RPB1_PLAFD
ID RPB1_PLAFD Reviewed; 2452 AA.
AC P14248;
DT 01-JAN-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1990, sequence version 1.
DT 03-AUG-2022, entry version 105.
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 largest subunit;
GN Name=RPII;
OS Plasmodium falciparum (isolate CDC / Honduras).
OC Eukaryota; Sar; Alveolata; Apicomplexa; Aconoidasida; Haemosporida;
OC Plasmodiidae; Plasmodium; Plasmodium (Laverania).
OX NCBI_TaxID=5836;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2690004; DOI=10.1093/nar/17.23.9621;
RA Li W.B., Bzik D.J., Gu H., Tanaka M., Fox B.A., Inselburg J.;
RT "An enlarged largest subunit of Plasmodium falciparum RNA polymerase II
RT defines conserved and variable RNA polymerase domains.";
RL Nucleic Acids Res. 17:9621-9636(1989).
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; X16561; CAA34560.1; -; Genomic_DNA.
DR PIR; S07485; RNZQ2L.
DR AlphaFoldDB; P14248; -.
DR SMR; P14248; -.
DR PRIDE; P14248; -.
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; -; 2.
DR Gene3D; 3.30.1360.140; -; 1.
DR Gene3D; 4.10.860.120; -; 1.
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; 4.
DR Pfam; PF04997; RNA_pol_Rpb1_1; 1.
DR Pfam; PF00623; RNA_pol_Rpb1_2; 1.
DR Pfam; PF04983; RNA_pol_Rpb1_3; 2.
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 SMART; SM00663; RPOLA_N; 1.
DR PROSITE; PS00115; RNA_POL_II_REPEAT; 9.
PE 3: Inferred from homology;
KW DNA-binding; DNA-directed RNA polymerase; Magnesium; Metal-binding;
KW Nucleotidyltransferase; Nucleus; Phosphoprotein; Repeat; Transcription;
KW Transferase; Zinc.
FT CHAIN 1..2452
FT /note="DNA-directed RNA polymerase II subunit RPB1"
FT /id="PRO_0000073942"
FT REPEAT 2251..2257
FT /note="1"
FT REPEAT 2265..2271
FT /note="2"
FT REPEAT 2290..2296
FT /note="3; approximate"
FT REPEAT 2297..2303
FT /note="4"
FT REPEAT 2304..2310
FT /note="5"
FT REPEAT 2311..2317
FT /note="6"
FT REPEAT 2318..2324
FT /note="7"
FT REPEAT 2325..2331
FT /note="8"
FT REPEAT 2332..2338
FT /note="9"
FT REPEAT 2339..2345
FT /note="10"
FT REPEAT 2346..2352
FT /note="11"
FT REPEAT 2361..2367
FT /note="12; approximate"
FT DNA_BIND 378..411
FT /evidence="ECO:0000250"
FT DNA_BIND 1182..1193
FT /evidence="ECO:0000255"
FT REGION 627..729
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 970..982
FT /note="Bridging helix"
FT REGION 1093..1128
FT /note="Leucine-zipper"
FT /evidence="ECO:0000255"
FT REGION 1143..1202
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1244..1293
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1261..1290
FT /note="6 X tandem repeats of [YLV]-D(3,4)"
FT REGION 1603..1640
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1653..1699
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1711..1827
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 2061..2246
FT /note="Highly diverged heptapeptide repeats"
FT REGION 2251..2367
FT /note="C-terminal domain (CTD); 12 X 7 AA approximate
FT tandem repeats of Y-S-P-T-S-P-[SYK]"
FT REGION 2258..2278
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 2296..2354
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 2427..2452
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 633..729
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1143..1170
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1178..1194
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1260..1292
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1613..1631
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1724..1742
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1744..1761
