UniProt Accession

 RPB2_HUMAN; P30876; A8K1A8; Q8IZ61 

Genbank Protein ID

 X63563; AK289823; CH471057; BC023503; AF055028 

Genbank Nucleotide ID

 CAA45124.1; BAF82512.1; EAX05519.1; AAH23503.2; AAC09367.1 

Protein Name

 DNA-directed RNA polymerase II subunit RPB2 

Protein Synonyms/Alias

 DNA-directed RNA polymerase II 140 kDa polypeptide; DNA-directed RNA polymerase II subunit B; RNA polymerase II subunit 2; RNA polymerase II subunit B2 

Gene Name

 POLR2B 

Gene Synonyms/Alias

  

Created Date

 July 27, 2013 

Organism

 Homo sapiens (Human) 

NCBI Taxa ID

 9606 

Lysine Modification

Position	Peptide	Type	References
87	EPPRYLLKFEQIYLS	ubiquitination	[1, 2]
95	FEQIYLSKPTHWERD	ubiquitination	[1, 2, 3, 4, 5, 6, 7, 8]
130	PLYVDITKTVIKEGE	ubiquitination	[1, 2, 7]
134	DITKTVIKEGEEQLQ	ubiquitination	[1, 2, 7]
146	QLQTQHQKTFIGKIP	ubiquitination	[1, 2, 3, 5, 7, 8]
151	HQKTFIGKIPIMLRS	ubiquitination	[1, 2, 3, 5, 6, 7, 8]
199	KVLIAQEKMATNTVY	ubiquitination	[1, 2, 7]
210	NTVYVFAKKDSKYAY	ubiquitination	[1, 2, 7]
211	TVYVFAKKDSKYAYT	ubiquitination	[2]
214	VFAKKDSKYAYTGEC	ubiquitination	[2]
248	ARGGQGAKKSAIGQR	ubiquitination	[1, 7]
249	RGGQGAKKSAIGQRI	ubiquitination	[1, 7]
264	VATLPYIKQEVPIII	ubiquitination	[1, 2, 4, 7]
340	EKRIKYAKEVLQKEM	ubiquitination	[1, 2, 6, 7]
345	YAKEVLQKEMLPHVG	ubiquitination	[2]
360	VSDFCETKKAYFLGY	ubiquitination	[2]
361	SDFCETKKAYFLGYM	ubiquitination	[2]
391	DRDHYGNKRLDLAGP	ubiquitination	[1, 2, 7]
413	GMFKNLLKEVRIYAQ	ubiquitination	[1]
421	EVRIYAQKFIDRGKD	ubiquitination	[1, 2, 3, 6, 8]
427	QKFIDRGKDFNLELA	ubiquitination	[1, 2]
436	FNLELAIKTRIISDG	ubiquitination	[1]
445	RIISDGLKYSLATGN	ubiquitination	[1, 2, 7]
457	TGNWGDQKKAHQARA	ubiquitination	[1, 2, 5, 7]
458	GNWGDQKKAHQARAG	ubiquitination	[2]
578	GCWVGIHKDPEQLMN	ubiquitination	[2]
630	RPLLIVEKQKLLLKK	ubiquitination	[1, 2, 5, 7]
632	LLIVEKQKLLLKKRH	ubiquitination	[2]
644	KRHIDQLKEREYNNY	ubiquitination	[1, 2, 5, 7]
730	TYQSAMGKQAMGVYI	ubiquitination	[1, 2, 5, 7]
756	HVLYYPQKPLVTTRS	ubiquitination	[1, 2, 3, 5, 6, 7, 8]
815	SVFYRSYKEQESKKG	acetylation	[9]
815	SVFYRSYKEQESKKG	ubiquitination	[1]
820	SYKEQESKKGFDQEE	acetylation	[9]
821	YKEQESKKGFDQEEV	ubiquitination	[1, 2, 7]
831	DQEEVFEKPTRETCQ	ubiquitination	[1, 2, 4, 5, 7]
847	MRHAIYDKLDDDGLI	ubiquitination	[1, 2, 3, 4, 7, 8]
869	GDDVIIGKTVTLPEN	ubiquitination	[1, 2, 4, 5, 7]
917	TLNQEGYKFCKIRVR	ubiquitination	[2]
934	RIPQIGDKFASRHGQ	ubiquitination	[1, 2, 3, 5, 6, 7, 8]
942	FASRHGQKGTCGIQY	ubiquitination	[2, 4]
988	LIECLQGKVSANKGE	ubiquitination	[2]
993	QGKVSANKGEIGDAT	ubiquitination	[1, 2, 4, 5, 6, 7]
1010	NDAVNVQKISNLLSD	ubiquitination	[1, 2, 6, 7]
1036	YNGFTGRKITSQIFI	ubiquitination	[1, 2, 5, 6]
1058	LKHMVDDKIHSRARG	ubiquitination	[1]
1143	ECRGCRNKTQISLVR	ubiquitination	[1, 2, 5, 7]

