RPB1_CAEBR
ID RPB1_CAEBR Reviewed; 1853 AA.
AC P35074; A8WZN7; Q61UE8;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-2005, sequence version 2.
DT 03-AUG-2022, entry version 122.
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=rpb-1; Synonyms=ama-1; ORFNames=CBG05355;
OS Caenorhabditis briggsae.
OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
OC Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae;
OC Caenorhabditis.
OX NCBI_TaxID=6238;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AF16;
RX PubMed=14624247; DOI=10.1371/journal.pbio.0000045;
RA Stein L.D., Bao Z., Blasiar D., Blumenthal T., Brent M.R., Chen N.,
RA Chinwalla A., Clarke L., Clee C., Coghlan A., Coulson A., D'Eustachio P.,
RA Fitch D.H.A., Fulton L.A., Fulton R.E., Griffiths-Jones S., Harris T.W.,
RA Hillier L.W., Kamath R., Kuwabara P.E., Mardis E.R., Marra M.A.,
RA Miner T.L., Minx P., Mullikin J.C., Plumb R.W., Rogers J., Schein J.E.,
RA Sohrmann M., Spieth J., Stajich J.E., Wei C., Willey D., Wilson R.K.,
RA Durbin R.M., Waterston R.H.;
RT "The genome sequence of Caenorhabditis briggsae: a platform for comparative
RT genomics.";
RL PLoS Biol. 1:166-192(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-66.
RA Bird D.M., Wilson M.A., Kaloshian I.;
RT "Analysis of 5' flanking sequences from the Caenorhabditis elegans ama-1
RT gene.";
RL Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases.
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. Involved in the transcription of several genes
CC including those involved in embryogenesis.
CC {ECO:0000250|UniProtKB:P16356, ECO:0000250|UniProtKB:P24928}.
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. Interacts with sig-7. {ECO:0000250|UniProtKB:P16356,
CC ECO:0000250|UniProtKB:P24928}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:P16356}.
CC Chromosome {ECO:0000250|UniProtKB:P16356}. Note=Localizes to punctate
CC nucleoplasmic structures in the nuclei of interphase somatic cells when
CC phosphorylated at 'Ser-5' of the C-terminal heptapeptide repeat. A
CC similar localization occurs in early developing oocytes when
CC phosphorylated at 'Ser-2' and 'Ser-5' of the C-terminal heptapeptide
CC repeat. Localizes to the nucleus of embryonic somatic and germline
CC cells when phosphorylated at 'Ser-2' of the C-terminal heptapeptide
CC repeat. Localizes to two discrete foci in the transcriptionally silent
CC germ line nucleus. Co-localizes with transcriptionally active chromatin
CC in all autosomes of mitotic and meiotic nuclei in germ cells.
CC {ECO:0000250|UniProtKB:P16356}.
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 and starts at the 3- to 4-cell embryonic stage.
CC This phosphorylation also occurs in the early stages of oocyte
CC development and is not detected in oocytes arrested at the meiotic
CC diakinesis stage. In the somatic lineage, phosphorylation at 'Ser-2' is
CC mediated by cdk-12 downstream of cdk-9 whereas in the germline lineage
CC cdk-12 phosphorylates 'Ser-2' independently of cdk-9. Phosphorylation
CC is likely mediated by cdk-7. May be dephosphorylated by fcp-1 in
CC diakinetic oocytes and in 1-cell and 2-cell embryos. Dephosphorylated
CC at 'Ser-5' of the heptapeptide repeat by ssup-72. The phosphorylation
CC state is believed to result from the balanced action of site-specific
CC CTD kinases and phosphatase, and a 'CTD code' that specifies the
CC position of Pol II within the transcription cycle has been proposed.
CC {ECO:0000250|UniProtKB:P16356, ECO:0000250|UniProtKB:P24928}.
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA27891.1; Type=Frameshift; Evidence={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; HE601337; CAP25847.3; -; Genomic_DNA.
DR EMBL; L23763; AAA27891.1; ALT_FRAME; Genomic_DNA.
DR RefSeq; XP_002634760.1; XM_002634714.1.
DR AlphaFoldDB; P35074; -.
DR SMR; P35074; -.
