UniProt Accession

 RPB1_HUMAN; P24928; A6NN93; B9EH88 

Genbank Protein ID

 X63564; X74874; X74873; X74872; X74871; X74870; AC113189; CH471108; BC137231 

Genbank Nucleotide ID

 CAA45125.1; CAA52862.1; CAA52862.1; CAA52862.1; CAA52862.1; CAA52862.1; EAW90181.1; AAI37232.1 

Protein Name

 DNA-directed RNA polymerase II subunit RPB1 

Protein Synonyms/Alias

 RNA polymerase II subunit B1; DNA-directed RNA polymerase II subunit A; DNA-directed RNA polymerase III largest subunit; RNA-directed RNA polymerase II subunit RPB1 

Gene Name

 POLR2A 

Gene Synonyms/Alias

 POLR2 

Created Date

 July 27, 2013 

Organism

 Homo sapiens (Human) 

NCBI Taxa ID

 9606 

Lysine Modification

Position	Peptide	Type	References
32	VLSPDELKRMSVTEG	ubiquitination	[1, 2, 3, 4, 5]
42	SVTEGGIKYPETTEG	ubiquitination	[1, 4, 6, 7, 8]
92	FGHIELAKPVFHVGF	ubiquitination	[4]
116	CVCFFCSKLLVDSNN	ubiquitination	[2, 4]
125	LVDSNNPKIKDILAK	ubiquitination	[4]
127	DSNNPKIKDILAKSK	ubiquitination	[4, 8]
132	KIKDILAKSKGQPKK	ubiquitination	[4]
149	THVYDLCKGKNICEG	ubiquitination	[2, 4, 8]
151	VYDLCKGKNICEGGE	ubiquitination	[2, 4]
163	GGEEMDNKFGVEQPE	ubiquitination	[2, 3, 4]
177	EGDEDLTKEKGHGGC	ubiquitination	[1, 2, 3, 5, 8]
179	DEDLTKEKGHGGCGR	ubiquitination	[4]
203	LELYAEWKHVNEDSQ	ubiquitination	[1, 4]
212	VNEDSQEKKILLSPE	ubiquitination	[1]
213	NEDSQEKKILLSPER	ubiquitination	[3, 4]
226	ERVHEIFKRISDEEC	ubiquitination	[4, 8]
279	NQDDLTHKLADIVKI	ubiquitination	[1, 2, 4, 8]
285	HKLADIVKINNQLRR	acetylation	[9, 10]
285	HKLADIVKINNQLRR	ubiquitination	[1, 2, 4, 5, 8, 11]
337	QKSGRPLKSLKQRLK	ubiquitination	[2]
417	NSQYPGAKYIIRDNG	ubiquitination	[1, 2, 4, 5, 8, 11]
434	IDLRFHPKPSDLHLQ	ubiquitination	[4]
445	LHLQTGYKVERHMCD	ubiquitination	[4, 8]
466	NRQPTLHKMSMMGHR	ubiquitination	[4]
581	VPQPAILKPRPLWTG	ubiquitination	[4]
619	DEDSGPYKHISPGDT	ubiquitination	[1, 2, 4, 5, 8, 11]
627	HISPGDTKVVVENGE	ubiquitination	[2]
642	LIMGILCKKSLGTSA	ubiquitination	[2, 4, 11]
643	IMGILCKKSLGTSAG	ubiquitination	[1, 4, 8]
707	QDIQNTIKKAKQDVI	ubiquitination	[1, 2, 4, 5, 6, 7, 8]
708	DIQNTIKKAKQDVIE	ubiquitination	[2, 4]
710	QNTIKKAKQDVIEVI	ubiquitination	[1, 2, 3, 4, 5, 8, 11]
719	DVIEVIEKAHNNELE	ubiquitination	[1, 2, 4, 8]
751	ILNDARDKTGSSAQK	ubiquitination	[1, 2, 4, 6, 7, 8, 12]
758	KTGSSAQKSLSEYNN	ubiquitination	[1, 2, 3, 4, 5, 6, 7, 8, 12, 13]
767	LSEYNNFKSMVVSGA	ubiquitination	[1, 2, 3, 4, 5, 6, 7, 8]
775	SMVVSGAKGSKINIS	ubiquitination	[1, 4, 5]
778	VSGAKGSKINISQVI	ubiquitination	[4]
796	GQQNVEGKRIPFGFK	ubiquitination	[1, 2, 3, 4, 5, 6, 7, 8, 11]
803	KRIPFGFKHRTLPHF	ubiquitination	[4]
812	RTLPHFIKDDYGPES	ubiquitination	[1, 2, 4, 5, 6, 7, 8]
853	GLIDTAVKTAETGYI	ubiquitination	[1, 2, 3, 4, 5, 8, 11]
866	YIQRRLIKSMESVMV	ubiquitination	[1, 2, 4, 5, 6, 7, 8, 11]
874	SMESVMVKYDATVRN	ubiquitination	[1, 2, 4]
910	FQNLATLKPSNKAFE	ubiquitination	[1, 2, 4, 5, 8, 12]
914	ATLKPSNKAFEKKFR	ubiquitination	[1, 2, 3, 4, 5, 8, 12]
918	PSNKAFEKKFRFDYT	ubiquitination	[1, 2, 4, 5]
919	SNKAFEKKFRFDYTN	ubiquitination	[4]
940	TLQEDLVKDVLSNAH	ubiquitination	[1, 2, 4, 5, 8, 11]
976	IFPTGDSKVVLPCNL	ubiquitination	[2, 3, 4, 8, 11]
992	RMIWNAQKIFHINPR	ubiquitination	[2, 3, 4, 5, 8]
1008	PSDLHPIKVVEGVKE	ubiquitination	[1, 2, 3, 4, 5, 6, 7, 8, 13]
1014	IKVVEGVKELSKKLV	ubiquitination	[1, 2, 4, 5, 8]
1019	GVKELSKKLVIVNGD	ubiquitination	[1, 3, 4, 5, 8]
1125	TLGVPRLKELINISK	ubiquitination	[1, 2, 3, 4, 6, 7, 8, 11]
1132	KELINISKKPKTPSL	ubiquitination	[2, 4, 8]
1133	ELINISKKPKTPSLT	ubiquitination	[4]
1135	INISKKPKTPSLTVF	ubiquitination	[4]
1155	ARDAERAKDILCRLE	ubiquitination	[4, 8]
1225	RKHMTDRKLTMEQIA	ubiquitination	[1, 2, 3, 4, 8]
1254	FNDDNAEKLVLRIRI	ubiquitination	[2, 4, 11]
1268	IMNSDENKMQEEEEV	ubiquitination	[1, 2, 4, 5]
1278	EEEEVVDKMDDDVFL	ubiquitination	[1, 2, 4, 8]
1317	HLPQTDNKKKIIITE	ubiquitination	[1, 4]
1318	LPQTDNKKKIIITED	ubiquitination	[4]
1319	PQTDNKKKIIITEDG	ubiquitination	[1, 4, 8, 13]
1350	LMRVLSEKDVDPVRT	ubiquitination	[1, 2, 3, 4, 5, 8, 11]
1429	QDTGPLMKCSFEETV	ubiquitination	[2]
1479	DLLLDAEKCKYGMEI	ubiquitination	[2]
1922	TYSPTSPKYSPTSPT	acetylation	[14]

