P24928 (RPB1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA-directed RNA polymerase II subunit RPB1
Short name=RNA polymerase II subunit B1
EC=2.7.7.6

Alternative name(s):
DNA-directed RNA polymerase II subunit A
DNA-directed RNA polymerase III largest subunit
RNA-directed RNA polymerase II subunit RPB1
EC=2.7.7.48

Gene names

Name:	POLR2A
Synonyms:	POLR2

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	1970 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.6 Ref.23
Catalytic activity	Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
Subunit structure	Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits. The phosphorylated C-terminal domain interacts with FNBP3 and SYNCRIP. Interacts with SAFB/SAFB1. Interacts with CCNL1 and MYO1C By similarity. Interacts with CCNL2 and SFRS19. Component of a complex which is at least composed of HTATSF1/Tat-SF1, the P-TEFb complex components CDK9 and CCNT1, RNA polymerase II, SUPT5H, and NCL/nucleolin. Interacts with PAF1. Interacts (via C-terminus) with FTSJD2, CTDSP1 and SCAF8. Interacts via the phosphorylated C-terminal domain with WDR82 and with SETD1A and SETD1B only in the presence of WDR82. Interacts with ATF7IP. When phosphorylated at 'Ser-5', interacts with MEN1; the unphosphorylated form, or phosphorylated at 'Ser-2' does not interact. Ref.7 Ref.9 Ref.10 Ref.11 Ref.12 Ref.13 Ref.15 Ref.16 Ref.18 Ref.19 Ref.21 Ref.22 Ref.24 Ref.27
Subcellular location	Nucleus Ref.6.
Post-translational modification	The tandem 7 residues repeats in the C-terminal domain (CTD) can be highly phosphorylated. The phosphorylation activates Pol II. Phosphorylation occurs mainly at residues 'Ser-2' and 'Ser-5' of the heptapeptide repeat and is mediated, at least, by CDK7 and CDK9. CDK7 phosphorylation of POLR2A associated with DNA promotes transcription initiation by triggering dissociation from DNA. The phosphorylation state is believed to result from the balanced action of site-specific CTD kinases and phosphatases, and a "CTD code" that specifies the position of Pol II within the transcription cycle has been proposed. Ref.14 Ref.17 Ref.20 Ref.25 Ref.26 Ref.28 Ref.29 Ref.30 Ref.31 Ref.33 Ref.35 Dephosphorylated by the protein phosphatase CTDSP1. Ref.14 Ref.17 Ref.20 Ref.25 Ref.26 Ref.28 Ref.29 Ref.30 Ref.31 Ref.33 Ref.35 Ubiquitinated by WWP2 leading to proteasomal degradation By similarity. Methylated at Arg-1810 by CARM1. Methylation occurs only when the CTD is hypophosphorylated, and phosphorylation at Ser-1805 and Ser-1808 prevent methylation (in vitro). It is assumed that methylation occurs prior to phosphorylation and transcription initiation. CTD methylation may facilitate the expression of select RNAs. Ref.14 Ref.17 Ref.20 Ref.25 Ref.26 Ref.28 Ref.29 Ref.30 Ref.31 Ref.33 Ref.35
Miscellaneous	The binding of ribonucleoside triphosphate to the RNA polymerase II transcribing complex probably involves a two-step mechanism. The initial binding seems to occur at the entry (E) site and involves a magnesium ion temporarily coordinated by three conserved aspartate residues of the two largest RNA Pol II subunits. The ribonucleoside triphosphate is transferred by a rotation to the nucleotide addition (A) site for pairing with the template DNA. The catalytic A site involves three conserved aspartate residues of the RNA Pol II largest subunit which permanently coordinate a second magnesium ion.
Sequence similarities	Belongs to the RNA polymerase beta' chain family.

