ID   RPB1A_TRYBB             Reviewed;        1766 AA.
AC   P17546;
DT   01-AUG-1990, integrated into UniProtKB/Swiss-Prot.
DT   01-AUG-1990, sequence version 1.
DT   03-AUG-2022, entry version 96.
DE   RecName: Full=DNA-directed RNA polymerase II subunit RPB1-A;
DE            Short=RNA polymerase II subunit B1-A;
DE            EC=2.7.7.6;
DE   AltName: Full=DNA-directed RNA polymerase II largest subunit A;
GN   Name=TRP4.8; Synonyms=polIIA;
OS   Trypanosoma brucei brucei.
OC   Eukaryota; Discoba; Euglenozoa; Kinetoplastea; Metakinetoplastina;
OC   Trypanosomatida; Trypanosomatidae; Trypanosoma.
OX   NCBI_TaxID=5702;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=2917367; DOI=10.1016/0092-8674(89)90581-3;
RA   Evers R., Hammer A., Koeck J., Waldemar J., Borst P., Memet S.,
RA   Cornelissen A.W.C.A.;
RT   "Trypanosoma brucei contains two RNA polymerase II largest subunit genes
RT   with an altered C-terminal domain.";
RL   Cell 56:585-597(1989).
RN   [2]
RP   FUNCTION, AND VARIANTS MET-131 AND ASN-472.
RX   PubMed=8497277; DOI=10.1128/mcb.13.6.3734-3743.1993;
RA   Chung H.M., Lee M.G., Dietrich P., Huang J., Van der Ploeg L.H.T.;
RT   "Disruption of largest subunit RNA polymerase II genes in Trypanosoma
RT   brucei.";
RL   Mol. Cell. Biol. 13:3734-3743(1993).
RN   [3]
RP   IDENTIFICATION IN THE RNA POLYMERASE II COMPLEX, AND IDENTIFICATION BY MASS
RP   SPECTROMETRY.
RX   PubMed=16962183; DOI=10.1016/j.molbiopara.2006.08.002;
RA   Das A., Li H., Liu T., Bellofatto V.;
RT   "Biochemical characterization of Trypanosoma brucei RNA polymerase II.";
RL   Mol. Biochem. Parasitol. 150:201-210(2006).
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 (By similarity). {ECO:0000250,
CC       ECO:0000269|PubMed:8497277}.
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.
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   -!- MISCELLANEOUS: Trypanosoma brucei contains two genes for the Pol II
CC       largest subunit. The presence of both, polIIA and polIIB genes, is not
CC       essential for viability and neither of the genes seem not to confer to
CC       alpha-amanitin-resistant transcription.
CC   -!- SIMILARITY: Belongs to the RNA polymerase beta' chain family.
CC       {ECO:0000305}.
CC   -!- CAUTION: Protein purification and mass spectrometry by PubMed:16962183
CC       do not differentiate between the TRP4.8/polIIA and TRP5.9/polIIB gene
CC       products. {ECO:0000305}.
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DR   EMBL; X13491; CAA31846.1; -; Genomic_DNA.
DR   PIR; A31875; A31875.
DR   AlphaFoldDB; P17546; -.
DR   SMR; P17546; -.
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:0006351; P:transcription, DNA-templated; 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; -; 1.
DR   InterPro; IPR045867; DNA-dir_RpoC_beta_prime.
DR   InterPro; IPR000722; RNA_pol_asu.
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   SMART; SM00663; RPOLA_N; 1.
PE   1: Evidence at protein level;
KW   DNA-binding; DNA-directed RNA polymerase; Magnesium; Metal-binding;
KW   Nucleotidyltransferase; Nucleus; Transcription; Transferase; Zinc.
