RPB1_PICGU
ID RPB1_PICGU Reviewed; 1579 AA.
AC A5DCV3; A5DCV0; Q6JE96; Q6JE97; Q6JE98;
DT 10-JUL-2007, integrated into UniProtKB/Swiss-Prot.
DT 10-JUL-2007, sequence version 2.
DT 03-AUG-2022, entry version 77.
DE RecName: Full=DNA-directed RNA polymerase II subunit RPB1;
DE Short=RNA polymerase II subunit 1;
DE Short=RNA polymerase II subunit B1;
DE EC=2.7.7.6;
DE AltName: Full=DNA-directed RNA polymerase III largest subunit;
DE Flags: Fragments;
GN Name=RPB1; ORFNames=PGUG_01108/01105;
OS Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539
OS / NBRC 10279 / NRRL Y-324) (Yeast) (Candida guilliermondii).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Debaryomycetaceae; Meyerozyma.
OX NCBI_TaxID=294746;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324;
RX PubMed=19465905; DOI=10.1038/nature08064;
RA Butler G., Rasmussen M.D., Lin M.F., Santos M.A.S., Sakthikumar S.,
RA Munro C.A., Rheinbay E., Grabherr M., Forche A., Reedy J.L., Agrafioti I.,
RA Arnaud M.B., Bates S., Brown A.J.P., Brunke S., Costanzo M.C.,
RA Fitzpatrick D.A., de Groot P.W.J., Harris D., Hoyer L.L., Hube B.,
RA Klis F.M., Kodira C., Lennard N., Logue M.E., Martin R., Neiman A.M.,
RA Nikolaou E., Quail M.A., Quinn J., Santos M.C., Schmitzberger F.F.,
RA Sherlock G., Shah P., Silverstein K.A.T., Skrzypek M.S., Soll D.,
RA Staggs R., Stansfield I., Stumpf M.P.H., Sudbery P.E., Srikantha T.,
RA Zeng Q., Berman J., Berriman M., Heitman J., Gow N.A.R., Lorenz M.C.,
RA Birren B.W., Kellis M., Cuomo C.A.;
RT "Evolution of pathogenicity and sexual reproduction in eight Candida
RT genomes.";
RL Nature 459:657-662(2009).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 88-295, AND VARIANT SER-198.
RC STRAIN=ATCC 46036 / CBS 2030 / IFO 10106 / NRRL Y-2075, MMRL 1635,
RC MMRL 1636, and MMRL 1759;
RX PubMed=15583292; DOI=10.1128/jcm.42.12.5624-5635.2004;
RA Diezmann S., Cox C.J., Schoenian G., Vilgalys R.J., Mitchell T.G.;
RT "Phylogeny and evolution of medical species of Candida and related taxa: a
RT multigenic analysis.";
RL J. Clin. Microbiol. 42:5624-5635(2004).
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=EDK37008.1; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=EDK37010.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; CH408155; EDK37008.1; ALT_FRAME; Genomic_DNA.
DR EMBL; CH408155; EDK37010.1; ALT_FRAME; Genomic_DNA.
DR EMBL; AY497711; AAT12588.1; -; Genomic_DNA.
DR EMBL; AY497732; AAT12608.1; -; Genomic_DNA.
DR EMBL; AY497733; AAT12609.1; -; Genomic_DNA.
DR EMBL; AY497734; AAT12610.1; -; Genomic_DNA.
DR RefSeq; XP_001487729.1; XM_001487679.1.
DR RefSeq; XP_001487731.1; XM_001487681.1.
DR AlphaFoldDB; A5DCV3; -.
DR SMR; A5DCV3; -.
DR STRING; 4929.XP_001487729.1; -.
DR PRIDE; A5DCV3; -.
DR EnsemblFungi; EDK37008; EDK37008; PGUG_01105.
DR EnsemblFungi; EDK37010; EDK37010; PGUG_01108.
DR GeneID; 5128694; -.
DR GeneID; 5128697; -.
DR KEGG; pgu:PGUG_01105; -.
DR KEGG; pgu:PGUG_01108; -.
DR eggNOG; KOG0260; Eukaryota.
DR HOGENOM; CLU_000487_1_1_1; -.
DR InParanoid; A5DCV3; -.
DR OrthoDB; 591636at2759; -.
DR Proteomes; UP000001997; Unassembled WGS sequence.
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; 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; 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; 2.
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; 15.
DR SMART; SM00663; RPOLA_N; 1.
DR PROSITE; PS00115; RNA_POL_II_REPEAT; 21.
PE 3: Inferred from homology;
KW DNA-binding; DNA-directed RNA polymerase; Magnesium; Metal-binding;
KW Nucleotidyltransferase; Nucleus; Phosphoprotein; Reference proteome;
KW Repeat; Transcription; Transferase; Zinc.
