RPB1_ASHGO
ID RPB1_ASHGO Reviewed; 1745 AA.
AC Q75A34; Q6JED0;
DT 31-AUG-2004, integrated into UniProtKB/Swiss-Prot.
DT 09-JAN-2013, sequence version 2.
DT 03-AUG-2022, entry version 106.
DE RecName: Full=DNA-directed RNA polymerase II subunit RPB1;
DE Short=RNA polymerase II subunit 1;
DE Short=RNA polymerase II subunit B1;
DE EC=2.7.7.6;
DE AltName: Full=DNA-directed RNA polymerase III largest subunit;
GN Name=RPB1; OrderedLocusNames=ADR086C;
OS Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
OS (Yeast) (Eremothecium gossypii).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Eremothecium.
OX NCBI_TaxID=284811;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056;
RX PubMed=15001715; DOI=10.1126/science.1095781;
RA Dietrich F.S., Voegeli S., Brachat S., Lerch A., Gates K., Steiner S.,
RA Mohr C., Poehlmann R., Luedi P., Choi S., Wing R.A., Flavier A.,
RA Gaffney T.D., Philippsen P.;
RT "The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces
RT cerevisiae genome.";
RL Science 304:304-307(2004).
RN [2]
RP GENOME REANNOTATION, AND SEQUENCE REVISION TO 1147.
RC STRAIN=ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056;
RX PubMed=23749448; DOI=10.1534/g3.112.002881;
RA Dietrich F.S., Voegeli S., Kuo S., Philippsen P.;
RT "Genomes of Ashbya fungi isolated from insects reveal four mating-type
RT loci, numerous translocations, lack of transposons, and distinct gene
RT duplications.";
RL G3 (Bethesda) 3:1225-1239(2013).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 85-291.
RC STRAIN=ATCC 8717 / IMI 31268;
RA Diezmann S., Cox C.J., Schoenian G., Vilgalys R.J., Mitchell T.G.;
RT "Molecular phylogeny and evolution of Candida and related species within
RT the order saccharomycetales as inferred from multilocus sequence
RT analysis.";
RL Submitted (DEC-2003) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription of
CC DNA into RNA using the four ribonucleoside triphosphates as substrates.
CC Largest and catalytic component of RNA polymerase II which synthesizes
CC mRNA precursors and many functional non-coding RNAs. Forms the
CC polymerase active center together with the second largest subunit. Pol
CC II is the central component of the basal RNA polymerase II
CC transcription machinery. It is composed of mobile elements that move
CC relative to each other. RPB1 is part of the core element with the
CC central large cleft, the clamp element that moves to open and close the
CC cleft and the jaws that are thought to grab the incoming DNA template.
CC At the start of transcription, a single-stranded DNA template strand of
CC the promoter is positioned within the central active site cleft of Pol
CC II. A bridging helix emanates from RPB1 and crosses the cleft near the
CC catalytic site and is thought to promote translocation of Pol II by
CC acting as a ratchet that moves the RNA-DNA hybrid through the active
CC site by switching from straight to bent conformations at each step of
CC nucleotide addition. During transcription elongation, Pol II moves on
CC the template as the transcript elongates. Elongation is influenced by
CC the phosphorylation status of the C-terminal domain (CTD) of Pol II
CC largest subunit (RPB1), which serves as a platform for assembly of
CC factors that regulate transcription initiation, elongation, termination
CC and mRNA processing (By similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate +
CC RNA(n+1); Xref=Rhea:RHEA:21248, Rhea:RHEA-COMP:14527, Rhea:RHEA-
CC COMP:17342, ChEBI:CHEBI:33019, ChEBI:CHEBI:61557, ChEBI:CHEBI:140395;
CC EC=2.7.7.6;
CC -!- SUBUNIT: Component of the RNA polymerase II (Pol II) complex consisting
CC of 12 subunits. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- DOMAIN: The C-terminal domain (CTD) serves as a platform for assembly
CC of factors that regulate transcription initiation, elongation,
CC termination and mRNA processing. {ECO:0000305}.
CC -!- PTM: The tandem 7 residues repeats in the C-terminal domain (CTD) can
CC be highly phosphorylated. The phosphorylation activates Pol II.
CC Phosphorylation occurs mainly at residues 'Ser-2' and 'Ser-5' of the
CC heptapeptide repeat. The phosphorylation state is believed to result
CC from the balanced action of site-specific CTD kinases and phosphatase,
CC and a 'CTD code' that specifies the position of Pol II within the
CC transcription cycle has been proposed (By similarity). {ECO:0000250}.
CC -!- MISCELLANEOUS: The binding of ribonucleoside triphosphate to the RNA
CC polymerase II transcribing complex probably involves a two-step
CC mechanism. The initial binding seems to occur at the entry (E) site and
CC involves a magnesium ion temporarily coordinated by three conserved
CC aspartate residues of the two largest RNA Pol II subunits. The
CC ribonucleoside triphosphate is transferred by a rotation to the
CC nucleotide addition (A) site for pairing with the template DNA. The
CC catalytic A site involves three conserved aspartate residues of the RNA
CC Pol II largest subunit which permanently coordinate a second magnesium
CC ion.