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] Global identification of modular cullin-RING ligase substrates.
 Emanuele MJ, Elia AE, Xu Q, Thoma CR, Izhar L, Leng Y, Guo A, Chen YN, Rush J, Hsu PW, Yen HC, Elledge SJ.
 Cell. 2011 Oct 14;147(2):459-74. [PMID: 21963094]
 [3] 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]
 [4] 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]
 [5] 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]
 [6] 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]
 [7] 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]
 [8] Integrated proteomic analysis of post-translational modifications by serial enrichment.
 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA.
 Nat Methods. 2013 Jul;10(7):634-7. [PMID: 23749302]
 [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]
 [10] Monoclonal antibody cocktail as an enrichment tool for acetylome analysis.
 Shaw PG, Chaerkady R, Zhang Z, Davidson NE, Pandey A.
 Anal Chem. 2011 May 15;83(10):3623-6. [PMID: 21466224]
 [11] 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]
 [12] Proteome-wide identification of ubiquitylation sites by conjugation of engineered lysine-less ubiquitin.
 Oshikawa K, Matsumoto M, Oyamada K, Nakayama KI.
 J Proteome Res. 2012 Feb 3;11(2):796-807. [PMID: 22053931]
 [13] 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]
 [14] Spermidine and resveratrol induce autophagy by distinct pathways converging on the acetylproteome.
 Morselli E, Mariño G, Bennetzen MV, Eisenberg T, Megalou E, Schroeder S, Cabrera S, Bénit P, Rustin P, Criollo A, Kepp O, Galluzzi L, Shen S, Malik SA, Maiuri MC, Horio Y, López-Otín C, Andersen JS, Tavernarakis N, Madeo F, Kroemer G.
 J Cell Biol. 2011 Feb 21;192(4):615-29. [PMID: 21339330] 

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. It is composed of mobile elements that move relative to each other. RPB1 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. At the start of transcription, a single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. 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. During transcription elongation, Pol II moves on the template as the transcript elongates. 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. Acts as a RNA- dependent RNA polymerase when associated with small delta antigen of Hepatitis delta virus, acting both as a replicate and transcriptase for the viral RNA circular genome. 

