CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-011059
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 E3 ubiquitin-protein ligase TOM1 
Protein Synonyms/Alias
 Suppressor of snRNA protein 2; Temperature-dependent organization in mitotic nucleus protein 1 
Gene Name
 TOM1 
Gene Synonyms/Alias
 SSR2; YDR457W; D8035.1 
Created Date
 July 27, 2013 
Organism
 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) 
NCBI Taxa ID
 559292 
Lysine Modification
Position
Peptide
Type
References
226FKKSSQQKNNINETQubiquitination[1]
278SIKASVAKAFSDDSGubiquitination[1]
2279EQEKLKNKNLLFNEAubiquitination[1]
Reference
 [1] Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.
 Swaney DL, Beltrao P, Starita L, Guo A, Rush J, Fields S, Krogan NJ, Villén J.
 Nat Methods. 2013 Jul;10(7):676-82. [PMID: 23749301] 
Functional Description
 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 subuni 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. 
Sequence Annotation
 DOMAIN 2932 3268 HECT.
 ACT_SITE 3235 3235 Glycyl thioester intermediate (By
 MOD_RES 1890 1890 Phosphoserine.
 MOD_RES 2096 2096 Phosphothreonine.
 MOD_RES 2119 2119 Phosphoserine.
 MOD_RES 2376 2376 Phosphoserine.
 MOD_RES 2406 2406 Phosphoserine.
 MOD_RES 2418 2418 Phosphoserine.  
Keyword
 Cell cycle; Complete proteome; Ligase; mRNA transport; Nucleus; Phosphoprotein; Reference proteome; rRNA processing; Transcription; Transcription regulation; Transport; Ubl conjugation pathway. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 3268 AA 
Protein Sequence
MVLFTRCEKA RKEKLAAGYK PLVDYLIDCD TPTFLERIEA IQEWDRSRDD LYVWIPILDR 60
MDGLLLKVAE KYKYKQDPKK ECEVKLVEME AHDVDYCLKM LKFTRRLLLN TENRFVYSSG 120
DVLMYLLNCP NFTIKLAVMR ILAILGERFV IAREKIVAHN IFGDHNLRKK TLKLALSLSS 180
SVMDEDGEHF SLVDLYFDKK KVPQKWRKLR FTHYTSNDFK KSSQQKNNIN ETQTSIKKVT 240
MTTQELCEHS LQQIFDKGMA LLPAESWFDF SIKASVAKAF SDDSGENIDL RNIIIETKLN 300
AIAFVNTIFS PPQVSSKLFE LDPYAFNSLT DLISLSETKI PKELRTDALF TLECISLKHV 360
WCSDIIRNLG GNISHGLLFQ ILRYIAKTLR EATDEIDEEY NVRFFYLISN LADVKPLHES 420
LFAAGLIPTL LEIVSIRNCP YKRTLASATH LLETFIDNSE TTTEFIENDG FTMLITSVAN 480
EIDFTLAHPE TWQPPKYSVV YYSISFRELA YIRSLLKLVL KLLSTDSGDR IRNLIDSPIL 540
VSLKKILENK LVFGLTLITY TLDVVQKVIN SEPTIYPVLV EAGLIPYVID NFPKLIGPSA 600
ELLSLLPDVV SAICLNPEGL KQVKEKGLIN NLFDFLLDAD HARILTGGDR STEYGTDIDE 660
LARHYPDLKA NIVEALCNVI RKMPSTFRNE REFLFTSPKD QKYFFHRKNE EILTDKEEHE 720
PAYWELLDKG TMLDTFTSVL FGMSLGNGSF SQVPQHLEAR DFLAIIFMEN PPYEYFTSVA 780
ISNVTEVLQY LDEKYEDYAF MDVMKVLNDQ LENLNDFLNS PNDRSFFLER DGENSVRSCH 840
SKLCRLAAIL NIVTNVYIDL TTLSCKRIMQ IYSYFDKRGF SLIKNLKLLF QKCALEEMYI 900
RQHMPDSVIT ETMPLPIVDV SGDGPPLQIY IDDPKKGDQK GKITSVKTRN TLQMRTILYT 960
LQSNTAILFR CFLRLSHSRN MDLEHKDLTT EVHIFENVVE NVIEMLKATE LEGHLPYILV 1020
LLNFNTFVFT IPKASPNSTE ILQTIPAYIF YQKGGYLLYL HIIRDLFTRM TKIKDLSSLD 1080
NINYIDESNG ILTLSCLINA LTFYNKSMQT ETMENVQSIG KYYVSIDDDY NIMKALTVPI 1140
KVMALAMILD LDKSDSLFKT QSRNVPYSVF KQLLSMLKNI FTNVNIYTKE LYELHWDLIF 1200
PPIKKISLFE QVGIPGDVAA NYLTDTGDDL PADNSIGLFS PEQWEKYKKL IGEDKSIYYP 1260
QPMQAQYYKG CSSKELDELR DTFFNDGLPS RIFTVLPFYP KLVNAFAKTL LQIFTKYDEP 1320
TEVFAGRILD RILETDLDDP ATLSSLIHLF GIFLNEKYIY QKASHLMQRF IEYLEKSLKP 1380
EHVNTPWFSK ALYVYEIILA KSELPHLEEL SKDVLLRYPL LSMAKVFRIP DPMKQKLFDI 1440
LIRVSDISNF YSALATSRIL IFYSRDELYA NNIARSGILS RLLKVIGSFQ KLDKINFLES 1500