CC -!- SIMILARITY: Belongs to the RNA polymerase beta' chain family.
CC {ECO:0000305}.
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DR EMBL; AE016817; AAS52006.2; -; Genomic_DNA.
DR EMBL; AY497699; AAT12576.1; -; Genomic_DNA.
DR RefSeq; NP_984182.2; NM_209535.2.
DR AlphaFoldDB; Q75A34; -.
DR SMR; Q75A34; -.
DR STRING; 33169.AAS52006; -.
DR EnsemblFungi; AAS52006; AAS52006; AGOS_ADR086C.
DR GeneID; 4620331; -.
DR KEGG; ago:AGOS_ADR086C; -.
DR eggNOG; KOG0260; Eukaryota.
DR HOGENOM; CLU_000487_3_0_1; -.
DR InParanoid; Q75A34; -.
DR OMA; SLLHICM; -.
DR Proteomes; UP000000591; Chromosome IV.
DR GO; GO:0000785; C:chromatin; IEA:EnsemblFungi.
DR GO; GO:0005665; C:RNA polymerase II, core complex; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0001055; F:RNA polymerase II activity; IEA:EnsemblFungi.
DR GO; GO:0003968; F:RNA-directed 5'-3' RNA polymerase activity; IEA:EnsemblFungi.
DR GO; GO:0006368; P:transcription elongation from RNA polymerase II promoter; IEA:EnsemblFungi.
DR GO; GO:0006367; P:transcription initiation from RNA polymerase II promoter; IEA:EnsemblFungi.
DR GO; GO:0019985; P:translesion synthesis; IEA:EnsemblFungi.
DR Gene3D; 1.10.132.30; -; 1.
DR Gene3D; 1.10.274.100; -; 1.
DR Gene3D; 3.30.1360.140; -; 1.
DR Gene3D; 4.10.860.120; -; 2.
DR InterPro; IPR045867; DNA-dir_RpoC_beta_prime.
DR InterPro; IPR000722; RNA_pol_asu.
DR InterPro; IPR000684; RNA_pol_II_repeat_euk.
DR InterPro; IPR006592; RNA_pol_N.
DR InterPro; IPR007080; RNA_pol_Rpb1_1.
DR InterPro; IPR007066; RNA_pol_Rpb1_3.
DR InterPro; IPR042102; RNA_pol_Rpb1_3_sf.
DR InterPro; IPR007083; RNA_pol_Rpb1_4.
DR InterPro; IPR007081; RNA_pol_Rpb1_5.
DR InterPro; IPR007075; RNA_pol_Rpb1_6.
DR InterPro; IPR007073; RNA_pol_Rpb1_7.
DR InterPro; IPR038593; RNA_pol_Rpb1_7_sf.
DR InterPro; IPR044893; RNA_pol_Rpb1_clamp_domain.
DR InterPro; IPR038120; Rpb1_funnel_sf.
DR PANTHER; PTHR19376; PTHR19376; 1.
DR Pfam; PF04997; RNA_pol_Rpb1_1; 1.
DR Pfam; PF00623; RNA_pol_Rpb1_2; 1.
DR Pfam; PF04983; RNA_pol_Rpb1_3; 1.
DR Pfam; PF05000; RNA_pol_Rpb1_4; 1.
DR Pfam; PF04998; RNA_pol_Rpb1_5; 1.
DR Pfam; PF04992; RNA_pol_Rpb1_6; 1.
DR Pfam; PF04990; RNA_pol_Rpb1_7; 1.
DR Pfam; PF05001; RNA_pol_Rpb1_R; 22.
DR SMART; SM00663; RPOLA_N; 1.
DR PROSITE; PS00115; RNA_POL_II_REPEAT; 23.
PE 3: Inferred from homology;
KW DNA-binding; DNA-directed RNA polymerase; Magnesium; Metal-binding;
KW Nucleotidyltransferase; Nucleus; Phosphoprotein; Reference proteome;
KW Repeat; Transcription; Transferase; Zinc.