FT CHAIN 1..1579
FT /note="DNA-directed RNA polymerase II subunit RPB1"
FT /id="PRO_0000295034"
FT REPEAT 1385..1391
FT /note="1"
FT REPEAT 1392..1398
FT /note="2"
FT REPEAT 1399..1405
FT /note="3"
FT REPEAT 1406..1412
FT /note="4"
FT REPEAT 1413..1419
FT /note="5"
FT REPEAT 1420..1426
FT /note="6"
FT REPEAT 1427..1433
FT /note="7"
FT REPEAT 1434..1440
FT /note="8"
FT REPEAT 1441..1447
FT /note="9"
FT REPEAT 1448..1454
FT /note="10"
FT REPEAT 1455..1461
FT /note="11"
FT REPEAT 1462..1468
FT /note="12"
FT REPEAT 1469..1475
FT /note="13"
FT REPEAT 1476..1482
FT /note="14"
FT REPEAT 1483..1489
FT /note="15"
FT REPEAT 1490..1496
FT /note="16"
FT REPEAT 1497..1503
FT /note="17; approximate"
FT REPEAT 1504..1510
FT /note="18"
FT REPEAT 1511..1517
FT /note="19"
FT REPEAT 1518..1524
FT /note="20"
FT REPEAT 1525..1531
FT /note="21"
FT REPEAT 1532..1538
FT /note="22"
FT REPEAT 1539..1545
FT /note="23"
FT REPEAT 1546..1552
FT /note="24"
FT REPEAT 1553..1559
FT /note="25; approximate"
FT REPEAT 1560..1566
FT /note="26; approximate"
FT REGION 642..654
FT /note="Bridging helix"
FT /evidence="ECO:0000250"
FT REGION 1382..1579
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1385..1566
FT /note="C-terminal domain (CTD); 26 X 7 AA approximate
FT tandem repeats of Y-S-P-T-S-P-[S-A-Q]"
FT COMPBIAS 1382..1568
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 171
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 485
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 485
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 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 VARIANT 198
FT /note="T -> S (in strain: MmRL 1635)"
FT /evidence="ECO:0000269|PubMed:15583292"
FT NON_CONS 566..567
FT /evidence="ECO:0000305"
SQ SEQUENCE 1579 AA; 175204 MW; 7BE0B14CC70852F8 CRC64;
MSRQFPHSSA PLRSVKEVQF GLLSPEEVRA ISVAKIEYPE TMDQATKRPR EGGLNDPRLG
SIDRNFKCQT CGEDMAECPG HFGHIELAKP VFHIGFIAKI KKVCECVCMH CGKLLLDESN
PAMAQAIRIR DPKKRFNAVW NLCKGKMICE ADVLQDDGEG NEPKRTSRGG CGHTQPVVRK
DGLKLWGTWK QNKNYDETEQ PERRLLTPSE ILNVFKHINS EDCVRLGFNE DYARPEWMLI
TVLPVPPPPV RPSIAFNDTA RGEDDLTFKL ADVIKANINV QRLELDGSPQ HVISEFEALL
QFHVATYMDN DIAGQPQALQ KTGRPIKSIR ARLKGKEGRL RGNLMGKRVD FSARTVISGD
PNLDLDQVGV PISIARTLTY PEIVTPYNIH RLTEYVRNGP NEHPGAKYVI RDTGDRIDLR
YNKRAGDIAL QYGWKVERHL MDDDPVLFNR QPSLHKMSMM CHRVKVMPYS TFRLNLSVTS
PYNADFDGDE MNLHVPQSPE TRAELSEICA VPLQIVSPQS NKPVMGIVQD TLCGVRKMTL
RDIFIEYDQV MNMLYWIPDW DGVIPPMNLK DLNNVKQMVV SGSKGSFINI SQMSACVGQQ
IVEGKRIPFG FADRSLPHFT KDDYSPESKG FVENSYLRGL TPQEFFFHAM AGREGLIDTA
VKTAETGYIQ RRLVKALEDI MVHYDGTTRN SLGDIIQFVY GEDGVDGTQV ESQSVDVIPG
TDESFERRYR VDLLDPEKCI RDSLLESGKE VRGDVNLQRV LDEEYEQLCN DRRYLREVCF
TNGDYTWPLP VNLRRIIQNA QQLFHGGRHK ASDLRLEEIV EGVKELCKKL LVLRGDSPLV
KESQENATLL FQCLVRSRLA TRRVIEEFRL NRMSFEWAMG EIETQFQKSL VHPGEMVGVI
AAQSIGEPAT QMTLNTFHYA GVSSKNVTLG VPRLKEILNV AKNIKTPALT VYLEKDIAAD
IEKAKVVQSA IEHTTLKNVT ASTEIFYDPD PRSTVLEEDY DTVEAYFAIP DEKVEESIEK
QSPWLLRLEL DRAKMLDKQL TMAQVAEKIS QNFGEDLFVI WSDDTADKLI IRCRVVRDPK
SLDEDVDAEE DQILKRIEAH MLESISLRGI QGITRVFMMQ HKLSLPDETG EFKQGQEWVL
ETDGVNLADV MAVPGVDAKR TYSNNFIEIL SVLGIEATRS ALFKEILNVI AFDGSYVNYR
HMALLVDVMT ARGHLMAITR HGINRADTGA LMRCSFEETV EILLEAGAAA ELDDCHGISE
NVVLGQLAPL GTGAFDVMVD DKILQSSPSN MSVPVGAAEG AGAYADDGGA TPYREYDMED
DKIQFEEGAG FSPIHTAPVS DGAGALTAYG GQPGSPSPTS PFAYGATSPA YGGASPGYGV
TSPTYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS
YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT
SPLYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPQYS PTSPAYSPTS PQYSPNSPQY
SPRSPLYSPD QNDDKDKKQ
