RPB1_ENCCU
ID RPB1_ENCCU Reviewed; 1599 AA.
AC Q8SSC4;
DT 31-AUG-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 03-AUG-2022, entry version 107.
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=ECU03_0290;
OS Encephalitozoon cuniculi (strain GB-M1) (Microsporidian parasite).
OC Eukaryota; Fungi; Fungi incertae sedis; Microsporidia; Unikaryonidae;
OC Encephalitozoon.
OX NCBI_TaxID=284813;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=GB-M1;
RX PubMed=11719806; DOI=10.1038/35106579;
RA Katinka M.D., Duprat S., Cornillot E., Metenier G., Thomarat F.,
RA Prensier G., Barbe V., Peyretaillade E., Brottier P., Wincker P.,
RA Delbac F., El Alaoui H., Peyret P., Saurin W., Gouy M., Weissenbach J.,
RA Vivares C.P.;
RT "Genome sequence and gene compaction of the eukaryote parasite
RT Encephalitozoon cuniculi.";
RL Nature 414:450-453(2001).
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; AL590443; CAD26175.1; -; Genomic_DNA.
DR RefSeq; NP_597540.1; NM_001040904.1.
DR AlphaFoldDB; Q8SSC4; -.
DR SMR; Q8SSC4; -.
DR STRING; 284813.Q8SSC4; -.
DR GeneID; 858702; -.
DR KEGG; ecu:ECU03_0290; -.
DR VEuPathDB; MicrosporidiaDB:ECU03_0290; -.
DR HOGENOM; CLU_000487_1_1_1; -.
DR InParanoid; Q8SSC4; -.
DR OMA; SLLHICM; -.
DR OrthoDB; 591636at2759; -.
DR Proteomes; UP000000819; Chromosome III.
DR GO; GO:0000428; C:DNA-directed RNA polymerase complex; IEA:UniProtKB-KW.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003899; F:DNA-directed 5'-3' RNA polymerase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006366; P:transcription by RNA polymerase II; IEA:InterPro.
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; 2.
DR Pfam; PF04990; RNA_pol_Rpb1_7; 1.
DR Pfam; PF05001; RNA_pol_Rpb1_R; 13.
DR SMART; SM00663; RPOLA_N; 1.
DR PROSITE; PS00115; RNA_POL_II_REPEAT; 14.
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..1599
FT /note="DNA-directed RNA polymerase II subunit RPB1"
FT /id="PRO_0000073943"
FT REPEAT 1473..1479
FT /note="1"
FT REPEAT 1480..1486
FT /note="2"
FT REPEAT 1487..1493
FT /note="3"
FT REPEAT 1494..1500
FT /note="4"
FT REPEAT 1501..1507
FT /note="5"
FT REPEAT 1508..1514
FT /note="6"
FT REPEAT 1515..1521
FT /note="7"
FT REPEAT 1522..1528
FT /note="8"
FT REPEAT 1529..1535
FT /note="9"
FT REPEAT 1536..1542
FT /note="10"
FT REPEAT 1543..1549
FT /note="11"
FT REPEAT 1550..1556
FT /note="12"
FT REPEAT 1557..1563
FT /note="13"
FT REPEAT 1564..1570
FT /note="14"
FT REGION 804..816
FT /note="Bridging helix"
FT REGION 1424..1446
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1464..1599
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1473..1570
FT /note="C-terminal domain (CTD); 14 X 7 AA approximate
FT tandem repeats of Y-S-P-[TS]-S-P-S"
FT COMPBIAS 1431..1446
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1465..1583
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1584..1599
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 61
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 64
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 71
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 74
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 101
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 104
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 131
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 143
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 450
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 450
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 452
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 452
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 454
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1599 AA; 177716 MW; 208FAE6AE3D6DCD8 CRC64;
MFEAKVKKQI KSIQFGLFSP DEVRNGSVAL IVHPEVMEGG VPKTGGLIDL RMGTTDRMYL
CQSCGGDNFS CPGHFGHIEL TKPMFHVGYI SKIKKVLECV CFYCSKIKIP RKGIKSTLSN
VWGMSKGRSV CEGEVLDNGR SGCGNKQPVI KREGLTLVAF MKGEESNEGK VMLNGERVYS
IFKKISDEDS VYMGFDLKYS RPEWMILTVL LVPPPAVRPS IVMEGSLRGE DDLTHKLADI
IKSNGYLKKY EQEGAPGHIV RDYEQLLQFH VATFIDNDIG GLPQALQKSG RPLKSLSARL
KGKEGRIRGN LMGKRVDFSA RTVITPDPNI SLEEVGVPLE IAKIHTFPEK VTSFNIDRLE
KLVRAGPNEH PGANYVLRSD GQKIDLNFNR SDIRLEEGYV VERHMQSGDV VLFNRQPSLH
KMSMMAHYAR VMGNKTFRLN LSVTSPYNAD FDGDEMNLHM PQSYTSKAEL EELALVSRQI
ISPQSNKPVM GIVQDTLTGL RLFTLRDTFL NEREVMSLLY AVNLEFCDIP LGDAVQTGLR
KGKDYDIMKI LRKPAIAKPM RLWTGKQVLS FVLPNLNYIG LSSEHDDDDK ENIGDTRVII
QDGYIHSGVI DKKAAGATQG GLVHIIFNDF GPKRAAQFFD GVQRMINAFM TGIHTFSMGI
GDTIADPKTV KVVESAIRKA KEEVSALIEN ARQNRLERLP GMTMKESFES HLNLVLNRAR
DVSGTSAQRS LSENNNMKTM VLAGSKGSFI NISQVTACVG QQNVEGKRIP FGFSHRTLPH
FVKDDYTGKS RGFVENSYLT GLDPEEFFFH AMGGREGLID TAIKTAETGY IQRRLVKALE
DAIVRQDESV RSGNGLVYQI KYGEDGFDAT FLESQKVDVK NFTKRYYIDM FGTEELEIKH
GQVSEEVYGM LSSDVDLQKL LDQEYEWLVG EIFEGPPILS VGEVDIERDY KVRDIYQSAV
MSPCNFTRIL ATAKRTFHLS TGDVSPYYIL EAHKHLTTSN RILNVLIRTN LSVKRVLLEH
RLNTEAFNWV VEVIDAKILK AKITPNEMVG TLAAQSVGEP ATQMTLNTFH LAGVASTVTM
GVPRLKEIFN VTKNLKTPSM KIYLDREHGK SIEAAKTIQN EIECLTVKDL CLFSEIYYDP
EITGTEISDD KDFVEAYFEF PDEDVDFSCL SPFLMRLVVD RAKLVGRGIN LEYVAMFIRK
ELGGGAHVIC SDENAVNMVV RVRTTKSEDE SLNFYTTALN SLLRLQLGGY KNVKKVYISE
DKDRKEWYLQ TDGICLSQIL GNPAVNSRLT ISNDLVEIAE TLGIEAARES ILRELTIVID
GNGSYVNYRH MSLLADVMTM RGYLCGITRH GVNKVGAGAL KRSSFEETVE ILLDAALVSE
KNICRGITEN IMMGQLAPMG TGNIEIMLDM KKLDKAIPLS NPVFKPNEPA TPVISTPSSD
SFSISSGNWS PTHLEMAYSR DLGERLSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS
YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT
SPSYSPTSPS YSVSMSSFSN KNKSKNQDGD KKRRNDGSF