Reference

 [1] Systematic and quantitative assessment of the ubiquitin-modified proteome.
 Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP.
 Mol Cell. 2011 Oct 21;44(2):325-40. [PMID: 21906983]
 [2] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [3] A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.
 Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, Choudhary C.
 Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. [PMID: 21890473]
 [4] Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels.
 Lee KA, Hammerle LP, Andrews PS, Stokes MP, Mustelin T, Silva JC, Black RA, Doedens JR.
 J Biol Chem. 2011 Dec 2;286(48):41530-8. [PMID: 21987572]
 [5] Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
 Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA.
 Mol Cell Proteomics. 2012 May;11(5):148-59. [PMID: 22505724]
 [6] Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass.
 Povlsen LK, Beli P, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker-Jensen S, Mailand N, Choudhary C.
 Nat Cell Biol. 2012 Oct;14(10):1089-98. [PMID: 23000965]
 [7] Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization.
 Sarraf SA, Raman M, Guarani-Pereira V, Sowa ME, Huttlin EL, Gygi SP, Harper JW.
 Nature. 2013 Apr 18;496(7445):372-6. [PMID: 23503661]
 [8] hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.
 Chen Z, Zhou Y, Song J, Zhang Z.
 Biochim Biophys Acta. 2013 Aug;1834(8):1461-7. [PMID: 23603789]
 [9] Regulation of cellular metabolism by protein lysine acetylation.
 Zhao S, Xu W, Jiang W, Yu W, Lin Y, Zhang T, Yao J, Zhou L, Zeng Y, Li H, Li Y, Shi J, An W, Hancock SM, He F, Qin L, Chin J, Yang P, Chen X, Lei Q, Xiong Y, Guan KL.
 Science. 2010 Feb 19;327(5968):1000-4. [PMID: 20167786] 

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 polymerase 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. It is composed of mobile elements that move relative to each other. RPB2 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template (By similarity). 

Sequence Annotation

 ZN_FING 1119 1140 C4-type.
 METAL 792 792 Magnesium; shared with RPB1 (By
 METAL 1119 1119 Zinc (By similarity).
 METAL 1122 1122 Zinc (By similarity).
 METAL 1137 1137 Zinc (By similarity).
 METAL 1140 1140 Zinc (By similarity).  

Keyword

 Complete proteome; DNA-directed RNA polymerase; Magnesium; Metal-binding; Nucleotidyltransferase; Nucleus; Reference proteome; Transcription; Transferase; Zinc; Zinc-finger. 

Sequence Source

 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 

Protein Length

 1174 AA 

Protein Sequence

Gene Ontology

 GO:0005665; C:DNA-directed RNA polymerase II, core complex; IDA:UniProtKB.
 GO:0003682; F:chromatin binding; IEA:Compara.
 GO:0003677; F:DNA binding; TAS:ProtInc.
 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:0006370; P:7-methylguanosine mRNA capping; TAS:Reactome.
 GO:0000398; P:mRNA splicing, via spliceosome; TAS:Reactome.
 GO:0050434; P:positive regulation of viral transcription; TAS:Reactome.
 GO:0006368; P:transcription elongation from RNA polymerase II promoter; TAS:Reactome.
 GO:0006367; P:transcription initiation from RNA polymerase II promoter; TAS:Reactome.
 GO:0006283; P:transcription-coupled nucleotide-excision repair; TAS:Reactome.
 GO:0022415; P:viral reproductive process; TAS:Reactome. 

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