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1773..1807
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 68
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 78
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 81
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 108
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 111
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 149
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 203
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 514
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 514
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 516
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 516
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 518
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
SQ SEQUENCE 2452 AA; 278168 MW; F995E117F617A48F CRC64;
MTVDLNIPYS ACELKRVKRL ELGVLDPEII KKISVCEIVN VDIYKDGFPR EGGLNDIRMG
TIDYRTLCGT CNMNVKYCPG HFGHIELAKP MYHYGFMNVV LNVLRCVCYH CGRLLCNVNS
SKVKYIEKIK VNSLRLRKLA ELCLGIRACD HSVEEEGLNI NDNSLNNFYN NDLSNLNMNQ
QMLLNKSNYT NIFEMVSKED VDCGCVQPKY SREGPNMYIQ FLHSSEEDID ESKRKLSAEE
ALEILKKIRK EEMSILGFNS DRCVPASLIL TCIPIPPPCA RPYVQYGNQR SEDDLTLKLL
DIVKTNIQLK RQTDRGAKSH VLQDLCSLLQ FHITTLFDND IPGMPIATTR SKKPIKAIRT
RLKGKEGRLR GNLMGKRVDF SARTVITGDP NLNIDYIGVP KSVAMTLTFC ETVTPLNYDN
LKKLVERGPY EWPGAKYIIR DNGTKYDLRH VRRNSEKELE YGYKVERHMT DEDYILFNRQ
PSLHKMSIMG HKAKILPYST FRLNLSVTSP YNADFDGDEM NLHLAQSHET RSEIKHLMIV
QRQIVSPQGN KPVMGIVQDS LLAIRKFTRR DNFLTKEEVM SLLIWIPYWN HVIPTPAIIK
PRALWTGKQI FSMLLQFDDM NIEDDKNDTA NNKVGRDVNT NVNKDSSKMN TSGNYYYGNS
TNDNTDDYLE KGNAYSRSGN NHPNSPLSIG DNINVGNVQQ NDMSSPNNNN NNNNNNNSNN
NNNNNIGGGI NSFKRFNMVK INLMRDSSTS SKDDNPYCSI NDGKVIIKNN ELLSGIICKR
TVGSSSGSLI HVLWHEMGPD KTKDFLSALQ KVTNNWLEYV GFTVSCSDII ASNKVLGKVR
EILDKSKSEV SKLVEKAQKG ELECQPGKSL YESFETRVNN ELNCAREMAG KVASESLDER
NNIFSMVASG SKGSIINISQ IISCVGQQNV EGKRIPFGFN HRSLPHFIKF DYGPESRGFV
SNSYLSGLTP QEVFFHAMGG REGIIDTACK TSETGYIQRR LIKAMEDVMV QYDRTVRNSY
GDIIQFLYGE DGMAGEYIED QIIDLMKLDN KEINKLYKYN FDEEPFGKDY YIGNKNDGSR
NTTYIDYNKQ NILNQEFEEL YKCKNYLCKE IFPDGDIRQH LPINMNRLIE YAKSQFPCIP
FVSNNNSTNN NNNNNNNNNI SNSRKLMDKG NLSSTHNHKE NKKRRKRRRR KNKFDKFKNE
NNELMSEIKK EYENNDLNNM MISKGDQSPF KGMNEFHMGV ADNDMGSDLG NNNNYNNDDF
VDDDYVDDDD YDDDDYDDDD YDDDDLDDDE NYSDNINIGG NRKYYGNTLK NNYDENSMLN
PIDVVHKVNN FLEKLVIIKQ INSNDTLSVE AQNNATILLK AHLRTYLNSK LLTQTHKVSV
KGLDWLLQEI EKIFYKSLCH PGECVGALAA QSIGEPATQM TLNTFHFAGV GSKNVTLGVP
RLKELINIVK NVKTPSTTIY LDDMVSNDQQ KAKDILTKLE YTTLKQLTSH AQIIYDPNTT
TTILEEDKSW VNEFYEFPDE DDTQYSLGEW VLRIQLTNIH VNEKKLTMKE IVYIIYSVFS
SDELDIIYTD DNSEDLVLRI RVKYLNGEYN FMNYDVVDNA NEQVDEQEED EEHLVANDRG
NYDETKNSTH PHHDYNNNTT NIFKSKVKNN ISSDINTKNE DSISINSSNN EQVKNINSSP
VSNNMHNNNN NNNNDSSNIN DIKVKNIKKE DGNEGALRGG GDSNTSALFG NKNSQKEDNI
VNNNNDNNDD DDEEEEEEDF LFGDHNVSPK NTKDGKNKNT NNKSNNNENK NKKSGNNNSN
NSNTYDDGDV DNDNDDDNDD NKSDITIKED NDVAFMKTST KNAEEDLELK NKNHIEHNIS
REDTEDTFLK KLMEQCLSTL KLRGIENITK VYMREESKIT YDSDNGKFVR SSHWVLDTDG
CNLENIFCAP QVDFKKTVSN DIVEIFEVLG IEAVRRALLK ELRTVISFDS SYVNYRHLSI
LCDVMTQKGY LMSITRHGIN RVDKGPLIKC SFEETVEILL EAAAFAQVDN LRGITENIML
GQLCKIGTGS FDIIIDNQKL NDANQNLETI QDLTSAGFTT PDSLHVITPD GLQSPVAINT
INSPLPFSPT YNANLLSPTA PIDNVNNLLS PQYNLQNYGD NVMSPTSKDI NNLDTLKLGG
KFSPTQSPKS PTSVMHSPFS PFDHQNQQPV DATNLLFSPK NNNIMNYNVF SPKPNINNNV
IQSPNIYSPN PMLDIFSPKP QINHNIYSPS YSPTSPTYNA NNAYYSPTSP KNQNDQMNVN
SQYNVMSPVY SVTSPKYSPT SPKYSPTSPK YSPTSPKYSP TSPKYSPTSP KYSPTSPKYS
PTSPKYSPTS PVAQNIASPN YSPYSITSPK FSPTSPAYSI SSPVYDKSGV VNAHQPMSPA
YILQSPVQIK QNVQDVNMFS PIQQAHVDEA KNDDPFSPMP YNIDEDEMKE NM