Ontologies

Keywords
Biological process	Transcription
Cellular component	DNA-directed RNA polymerase Nucleus
Coding sequence diversity	Polymorphism
Domain	Repeat
Ligand	DNA-binding Magnesium Metal-binding Zinc
Molecular function	Nucleotidyltransferase RNA-directed RNA polymerase Transferase
PTM	Acetylation Methylation Phosphoprotein Ubl conjugation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	mRNA capping Traceable author statement. Source: Reactome nuclear mRNA splicing, via spliceosome Traceable author statement. Source: Reactome positive regulation of viral transcription Traceable author statement. Source: Reactome protein phosphorylation Inferred from direct assay Ref.6. Source: GOC regulation of transcription, DNA-dependent Non-traceable author statement Ref.2. Source: UniProtKB transcription elongation from RNA polymerase II promoter Traceable author statement. Source: Reactome transcription initiation from RNA polymerase II promoter Traceable author statement. Source: Reactome transcription-coupled nucleotide-excision repair Traceable author statement. Source: Reactome viral reproduction Traceable author statement. Source: Reactome
Cellular component	DNA-directed RNA polymerase II, core complex Inferred from direct assay Ref.6. Source: UniProtKB
Molecular function	DNA binding Non-traceable author statement Ref.2. Source: UniProtKB DNA-directed RNA polymerase activity Non-traceable author statement Ref.2. Source: UniProtKB RNA-directed RNA polymerase activity Inferred from electronic annotation. Source: EC metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW ubiquitin protein ligase binding Inferred from physical interaction. Source: BHF-UCL
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
SUPT5H	O00267	2	EBI-295301,EBI-710464
XAB2	Q9HCS7	2	EBI-295301,EBI-295232

