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Protein

DNA-directed RNA polymerase II subunit RPB1

Gene

RPB1

Organism
Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (Yeast) (Eremothecium gossypii)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

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).By similarity

Catalytic activityi

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi67 – 671Zinc 1By similarity
Metal bindingi70 – 701Zinc 1By similarity
Metal bindingi77 – 771Zinc 1By similarity
Metal bindingi80 – 801Zinc 1By similarity
Metal bindingi107 – 1071Zinc 2By similarity
Metal bindingi110 – 1101Zinc 2By similarity
Metal bindingi148 – 1481Zinc 2By similarity
Metal bindingi167 – 1671Zinc 2By similarity
Metal bindingi481 – 4811Magnesium 1; catalyticBy similarity
Metal bindingi481 – 4811Magnesium 2; shared with RPB2By similarity
Metal bindingi483 – 4831Magnesium 1; catalyticBy similarity
Metal bindingi483 – 4831Magnesium 2; shared with RPB2By similarity
Metal bindingi485 – 4851Magnesium 1; catalyticBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

Transcription

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed RNA polymerase II subunit RPB1 (EC:2.7.7.6)
Short name:
RNA polymerase II subunit 1
Short name:
RNA polymerase II subunit B1
Alternative name(s):
DNA-directed RNA polymerase III largest subunit
Gene namesi
Name:RPB1
Ordered Locus Names:ADR086C
OrganismiAshbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (Yeast) (Eremothecium gossypii)
Taxonomic identifieri284811 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeEremothecium
Proteomesi
  • UP000000591 Componenti: Chromosome IV

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 17451745DNA-directed RNA polymerase II subunit RPB1PRO_0000073944Add
BLAST

Post-translational modificationi

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. The phosphorylation state is believed to result from the balanced action of site-specific CTD kinases and phosphatase, and a 'CTD code' that specifies the position of Pol II within the transcription cycle has been proposed (By similarity).By similarity

Keywords - PTMi

Phosphoprotein

Interactioni

Subunit structurei

Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits.By similarity

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati1552 – 155871
Repeati1559 – 156572
Repeati1566 – 157273
Repeati1573 – 157974
Repeati1580 – 158675
Repeati1587 – 159376
Repeati1594 – 160077
Repeati1601 – 160778
Repeati1608 – 161479
Repeati1615 – 1621710
Repeati1622 – 1628711
Repeati1629 – 1635712
Repeati1636 – 1642713
Repeati1643 – 1649714
Repeati1650 – 1656715
Repeati1657 – 1663716
Repeati1664 – 1670717
Repeati1671 – 1677718
Repeati1678 – 1684719
Repeati1685 – 1691720
Repeati1692 – 1698721
Repeati1699 – 1705722
Repeati1706 – 1712723
Repeati1713 – 1719724
Repeati1720 – 1726725; approximate

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni810 – 82213Bridging helixAdd
BLAST
Regioni1552 – 1726175C-terminal domain (CTD); 25 X 7 AA approximate tandem repeats of Y-S-P-T-S-P-[TSAN]Add
BLAST

Domaini

The C-terminal domain (CTD) serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing.Curated

Sequence similaritiesi

Belongs to the RNA polymerase beta' chain family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

HOGENOMiHOG000222975.
InParanoidiQ75A34.
KOiK03006.
OMAiTGDNSWP.
OrthoDBiEOG780RVQ.

