CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-002081
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 DNA-directed RNA polymerase II subunit RPB1 
Protein Synonyms/Alias
 RNA polymerase II subunit 1; RNA polymerase II subunit B1; DNA-directed RNA polymerase III largest subunit; RNA polymerase II subunit B220 
Gene Name
 RPO21 
Gene Synonyms/Alias
 RPB1; RPB220; SUA8; YDL140C; D2150 
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
143AAIWTLCKTKMVCETubiquitination[1]
145IWTLCKTKMVCETDVubiquitination[1]
186LKLVGSWKKDRATGDubiquitination[1]
368LDQVGVPKSIAKTLTubiquitination[1]
372GVPKSIAKTLTYPEVubiquitination[1]
687TETIAEAKKKVLDVTubiquitination[1]
689TIAEAKKKVLDVTKEubiquitination[1]
695KKVLDVTKEAQANLLubiquitination[1, 2, 3, 4]
705QANLLTAKHGMTLREubiquitination[1]
738RLAEVNLKDLNNVKQubiquitination[1]
744LKDLNNVKQMVMAGSubiquitination[1]
789RTLPHFSKDDYSPESubiquitination[1]
797DDYSPESKGFVENSYubiquitination[1]
830GLIDTAVKTAETGYIubiquitination[1]
843YIQRRLVKALEDIMVubiquitination[1]
895GSDAAFEKRYRVDLLubiquitination[1]
1003NLLVLRGKNEIIQNAubiquitination[1]
1039LQEYRLTKQAFDWVLubiquitination[1]
1093FAGVASKKVTSGVPRubiquitination[1]
1102TSGVPRLKEILNVAKubiquitination[1]
1205DRAAMNDKDLTMGQVubiquitination[1]
1246RCRVVRPKSLDAETEubiquitination[1, 4]
1286IERVVMMKYDRKVPSubiquitination[1]
1350AGRAALYKEVYNVIAubiquitination[1, 4]
1487VNADLDVKDELMFSPsumoylation[5]
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]
 [2] 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. 2003 Oct 28;100(22):12735-40. [PMID: 14557538]
 [3] Identification, analysis, and prediction of protein ubiquitination sites.
 Radivojac P, Vacic V, Haynes C, Cocklin RR, Mohan A, Heyen JW, Goebl MG, Iakoucheva LM.
 Proteins. 2010 Feb 1;78(2):365-80. [PMID: 19722269]
 [4] Sites of ubiquitin attachment in Saccharomyces cerevisiae.
 Starita LM, Lo RS, Eng JK, von Haller PD, Fields S.
 Proteomics. 2012 Jan;12(2):236-40. [PMID: 22106047]
 [5] Rpb1 sumoylation in response to UV radiation or transcriptional impairment in yeast.
 Chen X, Ding B, LeJeune D, Ruggiero C, Li S.
 PLoS One. 2009;4(4):e5267. [PMID: 19384408] 
Functional Description
 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. During a transcription cycle, Pol II, general transcription factors and the Mediator complex assemble as the preinitiation complex (PIC) at the promoter. 11-15 base pairs of DNA surrounding the transcription start site are melted and the single stranded DNA template strand of the promoter is positioned deeply within the central active site cleft of Pol II to form the open complex. After synthesis of about 30 bases of RNA, Pol II releases its contacts with the core promoter and the rest of the transcription machinery (promoter clearance) and enters the stage of transcription elongation in which it moves on the template as the transcript elongates. Pol II appears to oscillate between inactive and active conformations at each step of nucleotide addition. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing. Pol II is composed of mobile elements that move relative to each other. The core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. The clamp element (portions of RPB1, RPB2 and RPB3) is connected to the core through a set of flexible switches and moves to open and close the cleft. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. In elongating Pol II, the lid loop (RPB1) appears to act as a wedge to drive apart the DNA and RNA strands at the upstream end of the transcription bubble and guide the RNA strand toward the RNA exit groove located near the base of the largely unstructured CTD domain of RPB1. The rudder loop (RPB1) interacts with single stranded DNA after separation from the RNA strand, likely preventing reassociation with the exiting RNA. The cleft is surrounded by jaws: an upper jaw formed by portions of RBP1, RPB2 and RPB9, and a lower jaw, formed by RPB5 and portions of RBP1. The jaws are thought to grab the incoming DNA template, mainly by RPB5 direct contacts to DNA. 