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1970	1970	DNA-directed RNA polymerase II subunit RPB1		PRO_0000073940
Regions
	Repeat	1593 – 1599	7	1
	Repeat	1600 – 1606	7	2; approximate
	Repeat	1608 – 1614	7	3
	Repeat	1615 – 1621	7	4
	Repeat	1622 – 1628	7	5
	Repeat	1629 – 1635	7	6
	Repeat	1636 – 1642	7	7
	Repeat	1643 – 1649	7	8
	Repeat	1650 – 1656	7	9
	Repeat	1657 – 1663	7	10
	Repeat	1664 – 1670	7	11
	Repeat	1671 – 1677	7	12
	Repeat	1678 – 1684	7	13
	Repeat	1685 – 1691	7	14
	Repeat	1692 – 1698	7	15
	Repeat	1699 – 1705	7	16
	Repeat	1706 – 1712	7	17
	Repeat	1713 – 1719	7	18
	Repeat	1720 – 1726	7	19
	Repeat	1727 – 1733	7	20
	Repeat	1734 – 1740	7	21
	Repeat	1741 – 1747	7	22
	Repeat	1748 – 1754	7	23
	Repeat	1755 – 1761	7	24
	Repeat	1762 – 1768	7	25
	Repeat	1769 – 1775	7	26
	Repeat	1776 – 1782	7	27
	Repeat	1783 – 1789	7	28
	Repeat	1790 – 1796	7	29
	Repeat	1797 – 1803	7	30
	Repeat	1804 – 1810	7	31
	Repeat	1811 – 1817	7	32
	Repeat	1818 – 1824	7	33
	Repeat	1825 – 1831	7	34
	Repeat	1832 – 1838	7	35
	Repeat	1839 – 1845	7	36
	Repeat	1846 – 1852	7	37
	Repeat	1853 – 1859	7	38
	Repeat	1860 – 1866	7	39
	Repeat	1867 – 1873	7	40
	Repeat	1874 – 1880	7	41
	Repeat	1881 – 1887	7	42
	Repeat	1888 – 1894	7	43
	Repeat	1895 – 1901	7	44
	Repeat	1902 – 1908	7	45
	Repeat	1909 – 1915	7	46
	Repeat	1916 – 1922	7	47
	Repeat	1923 – 1929	7	48
	Repeat	1930 – 1936	7	49
	Repeat	1940 – 1946	7	50
	Repeat	1947 – 1953	7	51; approximate
	Repeat	1954 – 1960	7	52; approximate
	Region	833 – 845	13	Bridging helix
	Region	1593 – 1960	368	52 X 7 AA approximate tandem repeats of Y-[ST]-P-[STQ]-[ST]-P-[SRTEVKGN]
Sites
	Metal binding	71	1	Zinc 1 By similarity
	Metal binding	74	1	Zinc 1 By similarity
	Metal binding	81	1	Zinc 1 By similarity
	Metal binding	84	1	Zinc 1 By similarity
	Metal binding	111	1	Zinc 2 By similarity
	Metal binding	114	1	Zinc 2 By similarity
	Metal binding	154	1	Zinc 2 By similarity
	Metal binding	184	1	Zinc 2 By similarity
	Metal binding	495	1	Magnesium 1; catalytic By similarity
	Metal binding	495	1	Magnesium 2; shared with RPB2 By similarity
	Metal binding	497	1	Magnesium 1; catalytic By similarity
	Metal binding	497	1	Magnesium 2; shared with RPB2 By similarity
	Metal binding	499	1	Magnesium 1; catalytic By similarity
Amino acid modifications
	Modified residue	1	1	N-acetylmethionine Ref.26
	Modified residue	145	1	Phosphotyrosine Ref.17
	Modified residue	772	1	Phosphoserine Ref.20
	Modified residue	777	1	Phosphoserine Ref.20
	Modified residue	1810	1	Omega-N-methylated arginine; by CARM1 Ref.34
	Modified residue	1815	1	Phosphoserine Ref.31
	Modified residue	1839	1	Phosphotyrosine Ref.26
	Modified residue	1840	1	Phosphothreonine Ref.26
	Modified residue	1842	1	Phosphothreonine Ref.26
	Modified residue	1843	1	Phosphoserine Ref.26 Ref.31
	Modified residue	1845	1	Phosphoserine Ref.26
	Modified residue	1847	1	Phosphoserine Ref.26
	Modified residue	1849	1	Phosphoserine Ref.25 Ref.26
	Modified residue	1850	1	Phosphoserine Ref.26
	Modified residue	1853	1	Phosphotyrosine Ref.26 Ref.31
	Modified residue	1854	1	Phosphothreonine Ref.31
	Modified residue	1857	1	Phosphoserine Ref.26
	Modified residue	1871	1	Phosphoserine Ref.26
	Modified residue	1874	1	Phosphotyrosine Ref.25 Ref.26 Ref.31
	Modified residue	1875	1	Phosphoserine Ref.26
	Modified residue	1877	1	Phosphothreonine Ref.26
	Modified residue	1878	1	Phosphoserine Ref.26 Ref.31
	Modified residue	1881	1	Phosphotyrosine Ref.26
	Modified residue	1882	1	Phosphoserine Ref.26 Ref.31
	Modified residue	1884	1	Phosphothreonine Ref.26
	Modified residue	1888	1	Phosphotyrosine Ref.26
	Modified residue	1889	1	Phosphoserine Ref.26
	Modified residue	1891	1	Phosphothreonine Ref.25
	Modified residue	1892	1	Phosphoserine Ref.26
	Modified residue	1894	1	Phosphothreonine Ref.26
	Modified residue	1895	1	Phosphotyrosine Ref.26
	Modified residue	1896	1	Phosphoserine Ref.14 Ref.25 Ref.26
	Modified residue	1898	1	Phosphothreonine Ref.26
	Modified residue	1899	1	Phosphoserine Ref.26 Ref.31
	Modified residue	1902	1	Phosphotyrosine Ref.26
	Modified residue	1903	1	Phosphothreonine Ref.26
	Modified residue	1906	1	Phosphoserine Ref.26
	Modified residue	1909	1	Phosphotyrosine Ref.26 Ref.31
	Modified residue	1913	1	Phosphoserine Ref.31
	Modified residue	1917	1	Phosphoserine Ref.26 Ref.31
	Modified residue	1919	1	Phosphothreonine Ref.31
	Modified residue	1920	1	Phosphoserine Ref.31
	Modified residue	1923	1	Phosphotyrosine Ref.25 Ref.26
	Modified residue	1924	1	Phosphoserine Ref.26
	Modified residue	1926	1	Phosphothreonine Ref.26
	Modified residue	1927	1	Phosphoserine Ref.25 Ref.26
	Modified residue	1929	1	Phosphothreonine Ref.26
	Modified residue	1930	1	Phosphotyrosine Ref.26
	Modified residue	1931	1	Phosphoserine Ref.26
	Modified residue	1933	1	Phosphothreonine Ref.26
	Modified residue	1934	1	Phosphoserine Ref.14 Ref.25 Ref.26
	Modified residue	1962	1	Phosphoserine Ref.26
	Modified residue	1966	1	Phosphoserine Ref.26
Natural variations
	Natural variant	292	1	R → C. Corresponds to variant rs2229198 [ dbSNP | Ensembl ].		VAR_051872
Experimental info
	Mutagenesis	1810	1	R → A: Misexpression of a variety of small nuclear RNAs and small nucleolar RNAs. Ref.34
	Sequence conflict	1067	1	W → L in CAA52862. Ref.2
	Sequence conflict	1449	1	D → Y in CAA52862. Ref.2
	Sequence conflict	1835	1	A → T in CAA45125. Ref.1
	Sequence conflict	1835	1	A → T in CAA52862. Ref.2

