Reviewed, UniProtKB/Swiss-Prot P08775 (RPB1_MOUSE)

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

Gene names

Name:	Polr2a
Synonyms:	Rpii215, Rpo2-1

Organism

Mus musculus (Mouse)

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus

Protein attributes

Sequence length	1970 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
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 By similarity.
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, 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. Hyperphosphorylated form on tandem 7 residues repeats specifically interacts with SETD2 By similarity. Interacts with PAF1. Interacts (via C-terminus) with FTSJD2 By similarity. Interacts with MYO1C.
Subcellular location	Nucleus.
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 heptapepdtide repeat. The phosphorylation state is believed to result from the balanced action of site-specific CTD kinases and phosphataes, and a "CTD code" that specifies the position of Pol II within the transcription cycle has been proposed By similarity.
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 nucelotide 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. Contains 1 C2H2-type zinc finger.

Ontologies

Keywords
Biological process	Transcription
Cellular component	DNA-directed RNA polymerase Nucleus
Domain	Repeat Zinc-finger
Ligand	DNA-binding Magnesium Metal-binding Zinc
Molecular function	Nucleotidyltransferase Transferase
PTM	Phosphoprotein
Gene Ontology (GO)
Biological process	transcription from RNA polymerase II promoter Inferred from sequence or structural similarity. Source: UniProtKB
Cellular component	DNA-directed RNA polymerase II, core complex Inferred from sequence or structural similarity. Source: UniProtKB
Molecular function	DNA binding Inferred from direct assay. Source: MGI DNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: MGI zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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_0000073941
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
	Zinc finger	71 – 87	17	C2H2-type By similarity
	Region	833 – 845	13	Bridging helix
	Region	1593 – 1960	368	52 X 7 AA approximate tandem repeats of Y-[ST]-P-[STQ]-[ST]-P-[SRNTEVKGN]
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	145	1	Phosphotyrosine By similarity
	Modified residue	772	1	Phosphoserine By similarity
	Modified residue	777	1	Phosphoserine By similarity
	Modified residue	1849	1	Phosphoserine By similarity
	Modified residue	1874	1	Phosphotyrosine By similarity
	Modified residue	1878	1	Phosphoserine
	Modified residue	1891	1	Phosphothreonine By similarity
	Modified residue	1896	1	Phosphoserine By similarity
	Modified residue	1923	1	Phosphotyrosine
	Modified residue	1927	1	Phosphoserine
	Modified residue	1933	1	Phosphothreonine
	Modified residue	1934	1	Phosphoserine By similarity
Experimental info
	Sequence conflict	1498	1	P → R Ref.1
	Sequence conflict	1498	1	P → R Ref.2
	Sequence conflict	1499 – 1536	38	Missing Ref.1
	Sequence conflict	1499 – 1536	38	Missing Ref.2

Sequences

	Sequence		Length	Mass (Da)
	P08775-1 [UniParc]. Last modified March 1, 1992. Version 3. Checksum: 7D76F38FD92A657E	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 SYSPTSPKYT PTSPSYSPSS PEYTPASPKY 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]	"Cloning and sequence analysis of the mouse genomic locus encoding the largest subunit of RNA polymerase II." Ahearn J.M. Jr., Bartolomei M.S., West M.L., Cisek L.J., Corden J.L. J. Biol. Chem. 262:10695-10705(1987) [PubMed: 3038894] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Lineage-specific biology revealed by a finished genome assembly of the mouse." Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X., Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y., Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S. , Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R., Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K., Eichler E.E., Ponting C.P. PLoS Biol. 7:E1000112-E1000112(2009) [PubMed: 19468303] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: C57BL/6.
[3]	"A unique structure at the carboxyl terminus of the largest subunit of eukaryotic RNA polymerase II." Corden J.L., Cadena D.L., Ahearn J.M. Jr., Dahmus M.E. Proc. Natl. Acad. Sci. U.S.A. 82:7934-7938(1985) [PubMed: 2999785] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1587-1970.
[4]	"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: SEQUENCE REVISION, PRESENCE OF AN ADDITIONAL EXON.
[5]	"A myosin I isoform in the nucleus." Pestic-Dragovich L., Stojiljkovic L., Philimonenko A.A., Nowak G., Ke Y., Settlage R.E., Shabanowitz J., Hunt D.F., Hozak P., de Lanerolle P. Science 290:337-341(2000) [PubMed: 11030652] [Abstract] Cited for: INTERACTION WITH MYO1C.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	M12130, M14101 Genomic DNA. Translation: AAA40071.1. AL603707 Genomic DNA. Translation: CAI51953.1.
IPI	IPI00136207.
PIR	A28490.
RefSeq	NP_033115.1.
UniGene	Mm.16533
3D structure databases
HSSP	HSSP built from PDB template 1K83 based on UniProtKB P04050.
DisProt	DP00181.
ModBase	Search...
Protein-protein interaction databases
STRING	P08775.
PTM databases
PhosphoSite	P08775.
Proteomic databases
PRIDE	P08775.
Genome annotation databases
Ensembl	ENSMUST00000058470; ENSMUSP00000050771; ENSMUSG00000005198; Mus musculus. [Genome view]
GeneID	20020.
KEGG	mmu:20020.
UCSC	uc007jrk.1. mouse.
Organism-specific databases
MGI	MGI:98086. Polr2a.
Phylogenomic databases
HOGENOM	P08775.
HOVERGEN	P08775.
OMA	TSPHYSP.
Enzyme and pathway databases
BRENDA	2.7.7.6. 244.
Gene expression databases
ArrayExpress	P08775.
Bgee	P08775.
CleanEx	MM_POLR2A.
Genevestigator	P08775.
GermOnline	ENSMUSG00000005198. Mus musculus.
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]
Gene3D	G3DSA:2.40.40.30. RNA_pol_A. 1 hit. G3DSA:3.90.1120.10. RNA_pol_Rpb1_1. 1 hit. G3DSA:3.30.1360.90. RNA_pol_Rpb1_7. 1 hit.
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. 26 hits. [Graphical view]
SMART	SM00663. RPOLA_N. 1 hit. [Graphical view]
PROSITE	PS00115. RNA_POL_II_REPEAT. 42 hits. [Graphical view]
ProtoNet	Search...
Other Resources
SOURCE	Search...

Entry information

Entry name

RPB1_MOUSE

Accession

Primary (citable) accession number: P08775
Secondary accession number(s): Q5F298

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1988
Last sequence update:	March 1, 1992
Last modified:	November 3, 2009
This is version 104 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)