SCUD (Saccharomyces Cerevisiae Ubiquitination Database)


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Substrate Information

General Information
Standard nameRPB1
Systematic nameYDL140C
AliasRPB220, RPO21, SUA8
DescriptionDNA-directed RNA polymerase II subunit RPB1

Ubiquitination Features
NumberSiteTypeE2E3 ClassE3 SubclassSubstrate ReceptorUbiquitin ReceptorDUBEffect
1 MULTI HECTNARSP5   
2 MULTI HECTNARSP5   
3K695        
4 MULTI       
5 MULTI HECTNARSP5   
6 MULTI(K48-linked) RINGECSELA1  Proteasomal Degradation
7K330;K695MULTIUBC5HECTNARSP5   
8 MULTI    RPN10 Proteasomal Degradation
* Blank: not determined, NA: not applicable.

References
[1]EvidenceHigh MW Product Confirmation
Methodautoradiography (in vitro)
Reference"The large subunit of RNA polymerase II is a substrate of the Rsp5 ubiquitin-protein ligase."
Huibregtse JM, Yang JC, Beaudenon SL.
Proc Natl Acad Sci U S A. 94(8):3656-61 (1997) [9108033]
[2]EvidenceUb-conjugate Confirmation
MethodWestern blot
Reference"Rsp5 ubiquitin-protein ligase mediates DNA damage-induced degradation of the large subunit of RNA polymerase II in Saccharomyces cerevisiae."
Beaudenon SL, Huacani MR, Wang G, McDonnell DP, Huibregtse JM.
Mol Cell Biol. 19(10):6972-9 (1999) [10490634]
[3]EvidencePurification & Protein ID
Methodpurification (6xHis-Myc-ubiquitin), LC/MS
Reference"A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery."
Hitchcock AL, Auld K, Gygi SP, Silver PA.
Proc Natl Acad Sci U S A. 100(22):12735-40 (2003) [14557538]
[4]EvidencePurification & Protein ID
Methodpurification (ubiquitin-chain by UBA domain-containing protein, 6xHis-ubiquitin (two-step)), LC/MS
Reference"Analysis of polyubiquitin conjugates reveals that the Rpn10 substrate receptor contributes to the turnover of multiple proteasome targets."
Mayor T, Lipford JR, Graumann J, Smith GT, Deshaies RJ.
Mol Cell Proteomics. 4(6):741-51 (2005) [15699485]
[5]EvidenceUb-conjugate Confirmation
Methodluminescent assay (biotin-ubiquitin, GST-substrate)
Reference"A high throughput screen to identify substrates for the ubiquitin ligase Rsp5."
Kus B, Gajadhar A, Stanger K, Cho R, Sun W, Rouleau N, Lee T, Chan D, Wolting C, Edwards A, Bosse R, Rotin D.
J Biol Chem. 280(33):29470-8 (2005) [15955809]
[6]EvidenceUb-conjugate Confirmation
MethodWestern blot
Reference"ELA1 and CUL3 are required along with ELC1 for RNA polymerase II polyubiquitylation and degradation in DNA-damaged yeast cells."
Ribar B, Prakash L, Prakash S.
Mol Cell Biol. 27(8):3211-6 (2007) [17296727]
[7]EvidenceUb-conjugate Confirmation
MethodWestern blot
Reference"Communication between distant sites in RNA polymerase II through ubiquitylation factors and the polymerase CTD."
Somesh BP, Sigurdsson S, Saeki H, Erdjument-Bromage H, Tempst P, Svejstrup JQ.
Cell. 129(1):57-68 (2007) [17418786]
[8]EvidencePurification & Protein ID
Methodpurification (ubiquitin-chain by UBA domain-containing protein, 6xHis-ubiquitin (two-step)), LC/MS, validation (statistical quantitative analysis)
Reference"Quantitative profiling of ubiquitylated proteins reveals proteasome substrates and the substrate repertoire influenced by the Rpn10 receptor pathway."
Mayor T, Graumann J, Bryan J, MacCoss MJ, Deshaies RJ.
Mol Cell Proteomics. 6(11):1885-95 (2007) [17644757]

Cross References
Swiss-Prot accessionP04050
SGD YDL140C
Gene Ontology (GO)
Cellular componentGO:0005665DNA-directed RNA polymerase II, core complexTAS:SGD.
Cellular componentGO:0005739mitochondrionIDA:SGD.
Molecular functionGO:0003899DNA-directed RNA polymerase activityTAS:SGD.
Biological processGO:0006366transcription from RNA polymerase II promoterTAS:SGD.
EC number 2.7.7.6

Additional Features
Other Post Translational Modifications (PTM)
Residue indexType
621Phosphothreonine.