Sequences

	Sequence		Length	Mass (Da)
	P24928 [UniParc]. Last modified December 15, 2009. Version 2. Checksum: 28D6FD25693A6472	FASTA	1,970	217,176
	10 20 30 40 50 60 MHGGGPPSGD SACPLRTIKR VQFGVLSPDE LKRMSVTEGG IKYPETTEGG RPKLGGLMDP 70 80 90 100 110 120 RQGVIERTGR CQTCAGNMTE CPGHFGHIEL AKPVFHVGFL VKTMKVLRCV CFFCSKLLVD 130 140 150 160 170 180 SNNPKIKDIL AKSKGQPKKR LTHVYDLCKG KNICEGGEEM DNKFGVEQPE GDEDLTKEKG 190 200 210 220 230 240 HGGCGRYQPR IRRSGLELYA EWKHVNEDSQ EKKILLSPER VHEIFKRISD EECFVLGMEP 250 260 270 280 290 300 RYARPEWMIV TVLPVPPLSV RPAVVMQGSA RNQDDLTHKL ADIVKINNQL RRNEQNGAAA 310 320 330 340 350 360 HVIAEDVKLL QFHVATMVDN ELPGLPRAMQ KSGRPLKSLK QRLKGKEGRV RGNLMGKRVD 370 380 390 400 410 420 FSARTVITPD PNLSIDQVGV PRSIAANMTF AEIVTPFNID RLQELVRRGN SQYPGAKYII 430 440 450 460 470 480 RDNGDRIDLR FHPKPSDLHL QTGYKVERHM CDGDIVIFNR QPTLHKMSMM GHRVRILPWS 490 500 510 520 530 540 TFRLNLSVTT PYNADFDGDE MNLHLPQSLE TRAEIQELAM VPRMIVTPQS NRPVMGIVQD 550 560 570 580 590 600 TLTAVRKFTK RDVFLERGEV MNLLMFLSTW DGKVPQPAIL KPRPLWTGKQ IFSLIIPGHI 610 620 630 640 650 660 NCIRTHSTHP DDEDSGPYKH ISPGDTKVVV ENGELIMGIL CKKSLGTSAG SLVHISYLEM 670 680 690 700 710 720 GHDITRLFYS NIQTVINNWL LIEGHTIGIG DSIADSKTYQ DIQNTIKKAK QDVIEVIEKA 730 740 750 760 770 780 HNNELEPTPG NTLRQTFENQ VNRILNDARD KTGSSAQKSL SEYNNFKSMV VSGAKGSKIN 790 800 810 820 830 840 ISQVIAVVGQ QNVEGKRIPF GFKHRTLPHF IKDDYGPESR GFVENSYLAG LTPTEFFFHA 850 860 870 880 890 900 MGGREGLIDT AVKTAETGYI QRRLIKSMES VMVKYDATVR NSINQVVQLR YGEDGLAGES 910 920 930 940 950 960 VEFQNLATLK PSNKAFEKKF RFDYTNERAL RRTLQEDLVK DVLSNAHIQN ELEREFERMR 970 980 990 1000 1010 1020 EDREVLRVIF PTGDSKVVLP CNLLRMIWNA QKIFHINPRL PSDLHPIKVV EGVKELSKKL 1030 1040 1050 1060 1070 1080 VIVNGDDPLS RQAQENATLL FNIHLRSTLC SRRMAEEFRL SGEAFDWLLG EIESKFNQAI 1090 1100 1110 1120 1130 1140 AHPGEMVGAL AAQSLGEPAT QMTLNTFHYA GVSAKNVTLG VPRLKELINI SKKPKTPSLT 1150 1160 1170 1180 1190 1200 VFLLGQSARD AERAKDILCR LEHTTLRKVT ANTAIYYDPN PQSTVVAEDQ EWVNVYYEMP 1210 1220 1230 1240 1250 1260 DFDVARISPW LLRVELDRKH MTDRKLTMEQ IAEKINAGFG DDLNCIFNDD NAEKLVLRIR 1270 1280 1290 1300 1310 1320 IMNSDENKMQ EEEEVVDKMD DDVFLRCIES NMLTDMTLQG IEQISKVYMH LPQTDNKKKI 1330 1340 1350 1360 1370 1380 IITEDGEFKA LQEWILETDG VSLMRVLSEK DVDPVRTTSN DIVEIFTVLG IEAVRKALER 1390 1400 1410 1420 1430 1440 ELYHVISFDG SYVNYRHLAL LCDTMTCRGH LMAITRHGVN RQDTGPLMKC SFEETVDVLM 1450 1460 1470 1480 1490 1500 EAAAHGESDP MKGVSENIML GQLAPAGTGC FDLLLDAEKC KYGMEIPTNI PGLGAAGPTG 1510 1520 1530 1540 1550 1560 MFFGSAPSPM GGISPAMTPW NQGATPAYGA WSPSVGSGMT PGAAGFSPSA ASDASGFSPG 1570 1580 1590 1600 1610 1620 YSPAWSPTPG SPGSPGPSSP YIPSPGGAMS PSYSPTSPAY EPRSPGGYTP QSPSYSPTSP 1630 1640 1650 1660 1670 1680 SYSPTSPSYS PTSPNYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP 1690 1700 1710 1720 1730 1740 TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS 1750 1760 1770 1780 1790 1800 YSPTSPNYSP TSPNYTPTSP SYSPTSPSYS PTSPNYTPTS PNYSPTSPSY SPTSPSYSPT 1810 1820 1830 1840 1850 1860 SPSYSPSSPR YTPQSPTYTP SSPSYSPSSP SYSPASPKYT PTSPSYSPSS PEYTPTSPKY 1870 1880 1890 1900 1910 1920 SPTSPKYSPT SPKYSPTSPT YSPTTPKYSP TSPTYSPTSP VYTPTSPKYS PTSPTYSPTS 1930 1940 1950 1960 1970 PKYSPTSPTY SPTSPKGSTY SPTSPGYSPT SPTYSLTSPA ISPDDSDEEN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete sequence of the human RNA polymerase II largest subunit." Wintzerith M., Acker J., Vicaire S., Vigneron M., Kedinger C. Nucleic Acids Res. 20:910-910(1992) [PubMed: 1542581] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]	"The human gene encoding the largest subunit of RNA polymerase II." Mita K., Tsuji H., Morimyo M., Takahashi E., Nenoi M., Ichimura S., Yamauchi M., Hongo E., Hayashi A. Gene 159:285-286(1995) [PubMed: 7622068] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage." Zody M.C., Garber M., Adams D.J., Sharpe T., Harrow J., Lupski J.R., Nicholson C., Searle S.M., Wilming L., Young S.K., Abouelleil A., Allen N.R., Bi W., Bloom T., Borowsky M.L., Bugalter B.E., Butler J., Chang J.L. , Chen C.