SFLLLTRRCF ETTENVDALI RAEINRSFTA RPLGGGDDAV RELTTILEEK AHVVMRSPSQ 1560
FIDVLCETAR FHEFDDQGAL VDYSLKRFLG EKDKNTQASS TEKSDIYERT GIMHLLLSQL 1620
MAASEKDWLS EPANSSDLPE NKKAQLDPSR NPVCAYMIFL LKLLVELVSS YNQCKFEFLT 1680
FSRRNTYAER PRPRTTAINF FLYRLLDKPV GTDHDKHEAK RREVIGMLAR SVIIGFLATV 1740
QDDRTTKTDV KLADPHMNFI RKFAIEAIIK AIRNATSSSK LLESNHLKLD MWFRIITSMV 1800
YVQAPYLRQL LDSNKVEADQ YQLCKLVIDL GLPSVITEAM ASIDLNYPFS KKIFNVAVEA 1860
LNTISSTRNN FSEHFKIEDH DEVEDEVDES DKEEIPDMFK NSALGMYDVE DIEEDDDDDT 1920
SLIGDDDAMA FVDSDNGFEV VFSDEDDDMG EEDADDARSD SEENELSSEM QSSTADGTDV 1980
DYEVDDADGL IINIDQPSGD DEEMADYDAN ISHSSHSENE DDASMDVIEV YDDELSSGYD 2040
VDLSDYDVDE SDWDSGLSSL SISDEDSESS EDEPINSTRM GDSRRRWLIA EGVELTDDSQ 2100
GESEEDDRGV FRGIEHIFSN ENEPLFRVHD EMRHRNHHRS INRTHFHSAM SAPSLSLLNR 2160
GRRNQSNLIN PLGPTGLEQV ENDISDQVTV AGSGSRPRSH HLHFSEVLVS GSFFDEPVLD 2220
GIILKSTVSR WKDIFDMFYD SKTYANCIIP TVINRLYKVS LALQKDLENK REQEKLKNKN 2280
LLFNEAKVES HNSSDAISVE QDDIQESNVT HDDHEPVYVT IQGSEVDIGG TDIDPEFMNA 2340
LPDDIRADVF AQHVRERRAE ARLNSDHNVH SREIDSDFLE AIPEDIREGI LDTEAEEQRM 2400
FGRIGSSADV IRADDDVSNN DEEVENGLDH GNSNDRNNAD PEKKKPARIY FAPLIDRAGI 2460
ASLMKSVFIS KPYIQREIYH ELFYRLCSSK QNRNDLMNTF LFILSEGIID QHSLEKVYNI 2520
ISSRAMGHAK TTTVRQLPSD CTPLTVANQT IEILQSLIDA DSRLKYFLIA EHDNLIVNKA 2580
NNKSRKEALP DKKLRWPLWH LFSLLDRKLI TDESVLMDLL TRILQVCTKT LAVLSTSSNG 2640
KENLSKKFHL PSFDEDDLMK ILSIIMLDSC TTRVFQQTLN IIYNLSKLQG CMSIFTKHLV 2700
SLAISIMSKL KSALDGLSRE VGTITTGMEI NSELLQKFTL PSSDQAKLLK ILTTVDFLYT 2760
HKRKEEERNV KDLQSLYDKM NGGPVWSSLS ECLSQFEKSQ AINTSATILL PLIESLMVVC 2820
RRSDLSQNRN TAVKYEDAKL LDFSKTRVEN LFFPFTDAHK KLLNQMIRSN PKLMSGPFAL 2880
LVKNPKVLDF DNKRYFFNAK LKSDNQERPK LPITVRREQV FLDSYRALFF KTNDEIKNSK 2940
LEITFKGESG VDAGGVTREW YQVLSRQMFN PDYALFLPVP SDKTTFHPNR TSGINPEHLS 3000
FFKFIGMIIG KAIRDQCFLD CHFSREVYKN ILGRPVSLKD MESLDPDYYK SLVWILENDI 3060
TDIIEETFSV ETDDYGEHKV INLIEGGKDI IVTEANKQDY VKKVVEYKLQ TSVKEQMDNF 3120
LVGFYALISK DLITIFDEQE LELLISGLPD IDVDDWKNNT TYVNYTATCK EVSYFWRAVR 3180
SFDAEERAKL LQFVTGTSKV PLNGFKELSG VNGVCKFSIH RDFGSSERLP SSHTCFNQLN 3240
LPPYESYETL RGSLLLAINE GHEGFGLA 3268 
Gene Ontology
 GO:0016021; C:integral to membrane; ISM:SGD.
 GO:0005730; C:nucleolus; IDA:SGD.
 GO:0004842; F:ubiquitin-protein ligase activity; IDA:SGD.
 GO:0000448; P:cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
 GO:0000480; P:endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
 GO:0000447; P: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); IMP:SGD.
 GO:0000472; P:endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
 GO:0007067; P:mitosis; IMP:SGD.
 GO:0051028; P:mRNA transport; IEA:UniProtKB-KW.
 GO:0006913; P:nucleocytoplasmic transport; IMP:SGD.
 GO:0006997; P:nucleus organization; IMP:SGD.
 GO:0042787; P:protein ubiquitination involved in ubiquitin-dependent protein catabolic process; IMP:SGD.
 GO:0008361; P:regulation of cell size; IMP:SGD.
 GO:0006355; P:regulation of transcription, DNA-dependent; IEA:UniProtKB-KW.
 GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW. 
Interpro
 IPR016024; ARM-type_fold.
 IPR025527; DUF4414.
 IPR010309; E3_Ub_ligase_DUF908.
 IPR010314; E3_Ub_ligase_DUF913.
 IPR000569; HECT. 
Pfam
 PF14377; DUF4414
 PF06012; DUF908
 PF06025; DUF913
 PF00632; HECT 
SMART
 SM00119; HECTc 
PROSITE
 PS50237; HECT 
PRINTS