Sequence Information
Sequence length1733
Molecular weight191612

	---------+----------+----------+----------+----------+
MVGQQYSSAP LRTVKEVQFG LFSPEEVRAI SVAKIRFPET MDETQTRAKI   50
GGLNDPRLGS IDRNLKCQTC QEGMNECPGH FGHIDLAKPV FHVGFIAKIK   100
KVCECVCMHC GKLLLDEHNE LMRQALAIKD SKKRFAAIWT LCKTKMVCET   150
DVPSEDDPTQ LVSRGGCGNT QPTIRKDGLK LVGSWKKDRA TGDADEPELR   200
VLSTEEILNI FKHISVKDFT SLGFNEVFSR PEWMILTCLP VPPPPVRPSI   250
SFNESQRGED DLTFKLADIL KANISLETLE HNGAPHHAIE EAESLLQFHV   300
ATYMDNDIAG QPQALQKSGR PVKSIRARLK GKEGRIRGNL MGKRVDFSAR   350
TVISGDPNLE LDQVGVPKSI AKTLTYPEVV TPYNIDRLTQ LVRNGPNEHP   400
GAKYVIRDSG DRIDLRYSKR AGDIQLQYGW KVERHIMDND PVLFNRQPSL   450
HKMSMMAHRV KVIPYSTFRL NLSVTSPYNA DFDGDEMNLH VPQSEETRAE   500
LSQLCAVPLQ IVSPQSNKPC MGIVQDTLCG IRKLTLRDTF IELDQVLNML   550
YWVPDWDGVI PTPAIIKPKP LWSGKQILSV AIPNGIHLQR FDEGTTLLSP   600
KDNGMLIIDG QIIFGVVEKK TVGSSNGGLI HVVTREKGPQ VCAKLFGNIQ   650
KVVNFWLLHN GFSTGIGDTI ADGPTMREIT ETIAEAKKKV LDVTKEAQAN   700
LLTAKHGMTL RESFEDNVVR FLNEARDKAG RLAEVNLKDL NNVKQMVMAG   750
SKGSFINIAQ MSACVGQQSV EGKRIAFGFV DRTLPHFSKD DYSPESKGFV   800
ENSYLRGLTP QEFFFHAMGG REGLIDTAVK TAETGYIQRR LVKALEDIMV   850
HYDNTTRNSL GNVIQFIYGE DGMDAAHIEK QSLDTIGGSD AAFEKRYRVD   900
LLNTDHTLDP SLLESGSEIL GDLKLQVLLD EEYKQLVKDR KFLREVFVDG   950
EANWPLPVNI RRIIQNAQQT FHIDHTKPSD LTIKDIVLGV KDLQENLLVL   1000
RGKNEIIQNA QRDAVTLFCC LLRSRLATRR VLQEYRLTKQ AFDWVLSNIE   1050
AQFLRSVVHP GEMVGVLAAQ SIGEPATQMT LNTFHFAGVA SKKVTSGVPR   1100
LKEILNVAKN MKTPSLTVYL EPGHAADQEQ AKLIRSAIEH TTLKSVTIAS   1150
EIYYDPDPRS TVIPEDEEII QLHFSLLDEE AEQSFDQQSP WLLRLELDRA   1200
AMNDKDLTMG QVGERIKQTF KNDLFVIWSE DNDEKLIIRC RVVRPKSLDA   1250
ETEAEEDHML KKIENTMLEN ITLRGVENIE RVVMMKYDRK VPSPTGEYVK   1300
EPEWVLETDG VNLSEVMTVP GIDPTRIYTN SFIDIMEVLG IEAGRAALYK   1350
EVYNVIASDG SYVNYRHMAL LVDVMTTQGG LTSVTRHGFN RSNTGALMRC   1400
SFEETVEILF EAGASAELDD CRGVSENVIL GQMAPIGTGA FDVMIDEESL   1450
VKYMPEQKIT EIEDGQDGGV TPYSNESGLV NADLDVKDEL MFSPLVDSGS   1500
NDAMAGGFTA YGGADYGEAT SPFGAYGEAP TSPGFGVSSP GFSPTSPTYS   1550
PTSPAYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP   1600
TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT   1650
SPSYSPTSPA YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPNYSPTS   1700
PSYSPTSPGY SPGSPAYSPK QDEQKHNENE NSR                     1733

	* Ubiquitinated lysine is denoted as red color.