Sequence Annotation
 REPEAT 1549 1555 1.
 REPEAT 1556 1562 2.
 REPEAT 1563 1569 3.
 REPEAT 1570 1576 4.
 REPEAT 1577 1583 5.
 REPEAT 1584 1590 6.
 REPEAT 1591 1597 7.
 REPEAT 1598 1604 8.
 REPEAT 1605 1611 9.
 REPEAT 1612 1618 10.
 REPEAT 1619 1625 11.
 REPEAT 1626 1632 12.
 REPEAT 1633 1639 13.
 REPEAT 1640 1646 14.
 REPEAT 1647 1653 15.
 REPEAT 1654 1660 16.
 REPEAT 1661 1667 17.
 REPEAT 1668 1674 18.
 REPEAT 1675 1681 19.
 REPEAT 1682 1688 20.
 REPEAT 1689 1695 21.
 REPEAT 1696 1702 22.
 REPEAT 1703 1709 23.
 REPEAT 1710 1716 24; approximate.
 REGION 248 260 Lid loop.
 REGION 306 323 Rudder loop.
 REGION 810 822 Bridging helix.
 REGION 1549 1716 24 X 7 AA approximate tandem repeats of
 METAL 67 67 Zinc 1.
 METAL 70 70 Zinc 1.
 METAL 77 77 Zinc 1.
 METAL 80 80 Zinc 1.
 METAL 107 107 Zinc 2.
 METAL 110 110 Zinc 2.
 METAL 148 148 Zinc 2.
 METAL 167 167 Zinc 2.
 METAL 481 481 Magnesium 1; catalytic.
 METAL 481 481 Magnesium 2; shared with RPB2.
 METAL 483 483 Magnesium 1; catalytic.
 METAL 483 483 Magnesium 2; shared with RPB2.
 METAL 485 485 Magnesium 1; catalytic.
 MOD_RES 1471 1471 Phosphothreonine.
 CROSSLNK 695 695 Glycyl lysine isopeptide (Lys-Gly)  
Keyword
 3D-structure; Complete proteome; DNA-binding; DNA-directed RNA polymerase; Isopeptide bond; Magnesium; Metal-binding; Nucleotidyltransferase; Nucleus; Phosphoprotein; Reference proteome; Repeat; Transcription; Transferase; Ubl conjugation; Zinc. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1733 AA 
Protein Sequence
MVGQQYSSAP LRTVKEVQFG LFSPEEVRAI SVAKIRFPET MDETQTRAKI GGLNDPRLGS 60
IDRNLKCQTC QEGMNECPGH FGHIDLAKPV FHVGFIAKIK KVCECVCMHC GKLLLDEHNE 120
LMRQALAIKD SKKRFAAIWT LCKTKMVCET DVPSEDDPTQ LVSRGGCGNT QPTIRKDGLK 180
LVGSWKKDRA TGDADEPELR VLSTEEILNI FKHISVKDFT SLGFNEVFSR PEWMILTCLP 240
VPPPPVRPSI SFNESQRGED DLTFKLADIL KANISLETLE HNGAPHHAIE EAESLLQFHV 300
ATYMDNDIAG QPQALQKSGR PVKSIRARLK GKEGRIRGNL MGKRVDFSAR TVISGDPNLE 360
LDQVGVPKSI AKTLTYPEVV TPYNIDRLTQ LVRNGPNEHP GAKYVIRDSG DRIDLRYSKR 420
AGDIQLQYGW KVERHIMDND PVLFNRQPSL HKMSMMAHRV KVIPYSTFRL NLSVTSPYNA 480
DFDGDEMNLH VPQSEETRAE LSQLCAVPLQ IVSPQSNKPC MGIVQDTLCG IRKLTLRDTF 540
IELDQVLNML YWVPDWDGVI PTPAIIKPKP LWSGKQILSV AIPNGIHLQR FDEGTTLLSP 600
KDNGMLIIDG QIIFGVVEKK TVGSSNGGLI HVVTREKGPQ VCAKLFGNIQ KVVNFWLLHN 660