-K., Cook A., Corum B., Cuomo C.A., de Jong P.J., DeCaprio D., Dewar K., FitzGerald M., Gilbert J., Gibson R., Gnerre S., Goldstein S., Grafham D.V., Grocock R., Hafez N., Hagopian D.S., Hart E., Norman C.H., Humphray S., Jaffe D.B., Jones M., Kamal M., Khodiyar V.K., LaButti K., Laird G., Lehoczky J., Liu X., Lokyitsang T., Loveland J., Lui A., Macdonald P., Major J.E., Matthews L., Mauceli E., McCarroll S.A., Mihalev A.H., Mudge J., Nguyen C., Nicol R., O'Leary S.B., Osoegawa K., Schwartz D.C., Shaw-Smith C., Stankiewicz P., Steward C., Swarbreck D., Venkataraman V., Whittaker C.A., Yang X., Zimmer A.R., Bradley A., Hubbard T., Birren B.W., Rogers J., Lander E.S., Nusbaum C. Nature 440:1045-1049(2006) [PubMed: 16625196] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Brain.
[6]	"Immunoaffinity purification and functional characterization of human transcription factor IIH and RNA polymerase II from clonal cell lines that conditionally express epitope-tagged subunits of the multiprotein complexes." Kershnar E., Wu S.-Y., Chiang C.-M. J. Biol. Chem. 273:34444-34453(1998) [PubMed: 9852112] [Abstract] Cited for: FUNCTION, IDENTIFICATION IN THE RNA POLYMERASE II CORE-COMPLEX, SUBCELLULAR LOCATION.
[7]	"SAF-B couples transcription and pre-mRNA splicing to SAR/MAR elements." Nayler O., Straetling W., Bourquin J.-P., Stagljar I., Lindemann L., Jasper H., Hartmann A.M., Fackelmeyer F.O., Ullrich A., Stamm S. Nucleic Acids Res. 26:3542-3549(1998) [PubMed: 9671816] [Abstract] Cited for: INTERACTION WITH SAFB.
[8]	"A novel RNA polymerase II-containing complex potentiates Tat-enhanced HIV-1 transcription." Parada C.A., Roeder R.G. EMBO J. 18:3688-3701(1999) [PubMed: 10393184] [Abstract] Cited for: IDENTIFICATION IN A COMPLEX WITH HTATSF1; CCNT1; NCL; SUPT5H AND CDK9.
[9]	"Tat-SF1 protein associates with RAP30 and human SPT5 proteins." Kim J.B., Yamaguchi Y., Wada T., Handa H., Sharp P.A. Mol. Cell. Biol. 19:5960-5968(1999) [PubMed: 10454543] [Abstract] Cited for: INTERACTION WITH HTATSF1.
[10]	"The structure of an FF domain from human HYPA/FBP11." Allen M., Friedler A., Schon O., Bycroft M. J. Mol. Biol. 323:411-416(2002) [PubMed: 12381297] [Abstract] Cited for: INTERACTION WITH FNBP3.
[11]	"Hyperphosphorylated C-terminal repeat domain-associating proteins in the nuclear proteome link transcription to DNA/chromatin modification and RNA processing." Carty S.M., Greenleaf A.L. Mol. Cell. Proteomics 1:598-610(2002) [PubMed: 12376575] [Abstract] Cited for: INTERACTION WITH SYNCRIP.
[12]	"Cyclin L2, a novel RNA polymerase II-associated cyclin, is involved in pre-mRNA splicing and induces apoptosis of human hepatocellular carcinoma cells." Yang L., Li N., Wang C., Yu Y., Yuan L., Zhang M., Cao X. J. Biol. Chem. 279:11639-11648(2004) [PubMed: 14684736] [Abstract] Cited for: INTERACTION WITH CCNL2.
[13]	"Menin associates with a trithorax family histone methyltransferase complex and with the hoxc8 locus." Hughes C.M., Rozenblatt-Rosen O., Milne T.A., Copeland T.D., Levine S.S., Lee J.C., Hayes D.N., Shanmugam K.S., Bhattacharjee A., Biondi C.A., Kay G.F., Hayward N.K., Hess J.L., Meyerson M. Mol. Cell 13:587-597(2004) [PubMed: 14992727] [Abstract] Cited for: INTERACTION WITH MEN1.
