RPB1_DICDI
ID RPB1_DICDI Reviewed; 1727 AA.
AC P35084; Q54X42;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 04-DEC-2007, sequence version 2.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=DNA-directed RNA polymerase II subunit rpb1;
DE Short=RNA polymerase II subunit B1;
DE EC=2.7.7.6;
DE AltName: Full=DNA-directed RNA polymerase III subunit A;
GN Name=polr2a; Synonyms=rpb1, rpoA; ORFNames=DDB_G0279193;
OS Dictyostelium discoideum (Slime mold).
OC Eukaryota; Amoebozoa; Evosea; Eumycetozoa; Dictyostelia; Dictyosteliales;
OC Dictyosteliaceae; Dictyostelium.
OX NCBI_TaxID=44689;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AX4;
RX PubMed=15875012; DOI=10.1038/nature03481;
RA Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R.,
RA Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B.,
RA Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T.,
RA Lehmann R., Hamlin N., Davies R., Gaudet P., Fey P., Pilcher K., Chen G.,
RA Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N.,
RA Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E.,
RA Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N.,
RA Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D.,
RA Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T.,
RA Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D.,
RA Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A.,
RA Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M.,
RA Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A.,
RA Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y.,
RA Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C.,
RA Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R.,
RA Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.;
RT "The genome of the social amoeba Dictyostelium discoideum.";
RL Nature 435:43-57(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 826-1727.
RX PubMed=1482555; DOI=10.1139/o92-120;
RA Lam T.Y., Chan L., Yip P., Siu C.H.;
RT "The largest subunit of RNA polymerase II in Dictyostelium: conservation of
RT the unique tail domain and gene expression.";
RL Biochem. Cell Biol. 70:792-799(1992).
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|UniProtKB:P08775}.
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 heptapeptide 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. {ECO:0000250|UniProtKB:P24928}.
CC -!- SIMILARITY: Belongs to the RNA polymerase beta' chain family.
CC {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AAFI02000030; EAL67745.1; -; Genomic_DNA.
DR EMBL; S52651; AAB24966.1; -; mRNA.
DR PIR; A56823; A56823.
DR RefSeq; XP_641735.1; XM_636643.1.
DR AlphaFoldDB; P35084; -.
DR SMR; P35084; -.
DR STRING; 44689.DDB0215406; -.
DR PaxDb; P35084; -.
DR PRIDE; P35084; -.
DR EnsemblProtists; EAL67745; EAL67745; DDB_G0279193.
DR GeneID; 8621932; -.
DR KEGG; ddi:DDB_G0279193; -.
DR dictyBase; DDB_G0279193; rpb1.
DR eggNOG; KOG0260; Eukaryota.
DR HOGENOM; CLU_000487_3_0_1; -.
DR InParanoid; P35084; -.
DR OMA; SLLHICM; -.
DR PhylomeDB; P35084; -.
DR Reactome; R-DDI-113418; Formation of the Early Elongation Complex.
DR Reactome; R-DDI-674695; RNA Polymerase II Pre-transcription Events.
DR Reactome; R-DDI-6781823; Formation of TC-NER Pre-Incision Complex.
DR Reactome; R-DDI-6782135; Dual incision in TC-NER.
DR Reactome; R-DDI-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
DR Reactome; R-DDI-6796648; TP53 Regulates Transcription of DNA Repair Genes.
DR Reactome; R-DDI-6803529; FGFR2 alternative splicing.
DR Reactome; R-DDI-6807505; RNA polymerase II transcribes snRNA genes.
DR Reactome; R-DDI-72086; mRNA Capping.
DR Reactome; R-DDI-72163; mRNA Splicing - Major Pathway.
DR Reactome; R-DDI-72165; mRNA Splicing - Minor Pathway.
DR Reactome; R-DDI-73776; RNA Polymerase II Promoter Escape.
DR Reactome; R-DDI-73779; RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
DR Reactome; R-DDI-75953; RNA Polymerase II Transcription Initiation.