FT   CHAIN           1..1766
FT                   /note="DNA-directed RNA polymerase II subunit RPB1-A"
FT                   /id="PRO_0000073932"
FT   REGION          813..825
FT                   /note="Bridging helix"
FT   REGION          1660..1766
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1660..1695
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         69
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250"
FT   BINDING         72
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250"
FT   BINDING         79
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250"
FT   BINDING         82
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250"
FT   BINDING         487
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000250"
FT   BINDING         487
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         489
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000250"
FT   BINDING         489
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         491
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000250"
FT   VARIANT         131
FT                   /note="V -> M (in trypanosome isolates)"
FT                   /evidence="ECO:0000269|PubMed:8497277"
FT   VARIANT         472
FT                   /note="S -> N (in trypanosome isolates)"
FT                   /evidence="ECO:0000269|PubMed:8497277"
SQ   SEQUENCE   1766 AA;  196454 MW;  6CF20FB1FAE6166C CRC64;
     MSGGAALPVS QMELHKVNEV QFEIFKERQI KSYAVCLVEH AKSYANAADQ SGEASMICVW
     VPLTSNSACE TCHRKHPECP GHFGYIELAE PVFNIGVFDL VLLVLKCVCK TCGALLLNTR
     EQDVHKKLQH VTGLNRLRQV AKMAEAKCRV STSTEDDMGI DGFDSAPFNG GSGMGPGATR
     GCGASQPRVS RFYGIYPTLV IKAVHEEQDA EWHADKVRQV LDRVSDDDAR LMGFDPQRCH
     PRDLVLTVLP VPPPQVRPAI SFGGLRSDDE LTHQIMSIVK RNNQLRRDKE SDVQAAIDRS
     RALLQEHVAT YFNNASTYYK PTKVNDTKKL KSLTERLKGK YGRLRGNLMG KRVDFSARTV
     ITGDPNIDVD EVGVPFSVAM TLTFPERVNT VNKKRLTEFA RRTVYPSANY IHHPNGTITK
     LALLRDRSKV TLNIGDVVER HVINGDVVLF NRQPTLHRMS MMGHRVRVLN YSTFRLNLSC
     TTPYNADFDG DEMNLHVPQS LLTKAELIEM MMVPKNFVSP NKSAPCMGIV QDSLLGSYRL
     TDKDTFLDKY FVQSVALWLD LWQLPIPAIL KPRPLWTGKQ VFSLILPEVN HPATPQDRPP
     FPHNDSVVMI RRGQLLCGPI TKSIVGAAPG SLIHVIFNEH GSDEVARFIN GVQRVTTFFL
     LNFGFSVGVQ DTVADSDTLR QMNDVLVKTR RNVEKIGAAA NNRTLNRKAG MTLLQSFEAD
     VNSALNKCRE EAAKKALSNV RRTNSFKVMI EAGSKGTDLN ICQIAVFVGQ QNVAGSRIPF
     GFRRRTLPHF MLDDYGETSR GMANRGYVEG LKPHEFFFHT MAGREGLIDT AVKTSDTGYL
     QRKLIKALED VHAAYDGTVR NANDELIQFM YGEDGLDGAR IEGGQLFPLP FRDDKEMEDT
     YKYEYDVDGT FSGKVGGNYM DPHVRKMLRA DPQNVRKLQE EYEQLTADRE WSRKMLDLED
     RDKLKLNLPV NPGRLIQNAR STMGKRSQVS NLSPITIIDH VRKLQEDLMK LFPSYHRGGD
     GYIRNTLSRE RIESALTLFN VHLRQLLASK RVLKEYKLND RAFEYLLKEI RTKYHQSLTT
     PGENIGAIAA QSCGEPATQM TLNTFHNAGI SSKNVTLGVP RLLELLNVSR NQKHASMTVS
     LFPPYDEKRN AQKAQHLIEY CTLESITRRI QFIYDPDPRH TVVEADRDIL ELEWNVMDES
     DAELRIQEVV AGSPWVVRLE LDVDMVTDKA LDMKDVKQAI LRVDESYIIE TGMANNVRQR
     TIRMRSRYNE GADSIPKLKR EIPALLARVH LRGIPGVRRA LLKDTTEFTV DQATGKMSGN
     KIWAIDTDGT ALRRAFIGVV GEDGKNIINA VKTSSNKVPE VCSLLGIEAA RSKMLTELRE
     AYLAYGLNIN YRHYTILVDT ICQHGYLMAV SRSGINRSDT SGPLMRCSFE ETVKVLMAAA
     SFGECDPVRG VSANLVLGNQ ARVGTGLFDL VLNMAALQQA VPQAEAVAPG KDVNVYHSLG
     STLQQNIQSS IAYRPRDHDA TPFVNNASLF LRQGFGGGSS SAPVTASAPY NPSTTYHGGR
     LEASAVHRSQ AYSTSPALEY GGREASASQM YSVMSSASAF NPVSTRMSSV AHSYSEYSEA
     SSYHLQHSVA PTSMQASLPR TDNSMTMQGI GSVSVPYTPH AMSSAAPPSQ VYASTEVGRS
     HSEDSRSQSA LYVPTLSPTH AGYAIRGDEP STHRSDSNVM WREAGGGREQ DEEDDLSTNY
     MPTAKTPQQA APPTAAEFGD EEEEEQ