Sequence Annotation

 REPEAT 1593 1599 1.
 REPEAT 1600 1606 2; approximate.
 REPEAT 1608 1614 3.
 REPEAT 1615 1621 4.
 REPEAT 1622 1628 5.
 REPEAT 1629 1635 6.
 REPEAT 1636 1642 7.
 REPEAT 1643 1649 8.
 REPEAT 1650 1656 9.
 REPEAT 1657 1663 10.
 REPEAT 1664 1670 11.
 REPEAT 1671 1677 12.
 REPEAT 1678 1684 13.
 REPEAT 1685 1691 14.
 REPEAT 1692 1698 15.
 REPEAT 1699 1705 16.
 REPEAT 1706 1712 17.
 REPEAT 1713 1719 18.
 REPEAT 1720 1726 19.
 REPEAT 1727 1733 20.
 REPEAT 1734 1740 21.
 REPEAT 1741 1747 22.
 REPEAT 1748 1754 23.
 REPEAT 1755 1761 24.
 REPEAT 1762 1768 25.
 REPEAT 1769 1775 26.
 REPEAT 1776 1782 27.
 REPEAT 1783 1789 28.
 REPEAT 1790 1796 29.
 REPEAT 1797 1803 30.
 REPEAT 1804 1810 31.
 REPEAT 1811 1817 32.
 REPEAT 1818 1824 33.
 REPEAT 1825 1831 34.
 REPEAT 1832 1838 35.
 REPEAT 1839 1845 36.
 REPEAT 1846 1852 37.
 REPEAT 1853 1859 38.
 REPEAT 1860 1866 39.
 REPEAT 1867 1873 40.
 REPEAT 1874 1880 41.
 REPEAT 1881 1887 42.
 REPEAT 1888 1894 43.
 REPEAT 1895 1901 44.
 REPEAT 1902 1908 45.
 REPEAT 1909 1915 46.
 REPEAT 1916 1922 47.
 REPEAT 1923 1929 48.
 REPEAT 1930 1936 49.
 REPEAT 1940 1946 50.
 REPEAT 1947 1953 51; approximate.
 REPEAT 1954 1960 52; approximate.
 REGION 833 845 Bridging helix.
 REGION 1593 1960 52 X 7 AA approximate tandem repeats of
 METAL 71 71 Zinc 1 (By similarity).
 METAL 74 74 Zinc 1 (By similarity).
 METAL 81 81 Zinc 1 (By similarity).
 METAL 84 84 Zinc 1 (By similarity).
 METAL 111 111 Zinc 2 (By similarity).
 METAL 114 114 Zinc 2 (By similarity).
 METAL 154 154 Zinc 2 (By similarity).
 METAL 184 184 Zinc 2 (By similarity).
 METAL 495 495 Magnesium 1; catalytic (By similarity).
 METAL 495 495 Magnesium 2; shared with RPB2 (By
 METAL 497 497 Magnesium 1; catalytic (By similarity).
 METAL 497 497 Magnesium 2; shared with RPB2 (By
 METAL 499 499 Magnesium 1; catalytic (By similarity).
 MOD_RES 1 1 N-acetylmethionine.
 MOD_RES 1810 1810 Omega-N-methylated arginine; by CARM1.
 MOD_RES 1843 1843 Phosphoserine.
 MOD_RES 1849 1849 Phosphoserine.
 MOD_RES 1854 1854 Phosphothreonine.
 MOD_RES 1874 1874 Phosphotyrosine.
 MOD_RES 1878 1878 Phosphoserine.
 MOD_RES 1882 1882 Phosphoserine.
 MOD_RES 1896 1896 Phosphoserine.
 MOD_RES 1899 1899 Phosphoserine.
 MOD_RES 1909 1909 Phosphotyrosine.
 MOD_RES 1913 1913 Phosphoserine.
 MOD_RES 1917 1917 Phosphoserine.
 MOD_RES 1920 1920 Phosphoserine.
 MOD_RES 1923 1923 Phosphotyrosine.
 MOD_RES 1927 1927 Phosphoserine.
 MOD_RES 1931 1931 Phosphoserine.
 MOD_RES 1933 1933 Phosphothreonine (By similarity).
 MOD_RES 1934 1934 Phosphoserine.  

Keyword

 3D-structure; Acetylation; Complete proteome; DNA-binding; DNA-directed RNA polymerase; Magnesium; Metal-binding; Methylation; Nucleotidyltransferase; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Repeat; RNA-directed RNA polymerase; Transcription; Transferase; Ubl conjugation; Zinc. 

Sequence Source

 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 

Protein Length

 1970 AA 

Protein Sequence

Gene Ontology

 GO:0005665; C:DNA-directed RNA polymerase II, core complex; IDA:UniProtKB.
 GO:0003677; F:DNA binding; NAS:UniProtKB.
 GO:0003899; F:DNA-directed RNA polymerase activity; NAS:UniProtKB.
 GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
 GO:0003968; F:RNA-directed RNA polymerase activity; IEA:UniProtKB-KW.
 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:0006355; P:regulation of transcription, DNA-dependent; NAS:UniProtKB.
 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

 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