DR STRING; 6238.CBG05355; -.
DR PRIDE; P35074; -.
DR EnsemblMetazoa; CBG05355a.1; CBG05355a.1; WBGene00027817.
DR GeneID; 8576752; -.
DR KEGG; cbr:CBG_05355; -.
DR CTD; 8576752; -.
DR WormBase; CBG05355a; CBP01350; WBGene00027817; Cbr-rpb-1.
DR eggNOG; KOG0260; Eukaryota.
DR HOGENOM; CLU_000487_0_2_1; -.
DR InParanoid; P35074; -.
DR OMA; SLLHICM; -.
DR OrthoDB; 591636at2759; -.
DR Proteomes; UP000008549; Chromosome IV.
DR GO; GO:0005694; C:chromosome; IEA:UniProtKB-SubCell.
DR GO; GO:0005665; C:RNA polymerase II, core complex; IBA:GO_Central.
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; 1.
DR Pfam; PF04990; RNA_pol_Rpb1_7; 1.
DR Pfam; PF05001; RNA_pol_Rpb1_R; 24.
DR SMART; SM00663; RPOLA_N; 1.
DR PROSITE; PS00115; RNA_POL_II_REPEAT; 26.
PE 3: Inferred from homology;
KW Chromosome; DNA-binding; DNA-directed RNA polymerase; Magnesium;
KW Metal-binding; Nucleotidyltransferase; Nucleus; Phosphoprotein;
KW Reference proteome; Repeat; Transcription; Transferase; Zinc.
FT CHAIN 1..1853
FT /note="DNA-directed RNA polymerase II subunit RPB1"
FT /id="PRO_0000073934"
FT REPEAT 1592..1598
FT /note="1"
FT REPEAT 1599..1605
FT /note="2"
FT REPEAT 1616..1622
FT /note="3"
FT REPEAT 1623..1629
FT /note="4"
FT REPEAT 1630..1636
FT /note="5"
FT REPEAT 1637..1643
FT /note="6"
FT REPEAT 1644..1650
FT /note="7"
FT REPEAT 1651..1657
FT /note="8"
FT REPEAT 1658..1664
FT /note="9"
FT REPEAT 1665..1671
FT /note="10"
FT REPEAT 1679..1685
FT /note="11"
FT REPEAT 1686..1692
FT /note="12"
FT REPEAT 1693..1699
FT /note="13"
FT REPEAT 1700..1706
FT /note="14"
FT REPEAT 1707..1713
FT /note="15"
FT REPEAT 1717..1723
FT /note="16"
FT REPEAT 1724..1730
FT /note="17"
FT REPEAT 1731..1737
FT /note="18"
FT REPEAT 1752..1758
FT /note="19"
FT REPEAT 1759..1765
FT /note="20"
FT REPEAT 1779..1785
FT /note="21"
FT REPEAT 1786..1792
FT /note="22"
FT REPEAT 1800..1806
FT /note="23"
FT REPEAT 1821..1827
FT /note="24"
FT REPEAT 1828..1834
FT /note="25"
FT REPEAT 1842..1848
FT /note="26"
FT REGION 256..268
FT /note="Lid loop"
FT /evidence="ECO:0000250"
FT REGION 314..331
FT /note="Rudder loop"
FT /evidence="ECO:0000250"
FT REGION 827..839
FT /note="Bridging helix"
FT REGION 1520..1568
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1589..1853
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1592..1848
FT /note="C-terminal domain (CTD); 26 X 7 AA approximate
FT tandem repeats of Y-[ST]-P-[ST]-S-P-[AGKNQRST]"
FT COMPBIAS 1589..1801
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1810..1853
