Q75A34 (RPB1_ASHGO) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA-directed RNA polymerase II subunit RPB1
Short name=RNA polymerase II subunit 1
Short name=RNA polymerase II subunit B1
EC=2.7.7.6

Alternative name(s):
DNA-directed RNA polymerase III largest subunit

Gene names

Name:	RPB1
Ordered Locus Names:	ADR086C

Organism

Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (Yeast) (Eremothecium gossypii) [Complete proteome]

Taxonomic identifier

284811 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Eremothecium

Protein attributes

Sequence length	1745 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

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 By similarity.
Subcellular location	Nucleus By similarity.
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 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
Domain	Repeat
Ligand	DNA-binding Magnesium Metal-binding Zinc
Molecular function	Nucleotidyltransferase Transferase
PTM	Phosphoprotein
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	transcription from RNA polymerase II promoter Inferred from electronic annotation. Source: InterPro
Cellular component	DNA-directed RNA polymerase II, core complex Inferred from electronic annotation. Source: InterPro
Molecular function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW DNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW metal 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 – 1745	1745	DNA-directed RNA polymerase II subunit RPB1		PRO_0000073944
Regions
	Repeat	1552 – 1558	7	1
	Repeat	1559 – 1565	7	2
	Repeat	1566 – 1572	7	3
	Repeat	1573 – 1579	7	4
	Repeat	1580 – 1586	7	5
	Repeat	1587 – 1593	7	6
	Repeat	1594 – 1600	7	7
	Repeat	1601 – 1607	7	8
	Repeat	1608 – 1614	7	9
	Repeat	1615 – 1621	7	10
	Repeat	1622 – 1628	7	11
	Repeat	1629 – 1635	7	12
	Repeat	1636 – 1642	7	13
	Repeat	1643 – 1649	7	14
	Repeat	1650 – 1656	7	15
	Repeat	1657 – 1663	7	16
	Repeat	1664 – 1670	7	17
	Repeat	1671 – 1677	7	18
	Repeat	1678 – 1684	7	19
	Repeat	1685 – 1691	7	20
	Repeat	1692 – 1698	7	21
	Repeat	1699 – 1705	7	22
	Repeat	1706 – 1712	7	23
	Repeat	1713 – 1719	7	24
	Repeat	1720 – 1726	7	25; approximate
	Region	810 – 822	13	Bridging helix
	Region	1552 – 1726	175	25 X 7 AA approximate tandem repeats of Y-S-P-T-S-P-[TSAN]
Sites
	Metal binding	67	1	Zinc 1 By similarity
	Metal binding	70	1	Zinc 1 By similarity
	Metal binding	77	1	Zinc 1 By similarity
	Metal binding	80	1	Zinc 1 By similarity
	Metal binding	107	1	Zinc 2 By similarity
	Metal binding	110	1	Zinc 2 By similarity
	Metal binding	148	1	Zinc 2 By similarity
	Metal binding	167	1	Zinc 2 By similarity
	Metal binding	481	1	Magnesium 1; catalytic By similarity
	Metal binding	481	1	Magnesium 2; shared with RPB2 By similarity
	Metal binding	483	1	Magnesium 1; catalytic By similarity
	Metal binding	483	1	Magnesium 2; shared with RPB2 By similarity
	Metal binding	485	1	Magnesium 1; catalytic By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q75A34 [UniParc]. Last modified July 5, 2004. Version 1. Checksum: 60D5D74FFE1276DD	FASTA	1,745	193,375
	10 20 30 40 50 60 MVDFPYSSAP LRTIKEVQFG LFSPEEVRAI SVAKIEFPET MDETQMRAKV GGLNDPRLGS 70 80 90 100 110 120 IDRNFKCQTC GEGMNDCPGH FGHIELAKPV FHIGFISKIK KVCECVCMHC GKLLLDEYNE 130 140 150 160 170 180 LMRQAIKIKD PKRRFNAVWS LCKAKMVCDT EVPSEDDPSK YISRGGCGNA QPSIRKDGLS 190 200 210 220 230 240 LVGTWKKDKN AEDADQPEKR IISAEEILNV FKHISPEDSW RLGFNEDFSR PEWMLLTVLP 250 260 270 280 290 300 VPPPPVRPSI SFNESQRGED DLTYKLGDIL KANINVQRLE INGSPQHVIQ ESESLLQFHV 310 320 330 340 350 360 ATYMDNDIAG QPQAVQKSGR PIKSIRARLK GKEGRIRGNL MGKRVDFSAR TVISGDPNLD 370 380 390 400 410 420 LDQVGVPKSI AKTLTYPEVV TPYNIDRLTQ LVRNGPNEHP GAKYVIRDNG DRIDLRYSKR 430 440 450 460 470 480 AGDIQLQYGW KVERHIMDDD PVLFNRQPSL HKMSMMAHRV KVMPYSTFRL NLSVTSPYNA 490 500 510 520 530 540 DFDGDEMNLH VPQSEETRAE LSQLCAVPLQ IVSPQSNKPC MGIVQDTLCG IRKMTLRDTF 550 560 570 580 590 600 IELDQVLNML YWIPDWDGVI PTPTILKPKP LWSGKQLLSM AIPSGIHLQR FDEGTTYLSP 610 620 630 640 650 660 KDNGMLIIDG QIIFGVVDKK TVGSSSGGLI HVVTREKGPE VCAKLFGNIQ KVVNYWLLHN 670 680 690 700 710 720 GFSIGIGDTI ADEKTMREIT DAIALAKKKV EEVTKEAQAN LLTAKHGMTL RESFEDNVVR 730 740 750 760 770 780 YLNEARDKAG RSAEVNLKDL NNVKQMVSAG SKGSFINIAQ MSACVGQQSV EGKRIAFGFA 790 800 810 820 830 840 DRTLPHFSKD DYSPESKGFV ENSYLRGLTP QEFFFHAMGG REGLIDTAVK TAETGYIQRR 850 860 870 880 890 900 LVKALEDIMV HYDGTTRNSL GNIIQFVYGE DGMDAAHIEK QSIDTIPGSD LAFEKRYRID 910 920 930 940 950 960 LLNPNYALDP NLLESGTEIV GDLKLQNLLD EEYKQLVQDR HFLRKIFMDG EHNWPLPVNI 970 980 990 1000 1010 1020 RRIIQNAQQT FRIDSTKPTD LSIQDVVQGV RGLQERLLVL RGKSQILQEA QENAITLFCC 1030 1040 1050 1060 1070 1080 LLRSRLATRR VITEYRLTKQ TFEWVLNNIE AQFLRSIVHP GEMVGVLAAQ SIGEPATQMT 1090 1100 1110 1120 1130 1140 LNTFHFAGVA SKKVTSGVPR LKEILNVAKN MKTPSLTVYL EESYATDQEK AKLIRSAIEH 1150 1160 1170 1180 1190 1200 TTLKSVPVAS EIYYDPDPSS TVIEEDEEII QLHFSLMDEE TEASLKHQSP WLLRLELDRV 1210 1220 1230 1240 1250 1260 AMTDKDLTMG QVGEKIKETF KNDLFVIWSE DNAEKLIIRC RVVRDPKTLD AEAEAEEDHM 1270 1280 1290 1300 1310 1320 LKKIENTMLE SITLRGVQDI TRVVMMKYDR KVPSETGEYH KIPEWVLETD GVNLSEVMSV 1330 1340 1350 1360 1370 1380 PGVDPTRIYT NSFIDIMNVL GIEAGRAALY KEVYNVIASD GSYVNYRHMA LLVDVMTSQG 1390 1400 1410 1420 1430 1440 FLMSVTRHGF NRADTGALMR CSFEETVEIL FEAGAAAELD DCSGVSENVI LGQMAPIGTG 1450 1460 1470 1480 1490 1500 SFDVMIDDES LIKYMPEQKL STAVEVNDGG ATPYNSDAGL VNTKVDIKDE LMFSPLVEAG 1510 1520 1530 1540 1550 1560 TSDAIASGGF TAYGGADYGG ATSPFSGYGN GPTSPGFGDV SSPGFSPTSP AYSPTSPSYS 1570 1580 1590 1600 1610 1620 PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP 1630 1640 1650 1660 1670 1680 SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP 1690 1700 1710 1720 1730 1740 TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPQY SPRSPSYSPS FNNNDKEQKD ENGTH