GFSTGIGDTI ADGPTMREIT ETIAEAKKKV LDVTKEAQAN LLTAKHGMTL RESFEDNVVR 720
FLNEARDKAG RLAEVNLKDL NNVKQMVMAG SKGSFINIAQ MSACVGQQSV EGKRIAFGFV 780
DRTLPHFSKD DYSPESKGFV ENSYLRGLTP QEFFFHAMGG REGLIDTAVK TAETGYIQRR 840
LVKALEDIMV HYDNTTRNSL GNVIQFIYGE DGMDAAHIEK QSLDTIGGSD AAFEKRYRVD 900
LLNTDHTLDP SLLESGSEIL GDLKLQVLLD EEYKQLVKDR KFLREVFVDG EANWPLPVNI 960
RRIIQNAQQT FHIDHTKPSD LTIKDIVLGV KDLQENLLVL RGKNEIIQNA QRDAVTLFCC 1020
LLRSRLATRR VLQEYRLTKQ AFDWVLSNIE AQFLRSVVHP GEMVGVLAAQ SIGEPATQMT 1080
LNTFHFAGVA SKKVTSGVPR LKEILNVAKN MKTPSLTVYL EPGHAADQEQ AKLIRSAIEH 1140
TTLKSVTIAS EIYYDPDPRS TVIPEDEEII QLHFSLLDEE AEQSFDQQSP WLLRLELDRA 1200
AMNDKDLTMG QVGERIKQTF KNDLFVIWSE DNDEKLIIRC RVVRPKSLDA ETEAEEDHML 1260
KKIENTMLEN ITLRGVENIE RVVMMKYDRK VPSPTGEYVK EPEWVLETDG VNLSEVMTVP 1320
GIDPTRIYTN SFIDIMEVLG IEAGRAALYK EVYNVIASDG SYVNYRHMAL LVDVMTTQGG 1380
LTSVTRHGFN RSNTGALMRC SFEETVEILF EAGASAELDD CRGVSENVIL GQMAPIGTGA 1440
FDVMIDEESL VKYMPEQKIT EIEDGQDGGV TPYSNESGLV NADLDVKDEL MFSPLVDSGS 1500
NDAMAGGFTA YGGADYGEAT SPFGAYGEAP TSPGFGVSSP GFSPTSPTYS PTSPAYSPTS 1560
PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS 1620
PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPA YSPTSPSYSP TSPSYSPTSP 1680
SYSPTSPSYS PTSPNYSPTS PSYSPTSPGY SPGSPAYSPK QDEQKHNENE NSR 1733 
Gene Ontology
 GO:0005665; C:DNA-directed RNA polymerase II, core complex; IDA:SGD.
 GO:0005739; C:mitochondrion; IDA:SGD.
 GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
 GO:0003899; F:DNA-directed RNA polymerase activity; IEA:UniProtKB-KW.
 GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
 GO:0006366; P:transcription from RNA polymerase II promoter; IMP:SGD. 
Interpro
 IPR009010; Asp_de-COase-like_dom.
 IPR000722; RNA_pol_asu.
 IPR000684; RNA_pol_II_repeat_euk.
 IPR006592; RNA_pol_N.
 IPR007080; RNA_pol_Rpb1_1.
 IPR007066; RNA_pol_Rpb1_3.
 IPR007083; RNA_pol_Rpb1_4.
 IPR007081; RNA_pol_Rpb1_5.
 IPR007075; RNA_pol_Rpb1_6.
 IPR007073; RNA_pol_Rpb1_7. 
Pfam
 PF04997; RNA_pol_Rpb1_1
 PF00623; RNA_pol_Rpb1_2
 PF04983; RNA_pol_Rpb1_3
 PF05000; RNA_pol_Rpb1_4
 PF04998; RNA_pol_Rpb1_5
 PF04992; RNA_pol_Rpb1_6
 PF04990; RNA_pol_Rpb1_7
 PF05001; RNA_pol_Rpb1_R 
SMART
 SM00663; RPOLA_N 
PROSITE
 PS00115; RNA_POL_II_REPEAT 
PRINTS