CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-002664
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 DNA-directed RNA polymerase II subunit RPB2 
Protein Synonyms/Alias
 RNA polymerase II subunit 2; B150; DNA-directed RNA polymerase II 140 kDa polypeptide 
Gene Name
 RPB2 
Gene Synonyms/Alias
 RPB150; RPO22; YOR151C 
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
99FGKIYVTKPMVNESDubiquitination[1]
227GNIVQVFKKAAPSPIacetylation[2]
228NIVQVFKKAAPSPISubiquitination[1]
257FISTLQVKLYGREGSubiquitination[1]
270GSSARTIKATLPYIKubiquitination[1]
277KATLPYIKQDIPIVIubiquitination[3]
353EKRIQYAKDILQKEFubiquitination[1]
606TLRTLRRKGDINPEVubiquitination[1]
775TYQSAMGKQAMGVFLubiquitination[1]
801NILYYPQKPLGTTRAubiquitination[1]
864RSYMDQEKKYGMSITubiquitination[1]
914GEDVIIGKTTPISPDubiquitination[1]
979KIPQIGDKFASRHGQubiquitination[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]
 [2] Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae.
 Henriksen P, Wagner SA, Weinert BT, Sharma S, Bacinskaja G, Rehman M, Juffer AH, Walther TC, Lisby M, Choudhary C.
 Mol Cell Proteomics. 2012 Nov;11(11):1510-22. [PMID: 22865919]
 [3] 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] 
Functional Description
 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerases II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the 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. 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. The cleft is surrounded by jaws: an upper jaw formed by portions of RBP1, RPB2 and RPB9, and a lower jaw. The jaws are thought to grab the incoming DNA template. The fork loop 1 (RPB2) interacts with the RNA-DNA hybrid, possibly stabilizing it. 
Sequence Annotation
 ZN_FING 1163 1185 C4-type.
 REGION 467 478 Fork loop 1.
 METAL 837 837 Magnesium; shared with RPB1.
 METAL 1163 1163 Zinc.
 METAL 1166 1166 Zinc.
 METAL 1182 1182 Zinc.
 METAL 1185 1185 Zinc.
 MOD_RES 919 919 Phosphoserine.  
Keyword
 3D-structure; Complete proteome; Direct protein sequencing; DNA-directed RNA polymerase; Magnesium; Metal-binding; Nucleotidyltransferase; Nucleus; Phosphoprotein; Reference proteome; Transcription; Transferase; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1224 AA 
Protein Sequence
MSDLANSEKY YDEDPYGFED ESAPITAEDS WAVISAFFRE KGLVSQQLDS FNQFVDYTLQ 60
DIICEDSTLI LEQLAQHTTE SDNISRKYEI SFGKIYVTKP MVNESDGVTH ALYPQEARLR 120
NLTYSSGLFV DVKKRTYEAI DVPGRELKYE LIAEESEDDS ESGKVFIGRL PIMLRSKNCY 180
LSEATESDLY KLKECPFDMG GYFIINGSEK VLIAQERSAG NIVQVFKKAA PSPISHVAEI 240
RSALEKGSRF ISTLQVKLYG REGSSARTIK ATLPYIKQDI PIVIIFRALG IIPDGEILEH 300
ICYDVNDWQM LEMLKPCVED GFVIQDRETA LDFIGRRGTA LGIKKEKRIQ YAKDILQKEF 360
LPHITQLEGF ESRKAFFLGY MINRLLLCAL DRKDQDDRDH FGKKRLDLAG PLLAQLFKTL 420
FKKLTKDIFR YMQRTVEEAH DFNMKLAINA KTITSGLKYA LATGNWGEQK KAMSSRAGVS 480
QVLNRYTYSS TLSHLRRTNT PIGRDGKLAK PRQLHNTHWG LVCPAETPEG QACGLVKNLS 540
LMSCISVGTD PMPIITFLSE WGMEPLEDYV PHQSPDATRV FVNGVWHGVH RNPARLMETL 600
RTLRRKGDIN PEVSMIRDIR EKELKIFTDA GRVYRPLFIV EDDESLGHKE LKVRKGHIAK 660
LMATEYQDIE GGFEDVEEYT WSSLLNEGLV EYIDAEEEES ILIAMQPEDL EPAEANEEND 720
LDVDPAKRIR VSHHATTFTH CEIHPSMILG VAASIIPFPD HNQSPRNTYQ SAMGKQAMGV 780
FLTNYNVRMD TMANILYYPQ KPLGTTRAME YLKFRELPAG QNAIVAIACY SGYNQEDSMI 840
MNQSSIDRGL FRSLFFRSYM DQEKKYGMSI TETFEKPQRT NTLRMKHGTY DKLDDDGLIA 900
PGVRVSGEDV IIGKTTPISP DEEELGQRTA YHSKRDASTP LRSTENGIVD QVLVTTNQDG 960
LKFVKVRVRT TKIPQIGDKF ASRHGQKGTI GITYRREDMP FTAEGIVPDL IINPHAIPSR 1020
MTVAHLIECL LSKVAALSGN EGDASPFTDI TVEGISKLLR EHGYQSRGFE VMYNGHTGKK 1080
LMAQIFFGPT YYQRLRHMVD DKIHARARGP MQVLTRQPVE GRSRDGGLRF GEMERDCMIA 1140
HGAASFLKER LMEASDAFRV HICGICGLMT VIAKLNHNQF ECKGCDNKID IYQIHIPYAA 1200
KLLFQELMAM NITPRLYTDR SRDF 1224 
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:InterPro.
 GO:0003899; F:DNA-directed RNA polymerase activity; IEA:UniProtKB-KW.
 GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
 GO:0032549; F:ribonucleoside binding; IEA:InterPro.
 GO:0006366; P:transcription from RNA polymerase II promoter; IMP:SGD. 
Interpro
 IPR015712; DNA-dir_RNA_pol_su2.
 IPR007120; DNA-dir_RNA_pol_su2_6.
 IPR007121; RNA_pol_bsu_CS.
 IPR007644; RNA_pol_bsu_protrusion.
 IPR007642; RNA_pol_Rpb2_2.
 IPR007645; RNA_pol_Rpb2_3.
 IPR007646; RNA_pol_Rpb2_4.
 IPR007647; RNA_pol_Rpb2_5.
 IPR007641; RNA_pol_Rpb2_7.
 IPR014724; RNA_pol_RPB2_OB-fold. 
Pfam
 PF04563; RNA_pol_Rpb2_1
 PF04561; RNA_pol_Rpb2_2
 PF04565; RNA_pol_Rpb2_3
 PF04566; RNA_pol_Rpb2_4
 PF04567; RNA_pol_Rpb2_5
 PF00562; RNA_pol_Rpb2_6
 PF04560; RNA_pol_Rpb2_7 
SMART
  
PROSITE
 PS01166; RNA_POL_BETA 
PRINTS