FT CHAIN 1..1745
FT /note="DNA-directed RNA polymerase II subunit RPB1"
FT /id="PRO_0000073944"
FT REPEAT 1552..1558
FT /note="1"
FT REPEAT 1559..1565
FT /note="2"
FT REPEAT 1566..1572
FT /note="3"
FT REPEAT 1573..1579
FT /note="4"
FT REPEAT 1580..1586
FT /note="5"
FT REPEAT 1587..1593
FT /note="6"
FT REPEAT 1594..1600
FT /note="7"
FT REPEAT 1601..1607
FT /note="8"
FT REPEAT 1608..1614
FT /note="9"
FT REPEAT 1615..1621
FT /note="10"
FT REPEAT 1622..1628
FT /note="11"
FT REPEAT 1629..1635
FT /note="12"
FT REPEAT 1636..1642
FT /note="13"
FT REPEAT 1643..1649
FT /note="14"
FT REPEAT 1650..1656
FT /note="15"
FT REPEAT 1657..1663
FT /note="16"
FT REPEAT 1664..1670
FT /note="17"
FT REPEAT 1671..1677
FT /note="18"
FT REPEAT 1678..1684
FT /note="19"
FT REPEAT 1685..1691
FT /note="20"
FT REPEAT 1692..1698
FT /note="21"
FT REPEAT 1699..1705
FT /note="22"
FT REPEAT 1706..1712
FT /note="23"
FT REPEAT 1713..1719
FT /note="24"
FT REPEAT 1720..1726
FT /note="25; approximate"
FT REGION 810..822
FT /note="Bridging helix"
FT REGION 1530..1745
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1552..1726
FT /note="C-terminal domain (CTD); 25 X 7 AA approximate
FT tandem repeats of Y-S-P-T-S-P-[TSAN]"
FT COMPBIAS 1530..1733
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 67
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 70
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 77
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 80
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 107
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 110
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 148
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 167
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 481
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 481
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="ligand shared with RPB2"
FT /evidence="ECO:0000250"
FT BINDING 483
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 483
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="ligand shared with RPB2"
FT /evidence="ECO:0000250"
FT BINDING 485
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1745 AA; 193379 MW; B0E2943BC8A3B3AF CRC64;
MVDFPYSSAP LRTIKEVQFG LFSPEEVRAI SVAKIEFPET MDETQMRAKV GGLNDPRLGS
IDRNFKCQTC GEGMNDCPGH FGHIELAKPV FHIGFISKIK KVCECVCMHC GKLLLDEYNE
LMRQAIKIKD PKRRFNAVWS LCKAKMVCDT EVPSEDDPSK YISRGGCGNA QPSIRKDGLS
LVGTWKKDKN AEDADQPEKR IISAEEILNV FKHISPEDSW RLGFNEDFSR PEWMLLTVLP
VPPPPVRPSI SFNESQRGED DLTYKLGDIL KANINVQRLE INGSPQHVIQ ESESLLQFHV
ATYMDNDIAG QPQAVQKSGR PIKSIRARLK GKEGRIRGNL MGKRVDFSAR TVISGDPNLD
LDQVGVPKSI AKTLTYPEVV TPYNIDRLTQ LVRNGPNEHP GAKYVIRDNG DRIDLRYSKR
AGDIQLQYGW KVERHIMDDD PVLFNRQPSL HKMSMMAHRV KVMPYSTFRL NLSVTSPYNA
DFDGDEMNLH VPQSEETRAE LSQLCAVPLQ IVSPQSNKPC MGIVQDTLCG IRKMTLRDTF
IELDQVLNML YWIPDWDGVI PTPTILKPKP LWSGKQLLSM AIPSGIHLQR FDEGTTYLSP
KDNGMLIIDG QIIFGVVDKK TVGSSSGGLI HVVTREKGPE VCAKLFGNIQ KVVNYWLLHN
GFSIGIGDTI ADEKTMREIT DAIALAKKKV EEVTKEAQAN LLTAKHGMTL RESFEDNVVR
YLNEARDKAG RSAEVNLKDL NNVKQMVSAG SKGSFINIAQ MSACVGQQSV EGKRIAFGFA
DRTLPHFSKD DYSPESKGFV ENSYLRGLTP QEFFFHAMGG REGLIDTAVK TAETGYIQRR
LVKALEDIMV HYDGTTRNSL GNIIQFVYGE DGMDAAHIEK QSIDTIPGSD LAFEKRYRID
LLNPNYALDP NLLESGTEIV GDLKLQNLLD EEYKQLVQDR HFLRKIFMDG EHNWPLPVNI
RRIIQNAQQT FRIDSTKPTD LSIQDVVQGV RGLQERLLVL RGKSQILQEA QENAITLFCC
LLRSRLATRR VITEYRLTKQ TFEWVLNNIE AQFLRSIVHP GEMVGVLAAQ SIGEPATQMT
LNTFHFAGVA SKKVTSGVPR LKEILNVAKN MKTPSLTVYL EESYATDQEK AKLIRSAIEH
TTLKSVTVAS EIYYDPDPSS TVIEEDEEII QLHFSLMDEE TEASLKHQSP WLLRLELDRV
AMTDKDLTMG QVGEKIKETF KNDLFVIWSE DNAEKLIIRC RVVRDPKTLD AEAEAEEDHM
LKKIENTMLE SITLRGVQDI TRVVMMKYDR KVPSETGEYH KIPEWVLETD GVNLSEVMSV
PGVDPTRIYT NSFIDIMNVL GIEAGRAALY KEVYNVIASD GSYVNYRHMA LLVDVMTSQG
FLMSVTRHGF NRADTGALMR CSFEETVEIL FEAGAAAELD DCSGVSENVI LGQMAPIGTG
SFDVMIDDES LIKYMPEQKL STAVEVNDGG ATPYNSDAGL VNTKVDIKDE LMFSPLVEAG
TSDAIASGGF TAYGGADYGG ATSPFSGYGN GPTSPGFGDV SSPGFSPTSP AYSPTSPSYS
PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP
SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP
TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPQY SPRSPSYSPS FNNNDKEQKD
ENGTH