[14]	"Large-scale characterization of HeLa cell nuclear phosphoproteins." Beausoleil S.A., Jedrychowski M., Schwartz D., Elias J.E., Villen J., Li J., Cohn M.A., Cantley L.C., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 101:12130-12135(2004) [PubMed: 15302935] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1896 AND SER-1934, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[15]	"Expression of the C-terminal domain of novel human SR-A1 protein: interaction with the CTD domain of RNA polymerase II." Katsarou M.E., Papakyriakou A., Katsaros N., Scorilas A. Biochem. Biophys. Res. Commun. 334:61-68(2005) [PubMed: 15992770] [Abstract] Cited for: INTERACTION WITH SFRS19.
[16]	"Identification and characterization of a novel human histone H3 lysine 36 specific methyltransferase." Sun X.-J., Wei J., Wu X.-Y., Hu M., Wang L., Wang H.-H., Zhang Q.-H., Chen S.-J., Huang Q.-H., Chen Z. J. Biol. Chem. 280:35261-35271(2005) [PubMed: 16118227] [Abstract] Cited for: INTERACTION WITH SETD2.
[17]	"Immunoaffinity profiling of tyrosine phosphorylation in cancer cells." Rush J., Moritz A., Lee K.A., Guo A., Goss V.L., Spek E.J., Zhang H., Zha X.-M., Polakiewicz R.D., Comb M.J. Nat. Biotechnol. 23:94-101(2005) [PubMed: 15592455] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-145, MASS SPECTROMETRY.
[18]	"Solution structure of the Set2-Rpb1 interacting domain of human Set2 and its interaction with the hyperphosphorylated C-terminal domain of Rpb1." Li M., Phatnani H.P., Guan Z., Sage H., Greenleaf A.L., Zhou P. Proc. Natl. Acad. Sci. U.S.A. 102:17636-17641(2005) [PubMed: 16314571] [Abstract] Cited for: INTERACTION WITH SETD2.
[19]	"The human homologue of the RNA polymerase II-associated factor 1 (hPaf1), localized on the 19q13 amplicon, is associated with tumorigenesis." Moniaux N., Nemos C., Schmied B.M., Chauhan S.C., Deb S., Morikane K., Choudhury A., Vanlith M., Sutherlin M., Sikela J.M., Hollingsworth M.A., Batra S.K. Oncogene 25:3247-3257(2006) [PubMed: 16491129] [Abstract] Cited for: INTERACTION WITH PAF1 IN PAF1/RNA POLYMERASE II. Tissue: Fetal pancreas.
[20]	"Automated phosphoproteome analysis for cultured cancer cells by two-dimensional nanoLC-MS using a calcined titania/C18 biphasic column." Imami K., Sugiyama N., Kyono Y., Tomita M., Ishihama Y. Anal. Sci. 24:161-166(2008) [PubMed: 18187866] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-772 AND SER-777, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[21]	"The human interferon-regulated ISG95 protein interacts with RNA polymerase II and shows methyltransferase activity." Haline-Vaz T., Silva T.C.L., Zanchin N.I.T. Biochem. Biophys. Res. Commun. 372:719-724(2008) [PubMed: 18533109] [Abstract] Cited for: INTERACTION WITH FTSJD2.
[22]	"Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the carboxyl-terminal domain of RNA polymerase II." Becker R., Loll B., Meinhart A. J. Biol. Chem. 283:22659-22669(2008) [PubMed: 18550522] [Abstract] Cited for: INTERACTION WITH SCAF8.
[23]	"Transcription of hepatitis delta virus RNA by RNA polymerase II." Chang J., Nie X., Chang H.E., Han Z., Taylor J. J. Virol. 82:1118-1127(2008) [PubMed: 18032511] [Abstract] Cited for: FUNCTION AS RNA-DIRECTED RNA POLYMERASE.
[24]	"Wdr82 is a C-terminal domain-binding protein that recruits the Setd1A Histone H3-Lys4 methyltransferase complex to transcription start sites of transcribed human genes." Lee J.H., Skalnik D.G. Mol. Cell. Biol. 28:609-618(2008) [PubMed: 17998332] [Abstract] Cited for: INTERACTION WITH SETD1A; SETD1B AND WDR82.