Family and domain databases

InterProiIPR000722. 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]
PfamiPF04997. 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. 23 hits.
[Graphical view]
SMARTiSM00663. RPOLA_N. 1 hit.
[Graphical view]
PROSITEiPS00115. RNA_POL_II_REPEAT. 23 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q75A34-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVDFPYSSAP LRTIKEVQFG LFSPEEVRAI SVAKIEFPET MDETQMRAKV
60 70 80 90 100
GGLNDPRLGS IDRNFKCQTC GEGMNDCPGH FGHIELAKPV FHIGFISKIK
110 120 130 140 150
KVCECVCMHC GKLLLDEYNE LMRQAIKIKD PKRRFNAVWS LCKAKMVCDT
160 170 180 190 200
EVPSEDDPSK YISRGGCGNA QPSIRKDGLS LVGTWKKDKN AEDADQPEKR
210 220 230 240 250
IISAEEILNV FKHISPEDSW RLGFNEDFSR PEWMLLTVLP VPPPPVRPSI
260 270 280 290 300
SFNESQRGED DLTYKLGDIL KANINVQRLE INGSPQHVIQ ESESLLQFHV
310 320 330 340 350
ATYMDNDIAG QPQAVQKSGR PIKSIRARLK GKEGRIRGNL MGKRVDFSAR
360 370 380 390 400
TVISGDPNLD LDQVGVPKSI AKTLTYPEVV TPYNIDRLTQ LVRNGPNEHP
410 420 430 440 450
GAKYVIRDNG DRIDLRYSKR AGDIQLQYGW KVERHIMDDD PVLFNRQPSL
460 470 480 490 500
HKMSMMAHRV KVMPYSTFRL NLSVTSPYNA DFDGDEMNLH VPQSEETRAE
510 520 530 540 550
LSQLCAVPLQ IVSPQSNKPC MGIVQDTLCG IRKMTLRDTF IELDQVLNML
560 570 580 590 600
YWIPDWDGVI PTPTILKPKP LWSGKQLLSM AIPSGIHLQR FDEGTTYLSP
610 620 630 640 650
KDNGMLIIDG QIIFGVVDKK TVGSSSGGLI HVVTREKGPE VCAKLFGNIQ
660 670 680 690 700
KVVNYWLLHN GFSIGIGDTI ADEKTMREIT DAIALAKKKV EEVTKEAQAN
710 720 730 740 750
LLTAKHGMTL RESFEDNVVR YLNEARDKAG RSAEVNLKDL NNVKQMVSAG
760 770 780 790 800
SKGSFINIAQ MSACVGQQSV EGKRIAFGFA DRTLPHFSKD DYSPESKGFV
810 820 830 840 850
ENSYLRGLTP QEFFFHAMGG REGLIDTAVK TAETGYIQRR LVKALEDIMV
860 870 880 890 900
HYDGTTRNSL GNIIQFVYGE DGMDAAHIEK QSIDTIPGSD LAFEKRYRID
910 920 930 940 950
LLNPNYALDP NLLESGTEIV GDLKLQNLLD EEYKQLVQDR HFLRKIFMDG
960 970 980 990 1000
EHNWPLPVNI RRIIQNAQQT FRIDSTKPTD LSIQDVVQGV RGLQERLLVL
1010 1020 1030 1040 1050
RGKSQILQEA QENAITLFCC LLRSRLATRR VITEYRLTKQ TFEWVLNNIE
1060 1070 1080 1090 1100
AQFLRSIVHP GEMVGVLAAQ SIGEPATQMT LNTFHFAGVA SKKVTSGVPR
1110 1120 1130 1140 1150
LKEILNVAKN MKTPSLTVYL EESYATDQEK AKLIRSAIEH TTLKSVTVAS
1160 1170 1180 1190 1200
EIYYDPDPSS TVIEEDEEII QLHFSLMDEE TEASLKHQSP WLLRLELDRV
1210 1220 1230 1240 1250
AMTDKDLTMG QVGEKIKETF KNDLFVIWSE DNAEKLIIRC RVVRDPKTLD
1260 1270 1280 1290 1300
AEAEAEEDHM LKKIENTMLE SITLRGVQDI TRVVMMKYDR KVPSETGEYH
1310 1320 1330 1340 1350
KIPEWVLETD GVNLSEVMSV PGVDPTRIYT NSFIDIMNVL GIEAGRAALY
1360 1370 1380 1390 1400
KEVYNVIASD GSYVNYRHMA LLVDVMTSQG FLMSVTRHGF NRADTGALMR
1410 1420 1430 1440 1450
CSFEETVEIL FEAGAAAELD DCSGVSENVI LGQMAPIGTG SFDVMIDDES
1460 1470 1480 1490 1500
LIKYMPEQKL STAVEVNDGG ATPYNSDAGL VNTKVDIKDE LMFSPLVEAG
1510 1520 1530 1540 1550
TSDAIASGGF TAYGGADYGG ATSPFSGYGN GPTSPGFGDV SSPGFSPTSP
1560 1570 1580 1590 1600
AYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS
1610 1620 1630 1640 1650
YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY
1660 1670 1680 1690 1700
SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS
1710 1720 1730 1740
PTSPSYSPTS PSYSPTSPQY SPRSPSYSPS FNNNDKEQKD ENGTH
Length:1,745
Mass (Da):193,379
Last modified:January 9, 2013 - v2
Checksum:iB0E2943BC8A3B3AF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016817 Genomic DNA. Translation: AAS52006.2.
AY497699 Genomic DNA. Translation: AAT12576.1.
RefSeqiNP_984182.2. NM_209535.2.

Genome annotation databases

EnsemblFungiiAAS52006; AAS52006; AGOS_ADR086C.
GeneIDi4620331.
KEGGiago:AGOS_ADR086C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016817 Genomic DNA. Translation: AAS52006.2.
AY497699 Genomic DNA. Translation: AAT12576.1.
RefSeqiNP_984182.2. NM_209535.2.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiAAS52006; AAS52006; AGOS_ADR086C.
GeneIDi4620331.
KEGGiago:AGOS_ADR086C.

Phylogenomic databases

HOGENOMiHOG000222975.
InParanoidiQ75A34.
KOiK03006.
OMAiTGDNSWP.
OrthoDBiEOG780RVQ.

Family and domain databases

InterProiIPR000722. 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]
PfamiPF04997. 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. 23 hits.
[Graphical view]
SMARTiSM00663. RPOLA_N. 1 hit.
[Graphical view]
PROSITEiPS00115. RNA_POL_II_REPEAT. 23 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056.
  2. "Genomes of Ashbya fungi isolated from insects reveal four mating-type loci, numerous translocations, lack of transposons, and distinct gene duplications."
    Dietrich F.S., Voegeli S., Kuo S., Philippsen P.
    G3 (Bethesda) 3:1225-1239(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENOME REANNOTATION, SEQUENCE REVISION TO 1147.
    Strain: ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056.
  3. "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.

Entry informationi

Entry nameiRPB1_ASHGO
AccessioniPrimary (citable) accession number: Q75A34
Secondary accession number(s): Q6JED0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 31, 2004
Last sequence update: January 9, 2013
Last modified: May 11, 2016
This is version 78 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.