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 149
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 177
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
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 BINDING 491
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 493
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT CONFLICT 22
FT /note="I -> F (in Ref. 2; AAA27891)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1853 AA; 204442 MW; C055D4705E6C4AF1 CRC64;
MALVGVDFQA PLRTVCRVQF GILGPEEIKR MSVAHVEFPE VYENGKPKMG GLMDPRQGVI
DRRGRCMTCA GNLTDCPGHF GHLELAKPVF HIGFLTKSLK ILRCVCFYCG RLLIDKTNPR
VMDILKKTSG NPKKRLALIY DLCKSKSVCE GAAEKEDGLP DDMDDPMNEG KKVPAGCGRY
QPSYRRVGID INAEWKKNVN EDTQERKIML TAERVLEVFK QITDEDILVI GMDPQFARPE
WMICTVLPVP PLAVRPAVVT FGSAKNQDDL THKLSDIIKT NQQLQRNEAN GAAAHVLTDD
VRLLQYHVAT LVDNCIPGLP TATQKGGRPL KSIKQRLKGK EGRIRGNLMG KRVDFSARTV
ITADPNLPID TVGVPRTIAQ NLTFPEIVTP FNVDKLQELV NRGDTQYPGA KYIIRENGAR
VDLRYHPRAA DLHLQPGYRV ERHMKDGDII VFNRQPTLHK MSMMGHRVKI LPWSTFRMNL
SVTSPYNADF DGDEMNLHLP QSLETRAEIE EIAMVPRQLI TPQANKPVMG IVQDTLCAVR
MMTKRDIFID WPFMMDLLMY LPTWDGKVPQ PAILKPKPLW TGKQVFSLII PGNVNVLRTH
STHPDSEDSG PYKWISPGDT KVLIEHGELL SGIVCSKTVG KSAGNLLHVV ALELGHEIAA
NFYSHIQTVI NAWLLREGHT IGIGDTIADQ STYLDIQNTI RKAKQDVVDV IEKAHNDDLE
PTPGNTLRQT FENKVNQILN DARDRTGSSA QKSLSEFNNF KSMVVSGSKG SKINISQVIA
CVGQQNVEGK RIPFGFRHRT LPHFIKDDYG PESKGFVENS YLAGLTPSEF FFHAMGGREG
LIDTAVKTAE TGYIQRRLIK AMESVMVNYD GTVRNSLAQM VQLRYGEDGL DGMWVENQNM
PTMKPNNAVF ERDFRMDLTD NKFLRKNYSE DVVREIQEAQ DGISLVESEW SQLEEDRRLL
RKIFPRGDAK IVLPCNLQRL IWNAQKIFKV DLRKPVNLSP LHVINGVREL SKKLIIVSGN
DEISKQAQYN ATLLMNILLR STLCTKKMCT SAKLNTEAFD WLLGEIETRF QQAIAQPGEM
VGALAAQSLG EPATQMTLNT FHYAGVSAKN VTLGVPRLKE IINVSKQLKT PSLTVFLTGA
AAKDPEKAKD VLCKLEHTTL KKVTCNTAIY YDPDPKNTVI AEDEEWVSIF YEMPDHDLTR
TSPWLLRIEL DRKRMVDKKL TMEMIADRIH GGFGQDVHTI YTDDNAEKLV FRLRIAGEDK
GAEGQEEQVD KMEDDVFLRC IEANMLSDLT LQGIPAISKV YMNQPNTDDK KRIIITPEGG
FKAVADWILE TDGTALLRVL SERQIDPVRT TSNDICEIFE VLGIEAVRKS IEKEMDNVIS
FDGSYVNYRH LALLCDVMTA KGHLMAITRH GINRQEVGAL MRCSFEETVD ILMEASVHAE
VDPVKGVSEN IMLGQLARCG TGCFDLVLDV EKCKHGMEIP QNVVMGAGIY GGGFAGSPSR
EFSPAHSPWN SGVTPNYSGP WSPTGGMSPS AGFSPAGNLD GGASPFNEGG WSPASPGDPL
GALSPRTPAY GGMSPGVYSP ASPGFSMTSP HYSPTSPSYS PTSPAHHGQS PVSPSYSPTS
PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPSSPRYS
PTSPTYSPTS PTYSPTSPTY SPTSPTYSPT SPSYEGYSPS SPKYSPSSPT YSPTSPSYSP
TSPQYSPTSP QYSPSSPTYT PSSPTYNPTS PRAFSSPQYS PTSPTYSPTS PSYTPSSPQY
SPTSPTYTPS PADQPGTSNQ YSPSSPTYSP SSPTYSPASP SYSPSSPTYD PQN