[25]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed: 18669648] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1849; TYR-1874; THR-1891; SER-1896; TYR-1923; SER-1927 AND SER-1934, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[26]	"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach." Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S. Anal. Chem. 81:4493-4501(2009) [PubMed: 19413330] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-1839; THR-1840; THR-1842; SER-1843; SER-1845; SER-1847; SER-1849; SER-1850; TYR-1853; SER-1857; SER-1871; TYR-1874; SER-1875; THR-1877; SER-1878; TYR-1881; SER-1882; THR-1884; TYR-1888; SER-1889; SER-1892; THR-1894; TYR-1895; SER-1896; THR-1898; SER-1899; TYR-1902; THR-1903; SER-1906; TYR-1909; SER-1917; TYR-1923; SER-1924; THR-1926; SER-1927; THR-1929; TYR-1930; SER-1931; THR-1933; SER-1934; SER-1962 AND SER-1966, MASS SPECTROMETRY. Tissue: Embryonic kidney.
[27]	"MCAF1/AM is involved in Sp1-mediated maintenance of cancer-associated telomerase activity." Liu L., Ishihara K., Ichimura T., Fujita N., Hino S., Tomita S., Watanabe S., Saitoh N., Ito T., Nakao M. J. Biol. Chem. 284:5165-5174(2009) [PubMed: 19106100] [Abstract] Cited for: INTERACTION WITH ATF7IP.
[28]	"TFIIH kinase places bivalent marks on the carboxy-terminal domain of RNA polymerase II." Akhtar M.S., Heidemann M., Tietjen J.R., Zhang D.W., Chapman R.D., Eick D., Ansari A.Z. Mol. Cell 34:387-393(2009) [PubMed: 19450536] [Abstract] Cited for: PHOSPHORYLATION BY CDK7.
[29]	"TFIIH-associated Cdk7 kinase functions in phosphorylation of C-terminal domain Ser7 residues, promoter-proximal pausing, and termination by RNA polymerase II." Glover-Cutter K., Larochelle S., Erickson B., Zhang C., Shokat K., Fisher R.P., Bentley D.L. Mol. Cell. Biol. 29:5455-5464(2009) [PubMed: 19667075] [Abstract] Cited for: PHOSPHORYLATION BY CDK7 AND CDK9.
[30]	"Binding to DNA of the RNA-polymerase II C-terminal domain allows discrimination between Cdk7 and Cdk9 phosphorylation." Lolli G. Nucleic Acids Res. 37:1260-1268(2009) [PubMed: 19136461] [Abstract] Cited for: PHOSPHORYLATION BY CDK7.
[31]	"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions." Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K. Sci. Signal. 2:RA46-RA46(2009) [PubMed: 19690332] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1815; SER-1843; TYR-1853; THR-1854; TYR-1874; SER-1878; SER-1882; SER-1899; TYR-1909; SER-1913; SER-1917; THR-1919 AND SER-1920, MASS SPECTROMETRY. Tissue: Leukemic T-cell.
[32]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed: 21269460] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[33]	"Transcription factor IIS cooperates with the E3 ligase UBR5 to ubiquitinate the CDK9 subunit of the positive transcription elongation factor B." Cojocaru M., Bouchard A., Cloutier P., Cooper J.J., Varzavand K., Price D.H., Coulombe B. J. Biol. Chem. 286:5012-5022(2011) [PubMed: 21127351] [Abstract] Cited for: PHOSPHORYLATION BY CDK9.
[34]	"The C-terminal domain of RNA polymerase II is modified by site-specific methylation." Sims R.J. III, Rojas L.A., Beck D., Bonasio R., Schuller R., Drury W.J. III, Eick D., Reinberg D. Science 332:99-103(2011) [PubMed: 21454787] [Abstract] Cited for: METHYLATION AT ARG-1810 BY CARM1, MUTAGENESIS OF ARG-1810.
[35]	"Determinants for dephosphorylation of the RNA polymerase II C-terminal domain by Scp1." Zhang Y., Kim Y., Genoud N., Gao J., Kelly J.W., Pfaff S.L., Gill G.N., Dixon J.E., Noel J.P. Mol. Cell 24:759-770(2006) [PubMed: 17157258] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 1796-1803 IN COMPLEX WITH CTDSP1, DEPHOSPHORYLATION.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X63564 mRNA. Translation: CAA45125.1.
X74874 , X74873, X74872, X74871, X74870 Genomic DNA. Translation: CAA52862.1.
AC113189 Genomic DNA. No translation available.
CH471108 Genomic DNA. Translation: EAW90181.1.
BC137231 mRNA. Translation: AAI37232.1.

