit.
InterProiView protein in InterPro
IPR011989. ARM-like.
IPR016024. ARM-type_fold.
IPR025527. DUF4414.
IPR010309. E3_Ub_ligase_DUF908.
IPR010314. E3_Ub_ligase_DUF913.
IPR000569. HECT_dom.
PfamiView protein in Pfam
PF14377. DUF4414. 1 hit.
PF06012. DUF908. 1 hit.
PF06025. DUF913. 1 hit.
PF00632. HECT. 1 hit.
SMARTiView protein in SMART
SM00119. HECTc. 1 hit.
SUPFAMiSSF48371. SSF48371. 2 hits.
SSF56204. SSF56204. 1 hit.
PROSITEiView protein in PROSITE
PS50237. HECT. 1 hit.

Sequencei

Sequence statusi: Complete.

Q03280-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVLFTRCEKA RKEKLAAGYK PLVDYLIDCD TPTFLERIEA IQEWDRSRDD
60 70 80 90 100
LYVWIPILDR MDGLLLKVAE KYKYKQDPKK ECEVKLVEME AHDVDYCLKM
110 120 130 140 150
LKFTRRLLLN TENRFVYSSG DVLMYLLNCP NFTIKLAVMR ILAILGERFV
160 170 180 190 200
IAREKIVAHN IFGDHNLRKK TLKLALSLSS SVMDEDGEHF SLVDLYFDKK
210 220 230 240 250
KVPQKWRKLR FTHYTSNDFK KSSQQKNNIN ETQTSIKKVT MTTQELCEHS
260 270 280 290 300
LQQIFDKGMA LLPAESWFDF SIKASVAKAF SDDSGENIDL RNIIIETKLN
310 320 330 340 350
AIAFVNTIFS PPQVSSKLFE LDPYAFNSLT DLISLSETKI PKELRTDALF
360 370 380 390 400
TLECISLKHV WCSDIIRNLG GNISHGLLFQ ILRYIAKTLR EATDEIDEEY
410 420 430 440 450
NVRFFYLISN LADVKPLHES LFAAGLIPTL LEIVSIRNCP YKRTLASATH
460 470 480 490 500
LLETFIDNSE TTTEFIENDG FTMLITSVAN EIDFTLAHPE TWQPPKYSVV
510 520 530 540 550
YYSISFRELA YIRSLLKLVL KLLSTDSGDR IRNLIDSPIL VSLKKILENK
560 570 580 590 600
LVFGLTLITY TLDVVQKVIN SEPTIYPVLV EAGLIPYVID NFPKLIGPSA
610 620 630 640 650
ELLSLLPDVV SAICLNPEGL KQVKEKGLIN NLFDFLLDAD HARILTGGDR
660 670 680 690 700
STEYGTDIDE LARHYPDLKA NIVEALCNVI RKMPSTFRNE REFLFTSPKD
710 720 730 740 750
QKYFFHRKNE EILTDKEEHE PAYWELLDKG TMLDTFTSVL FGMSLGNGSF
760 770 780 790 800
SQVPQHLEAR DFLAIIFMEN PPYEYFTSVA ISNVTEVLQY LDEKYEDYAF
810 820 830 840 850
MDVMKVLNDQ LENLNDFLNS PNDRSFFLER DGENSVRSCH SKLCRLAAIL
860 870 880 890 900
NIVTNVYIDL TTLSCKRIMQ IYSYFDKRGF SLIKNLKLLF QKCALEEMYI
910 920 930 940 950
RQHMPDSVIT ETMPLPIVDV SGDGPPLQIY IDDPKKGDQK GKITSVKTRN
960 970 980 990 1000
TLQMRTILYT LQSNTAILFR CFLRLSHSRN MDLEHKDLTT EVHIFENVVE
1010 1020 1030 1040 1050
NVIEMLKATE LEGHLPYILV LLNFNTFVFT IPKASPNSTE ILQTIPAYIF
1060 1070 1080 1090 1100