DR Reactome; R-DDI-75955; RNA Polymerase II Transcription Elongation.
DR Reactome; R-DDI-76042; RNA Polymerase II Transcription Initiation And Promoter Clearance.
DR Reactome; R-DDI-77075; RNA Pol II CTD phosphorylation and interaction with CE.
DR Reactome; R-DDI-9018519; Estrogen-dependent gene expression.
DR PRO; PR:P35084; -.
DR Proteomes; UP000002195; Chromosome 3.
DR GO; GO:0005634; C:nucleus; IDA:dictyBase.
DR GO; GO:0005665; C:RNA polymerase II, core complex; ISS:dictyBase.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003899; F:DNA-directed 5'-3' RNA polymerase activity; ISS:dictyBase.
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; 1.
DR Pfam; PF04990; RNA_pol_Rpb1_7; 1.
DR Pfam; PF05001; RNA_pol_Rpb1_R; 10.
DR SMART; SM00663; RPOLA_N; 1.
DR PROSITE; PS00115; RNA_POL_II_REPEAT; 22.
PE 2: Evidence at transcript level;
KW DNA-binding; DNA-directed RNA polymerase; Magnesium; Metal-binding;
KW Nucleotidyltransferase; Nucleus; Phosphoprotein; Reference proteome;
KW Repeat; Transcription; Transferase; Zinc.
FT CHAIN 1..1727
FT /note="DNA-directed RNA polymerase II subunit rpb1"
FT /id="PRO_0000073936"
FT REPEAT 1553..1559
FT /note="1"
FT REPEAT 1560..1566
FT /note="2"
FT REPEAT 1567..1573
FT /note="3"
FT REPEAT 1574..1580
FT /note="4"
FT REPEAT 1581..1587
FT /note="5"
FT REPEAT 1588..1594
FT /note="6"
FT REPEAT 1595..1601
FT /note="7"
FT REPEAT 1602..1608
FT /note="8"
FT REPEAT 1609..1615
FT /note="9"
FT REPEAT 1616..1622
FT /note="10"
FT REPEAT 1623..1629
FT /note="11"
FT REPEAT 1630..1636
FT /note="12"
FT REPEAT 1637..1643
FT /note="13"
FT REPEAT 1644..1650
FT /note="14"
FT REPEAT 1651..1657
FT /note="15"
FT REPEAT 1658..1664
FT /note="16"
FT REPEAT 1665..1671
FT /note="17"
FT REPEAT 1672..1678
FT /note="18"
FT REPEAT 1679..1685
FT /note="19"
FT REPEAT 1686..1692
FT /note="20"
FT REPEAT 1693..1699
FT /note="21"
FT REPEAT 1700..1706
FT /note="22"
FT REPEAT 1707..1713
FT /note="23"
FT REGION 819..831
FT /note="Bridging helix"
FT /evidence="ECO:0000250"
FT REGION 1478..1512
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1551..1727
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1553..1713
FT /note="C-terminal domain (CTD); 23 X 7 AA tandem repeats of
FT Y-S-P-[ST]-S-P-[FST]"
FT COMPBIAS 1483..1503
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1551..1721
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 66
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 69
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 76
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 79
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 106
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 109
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 147