IPI

IPI00031627.

PIR

I38186.
S21054.

RefSeq

NP_000928.1. NM_000937.4.

UniGene

Hs.270017.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2GHQ	X-ray	2.05	C/D	1795-1803	[»]
2GHT	X-ray	1.80	C/D	1796-1803	[»]

ProteinModelPortal

P24928.

SMR

P24928. Positions 16-903, 1054-1477.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-29011N.

IntAct

P24928. 20 interactions.

MINT

MINT-156582.

STRING

P24928.

PTM databases

PhosphoSite

P24928.

Polymorphism databases

DMDM

281185484.

Proteomic databases

PRIDE

P24928.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000322644; ENSP00000314949; ENSG00000181222.

GeneID

5430.

KEGG

hsa:5430.

UCSC

uc002ghf.2. human.

Organism-specific databases

CTD

5430.

GeneCards

GC17P007387.

H-InvDB

HIX0039202.

HGNC

HGNC:9187. POLR2A.

HPA

CAB012226.
CAB016388.
CAB022311.
HPA021563.

MIM

180660. gene+phenotype.

neXtProt

NX_P24928.

PharmGKB

PA33507.

GenAtlas

Search...

Phylogenomic databases

eggNOG

prNOG15419.

HOGENOM

HBG499785.

HOVERGEN

HBG004339.

InParanoid

P24928.

OMA

SPTSPHY.

OrthoDB

EOG4JWVCM.

PhylomeDB

P24928.

Enzyme and pathway databases

Reactome

REACT_12472. Regulatory RNA pathways.
REACT_1675. mRNA Processing.
REACT_1788. Transcription.
REACT_1892. Elongation arrest and recovery.
REACT_216. DNA Repair.
REACT_6185. HIV Infection.
REACT_71. Gene Expression.
REACT_769. Pausing and recovery of elongation.

Gene expression databases

ArrayExpress

P24928.

Bgee

P24928.

CleanEx

HS_POLR2A.

Genevestigator

P24928.

GermOnline

ENSG00000181222. Homo sapiens.

Family and domain databases

InterPro

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.
[Graphical view]

KO

K03006.

Pfam

PF04997. RNA_pol_Rpb1_1. 1 hit.
PF00623. RNA_pol_Rpb1_2. 1 hit.
PF04983. RNA_pol_Rpb1_3. 1 hit.
PF05000. RNA_pol_Rpb1_4. 1 hit.
PF04998. RNA_pol_Rpb1_5. 1 hit.
PF04992. RNA_pol_Rpb1_6. 1 hit.
PF04990. RNA_pol_Rpb1_7. 1 hit.
PF05001. RNA_pol_Rpb1_R. 46 hits.
[Graphical view]

SMART

SM00663. RPOLA_N. 1 hit.
[Graphical view]

PROSITE

PS00115. RNA_POL_II_REPEAT. 42 hits.
[Graphical view]

ProtoNet

Search...

Other

NextBio

21009.

SOURCE

Search...

Entry information

Entry name

RPB1_HUMAN

Accession

Primary (citable) accession number: P24928
Secondary accession number(s): A6NN93, B9EH88

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 1, 1992
Last sequence update:	December 15, 2009
Last modified:	January 25, 2012
This is version 133 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.