YQKGGYLLYL HIIRDLFTRM TKIKDLSSLD NINYIDESNG ILTLSCLINA
1110 1120 1130 1140 1150
LTFYNKSMQT ETMENVQSIG KYYVSIDDDY NIMKALTVPI KVMALAMILD
1160 1170 1180 1190 1200
LDKSDSLFKT QSRNVPYSVF KQLLSMLKNI FTNVNIYTKE LYELHWDLIF
1210 1220 1230 1240 1250
PPIKKISLFE QVGIPGDVAA NYLTDTGDDL PADNSIGLFS PEQWEKYKKL
1260 1270 1280 1290 1300
IGEDKSIYYP QPMQAQYYKG CSSKELDELR DTFFNDGLPS RIFTVLPFYP
1310 1320 1330 1340 1350
KLVNAFAKTL LQIFTKYDEP TEVFAGRILD RILETDLDDP ATLSSLIHLF
1360 1370 1380 1390 1400
GIFLNEKYIY QKASHLMQRF IEYLEKSLKP EHVNTPWFSK ALYVYEIILA
1410 1420 1430 1440 1450
KSELPHLEEL SKDVLLRYPL LSMAKVFRIP DPMKQKLFDI LIRVSDISNF
1460 1470 1480 1490 1500
YSALATSRIL IFYSRDELYA NNIARSGILS RLLKVIGSFQ KLDKINFLES
1510 1520 1530 1540 1550
SFLLLTRRCF ETTENVDALI RAEINRSFTA RPLGGGDDAV RELTTILEEK
1560 1570 1580 1590 1600
AHVVMRSPSQ FIDVLCETAR FHEFDDQGAL VDYSLKRFLG EKDKNTQASS
1610 1620 1630 1640 1650
TEKSDIYERT GIMHLLLSQL MAASEKDWLS EPANSSDLPE NKKAQLDPSR
1660 1670 1680 1690 1700
NPVCAYMIFL LKLLVELVSS YNQCKFEFLT FSRRNTYAER PRPRTTAINF
1710 1720 1730 1740 1750
FLYRLLDKPV GTDHDKHEAK RREVIGMLAR SVIIGFLATV QDDRTTKTDV
1760 1770 1780 1790 1800
KLADPHMNFI RKFAIEAIIK AIRNATSSSK LLESNHLKLD MWFRIITSMV
1810 1820 1830 1840 1850
YVQAPYLRQL LDSNKVEADQ YQLCKLVIDL GLPSVITEAM ASIDLNYPFS
1860 1870 1880 1890 1900
KKIFNVAVEA LNTISSTRNN FSEHFKIEDH DEVEDEVDES DKEEIPDMFK
1910 1920 1930 1940 1950
NSALGMYDVE DIEEDDDDDT SLIGDDDAMA FVDSDNGFEV VFSDEDDDMG
1960 1970 1980 1990 2000
EEDADDARSD SEENELSSEM QSSTADGTDV DYEVDDADGL IINIDQPSGD
2010 2020 2030 2040 2050
DEEMADYDAN ISHSSHSENE DDASMDVIEV YDDELSSGYD VDLSDYDVDE
2060 2070 2080 2090 2100
SDWDSGLSSL SISDEDSESS EDEPINSTRM GDSRRRWLIA EGVELTDDSQ
2110 2120 2130 2140 2150
GESEEDDRGV FRGIEHIFSN ENEPLFRVHD EMRHRNHHRS INRTHFHSAM
2160 2170 2180 2190 2200
SAPSLSLLNR GRRNQSNLIN PLGPTGLEQV ENDISDQVTV AGSGSRPRSH
2210 2220 2230 2240 2250
HLHFSEVLVS GSFFDEPVLD GIILKSTVSR WKDIFDMFYD SKTYANCIIP
2260 2270 2280 2290 2300
TVINRLYKVS LALQKDLENK REQEKLKNKN LLFNEAKVES HNSSDAISVE
2310 2320 2330 2340 2350
QDDIQESNVT HDDHEPVYVT IQGSEVDIGG TDIDPEFMNA LPDDIRADVF
2360 2370 2380 2390 2400
AQHVRERRAE ARLNSDHNVH SREIDSDFLE AIPEDIREGI LDTEAEEQRM
2410 2420 2430 2440 2450