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 175
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 486
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 486
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 488
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 488
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 490
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT CONFLICT 849
FT /note="R -> C (in Ref. 2; AAB24966)"
FT /evidence="ECO:0000305"
FT CONFLICT 1121..1122
FT /note="KE -> NQ (in Ref. 2; AAB24966)"
FT /evidence="ECO:0000305"
FT CONFLICT 1305
FT /note="D -> E (in Ref. 2; AAB24966)"
FT /evidence="ECO:0000305"
FT CONFLICT 1314
FT /note="G -> S (in Ref. 2; AAB24966)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1727 AA; 192740 MW; 6A72F20A508EC68E CRC64;
MAAFFPPSSA ELRKVKRVQF GILSPDEIRN MSVARVEHPE TYENGKPKAG GLLDPAMGTI
DKTQRCQTCS GTMAECPGHF GHIELAKPVF HIGFIDTVLK ILRCVCYHCS KLLTDTNEHS
FRQALKIRNQ KHRLNAVVDC CKNKKVCAIG GEEEEEHDLS KTDEELDKPV KHGGCGNVLP
KITKEDLKII VEFKDVTDES IEKKSVLSAE RVLNILKRIK DEDSRAMGIN PDWARADWMI
ATVLPVPPPP VRPSIMMDTS TRGEDDLTHK LADIVKANRE LQRQEKNGAP AHIIAEATQF
LQFHVATYVD NEIPGLPQAQ QRSGRPLKSI RQRLKGKEGR IRGNLMGKRV DFSARTVITA
DPNLSIDQVG VPRSIALNLT YPETVTPFNI DKMRELIRNG PSEHPGAKYI IREDGTRFDL
RFVKKVSDTH LECGYKVERH INDGDVVIFN RQPSLHKMSM MGHRIKVMPY STFRLNLSVT
SPYNADFDGD EMNLHVPQTL ETRAEVIEIM MVPRQIVSPQ SNRPVMGIVQ DTLLGSRLFT
KRDCFMEKDL VMNILMWLPS WDGKVPPPAI LKPKQLWTGK QLFSLIIPDI NLIRFTSTHN
DKEPNECSAG DTRVIIERGE LLAGILCKRS LGAANGSIIH VVMNEHGHDT CRLFIDQTQT
VVNHWLINRG FTMGIGDTIA DSATMAKVTL TISSAKNQVK ELIIKAQNKQ FECQPGKSVI
ETFEQKVNQV LNKARDTAGS SAQDSLSEDN NLKAMVTAGS KGSFINISQM MACVGQQNVE
GKRIPFGFQS RTLPHFTKDD YGPESRGFVE NSYLRGLTPQ EFFFHAMGGR EGLIDTAVKT
SETGYIQRRL VKAMEDVSIK YDATVRNSLG DVIQFAYGED GIDGCFVENQ SIDSLRKDNT
ELERMYRHQV DKPDYGDGWM DPLVIEHVRN DSLTRDTLEK EFERIKSDRS LLRNEIIPSG
EANWPLPVNL RRLINNAQKL FNIDIRRVSD LNPAVVVLEI EKLVARLKII ATADTTEDDE
NFNRAWAEVY FNATMLFSIL VRSTFASKRV LTEFRLTEKA FLWVCGEIES KFLQALAHPG
EMVGALAAQS IGEPATQMTL NTFHYAGVSS KNVTLGVPRL KEIINIAKQV KTPSLTIYLK
PHMARDMDRA KIVKSQLEYT TLANVTSATE IYYDPDPQNT IISEDAEFVN SYFELPDEEI
DVHSMSPWLL RIELDRGMVT DKKLTMADIT QCVVRDFGLS LNCIFSDDNA EKLILRIRMV
ESQETKGTDN DDDDQFLRRI ESNMLSEMVL RGIKGIKKVF MRTDDKIPKV TENGGFGVRE
EWILDTDGVS LLEVMSHPDV DHTRTTSNDI VEIIQVLGIE AVRNALLKEL RAVISFDGSY
VNYRHLAILA DVMTYRGHLM AITRHGINRV ETGPLMRCSF EETVEILMDA AMFSETDDVK
GVTENIILGQ LPPLGTGSFE VFLNQDMIKN AHSIALPEPS NVSYPDTPGS QTPSYSYGDG
STTPFHNPYD APLSPFNETF RGDFSPSAMN SPGYNANKSY GSSYQYFPQS PTYSPTSPSY
SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP FYSPTSPSYS PTSPSYSPTS
PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS
PTSPSYSPSS PSYSPSSPSY SPSSPSYSPS SPTFTNKYNY QPNNKKK
