RPB1B_TRYBB
ID RPB1B_TRYBB Reviewed; 1766 AA.
AC P17545;
DT 01-AUG-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1990, sequence version 1.
DT 03-AUG-2022, entry version 95.
DE RecName: Full=DNA-directed RNA polymerase II subunit RPB1-B;
DE Short=RNA polymerase II subunit B1-B;
DE EC=2.7.7.6;
DE AltName: Full=DNA-directed RNA polymerase II largest subunit B;
GN Name=TRP5.9; Synonyms=polIIB;
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.
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; X13492; CAA31847.1; -; Genomic_DNA.
DR PIR; B31875; B31875.
DR AlphaFoldDB; P17545; -.
DR SMR; P17545; -.
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-B"
FT /id="PRO_0000073931"
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"
SQ SEQUENCE 1766 AA; 196527 MW; 5BF2239EC30F1FEB CRC64;
MSGGAALPVS QMELHKVNEV QFEIFKERQI KSYAVCLVEH AKSYANAADQ SGEASMICVW
VPLTSNSACE TCHRKHPECP GHFGYIELAE PVFNIGVFDL VLLVLKCVCK TCGALLLNTR
EQDVHKKLQH MTGLNRLRQV 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 INKKRLTEFA RRTVYPSANY IHHPNGTITK
LALLRDRSKV TLNIGDVVER HVINGDVVLF NRQPTLHRMS MMGHRVRVLN YNTFRLNLSC
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