FGRIGSSADV IRADDDVSNN DEEVENGLDH GNSNDRNNAD PEKKKPARIY
2460 2470 2480 2490 2500
FAPLIDRAGI ASLMKSVFIS KPYIQREIYH ELFYRLCSSK QNRNDLMNTF
2510 2520 2530 2540 2550
LFILSEGIID QHSLEKVYNI ISSRAMGHAK TTTVRQLPSD CTPLTVANQT
2560 2570 2580 2590 2600
IEILQSLIDA DSRLKYFLIA EHDNLIVNKA NNKSRKEALP DKKLRWPLWH
2610 2620 2630 2640 2650
LFSLLDRKLI TDESVLMDLL TRILQVCTKT LAVLSTSSNG KENLSKKFHL
2660 2670 2680 2690 2700
PSFDEDDLMK ILSIIMLDSC TTRVFQQTLN IIYNLSKLQG CMSIFTKHLV
2710 2720 2730 2740 2750
SLAISIMSKL KSALDGLSRE VGTITTGMEI NSELLQKFTL PSSDQAKLLK
2760 2770 2780 2790 2800
ILTTVDFLYT HKRKEEERNV KDLQSLYDKM NGGPVWSSLS ECLSQFEKSQ
2810 2820 2830 2840 2850
AINTSATILL PLIESLMVVC RRSDLSQNRN TAVKYEDAKL LDFSKTRVEN
2860 2870 2880 2890 2900
LFFPFTDAHK KLLNQMIRSN PKLMSGPFAL LVKNPKVLDF DNKRYFFNAK
2910 2920 2930 2940 2950
LKSDNQERPK LPITVRREQV FLDSYRALFF KTNDEIKNSK LEITFKGESG
2960 2970 2980 2990 3000
VDAGGVTREW YQVLSRQMFN PDYALFLPVP SDKTTFHPNR TSGINPEHLS
3010 3020 3030 3040 3050
FFKFIGMIIG KAIRDQCFLD CHFSREVYKN ILGRPVSLKD MESLDPDYYK
3060 3070 3080 3090 3100
SLVWILENDI TDIIEETFSV ETDDYGEHKV INLIEGGKDI IVTEANKQDY
3110 3120 3130 3140 3150
VKKVVEYKLQ TSVKEQMDNF LVGFYALISK DLITIFDEQE LELLISGLPD
3160 3170 3180 3190 3200
IDVDDWKNNT TYVNYTATCK EVSYFWRAVR SFDAEERAKL LQFVTGTSKV
3210 3220 3230 3240 3250
PLNGFKELSG VNGVCKFSIH RDFGSSERLP SSHTCFNQLN LPPYESYETL
3260
RGSLLLAINE GHEGFGLA
Length:3,268
Mass (Da):374,185
Last modified:November 1, 1996 - v1
Checksum:i8F71F3493D70A6C9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U33050 Genomic DNA. Translation: AAB64910.1.
D63905 Genomic DNA. Translation: BAA21482.1.
BK006938 Genomic DNA. Translation: DAA12291.1.
PIRiS69625.
RefSeqiNP_010745.3. NM_001180765.3.

Genome annotation databases

EnsemblFungiiYDR457W; YDR457W; YDR457W.
GeneIDi852068.
KEGGisce:YDR457W.

Similar proteinsi

Entry informationi

Entry nameiTOM1_YEAST
AccessioniPrimary (citable) accession number: Q03280
Secondary accession number(s): D6VT81, Q7LIK7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: November 1, 1996
Last modified: July 5, 2017
This is version 163 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

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