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome." Dietrich F.S., Voegeli S., Brachat S., Lerch A., Gates K., Steiner S., Mohr C., Poehlmann R., Luedi P., Choi S., Wing R.A., Flavier A., Gaffney T.D., Philippsen P. Science 304:304-307(2004) [PubMed: 15001715] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056.
[2]	"Molecular phylogeny and evolution of Candida and related species within the order saccharomycetales as inferred from multilocus sequence analysis." Diezmann S., Cox C.J., Schoenian G., Vilgalys R.J., Mitchell T.G. Submitted (DEC-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 85-291. Strain: ATCC 8717 / IMI 31268.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE016817 Genomic DNA. Translation: AAS52006.1. AY497699 Genomic DNA. Translation: AAT12576.1.
RefSeq	NP_984182.2. NM_209535.2.
3D structure databases
ProteinModelPortal	Q75A34.
ModBase	Search...
Protein-protein interaction databases
STRING	Q75A34.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	4620331.
GenomeReviews	Gene locus ADR086C in contig AE016817_GR.
KEGG	ago:AGOS_ADR086C.
NMPDR	fig|33169.1.peg.1827.
Organism-specific databases
AGD	ADR086C.
Phylogenomic databases
eggNOG	fuNOG04507.
HOGENOM	HBG499785.
OMA	SPTSPHY.
OrthoDB	EOG4J14H5.
PhylomeDB	Q75A34.
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. 14 hits. [Graphical view]
SMART	SM00663. RPOLA_N. 1 hit. [Graphical view]
PROSITE	PS00115. RNA_POL_II_REPEAT. 23 hits. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RPB1_ASHGO

Accession

Primary (citable) accession number: Q75A34
Secondary accession number(s): Q6JED0

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 31, 2004
Last sequence update:	July 5, 2004
Last modified:	December 14, 2011
This is version 55 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program