(data stored in ACNUC11299 zone)

SWISSPROT: RPB1_SCHPO

ID   RPB1_SCHPO              Reviewed;        1752 AA.
AC   P36594;
DT   01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-1994, sequence version 1.
DT   05-JUL-2017, entry version 145.
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;
GN   Name=rpb1; ORFNames=SPBC28F2.12;
OS   Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina;
OC   Schizosaccharomycetes; Schizosaccharomycetales;
OC   Schizosaccharomycetaceae; Schizosaccharomyces.
OX   NCBI_TaxID=284812;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=972 / ATCC 24843;
RX   PubMed=2011520; DOI=10.1093/nar/19.3.461;
RA   Azuma Y., Yarnagishi M., Ueshima R., Ishihama A.;
RT   "Cloning and sequence determination of the Schizosaccharomyces pombe
RT   rpb1 gene encoding the largest subunit of RNA polymerase II.";
RL   Nucleic Acids Res. 19:461-468(1991).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=972 / ATCC 24843;
RX   PubMed=11859360; DOI=10.1038/nature724;
RA   Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A.,
RA   Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S.,
RA   Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M.,
RA   Collins M., Connor R., Cronin A., Davis P., Feltwell T., Fraser A.,
RA   Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G.,
RA   Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K.,
RA   James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J.,
RA   Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C.,
RA   Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E.,
RA   Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S.,
RA   Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K.,
RA   Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S.,
RA   Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B.,
RA   Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S.,
RA   Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D.,
RA   Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R.,
RA   Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B.,
RA   Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S.,
RA   Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M.,
RA   Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G.,
RA   Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J.,
RA   Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L.,
RA   Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J.,
RA   Shpakovski G.V., Ussery D., Barrell B.G., Nurse P.;
RT   "The genome sequence of Schizosaccharomyces pombe.";
RL   Nature 415:871-880(2002).
RN   [3]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1489; SER-1499;
RP   SER-1506; SER-1529 AND TYR-1531, AND IDENTIFICATION BY MASS
RP   SPECTROMETRY.
RX   PubMed=18257517; DOI=10.1021/pr7006335;
RA   Wilson-Grady J.T., Villen J., Gygi S.P.;
RT   "Phosphoproteome analysis of fission yeast.";
RL   J. Proteome Res. 7:1088-1097(2008).
CC   -!- FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription
CC       of DNA into RNA using the four ribonucleoside triphosphates as
CC       substrates. Largest and catalytic component of RNA polymerase II
CC       which synthesizes mRNA precursors and many functional non-coding
CC       RNAs. Forms the polymerase active center together with the second
CC       largest subunit. Pol II is the central component of the basal RNA
CC       polymerase II transcription machinery. It is composed of mobile
CC       elements that move relative to each other. RPB1 is part of the
CC       core element with the central large cleft, the clamp element that
CC       moves to open and close the cleft and the jaws that are thought to
CC       grab the incoming DNA template. At the start of transcription, a
CC       single-stranded DNA template strand of the promoter is positioned
CC       within the central active site cleft of Pol II. A bridging helix
CC       emanates from RPB1 and crosses the cleft near the catalytic site
CC       and is thought to promote translocation of Pol II by acting as a
CC       ratchet that moves the RNA-DNA hybrid through the active site by
CC       switching from straight to bent conformations at each step of
CC       nucleotide addition. During transcription elongation, Pol II moves
CC       on the template as the transcript elongates. Elongation is
CC       influenced by the phosphorylation status of the C-terminal domain
CC       (CTD) of Pol II largest subunit (RPB1), which serves as a platform
CC       for assembly of factors that regulate transcription initiation,
CC       elongation, termination and mRNA processing (By similarity).
CC       {ECO:0000250}.
CC   -!- CATALYTIC ACTIVITY: Nucleoside triphosphate + RNA(n) = diphosphate
CC       + RNA(n+1).
CC   -!- SUBUNIT: Component of the RNA polymerase II (Pol II) complex
CC       consisting of 12 subunits. {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC   -!- DOMAIN: The C-terminal domain (CTD) serves as a platform for
CC       assembly of factors that regulate transcription initiation,
CC       elongation, termination and mRNA processing. {ECO:0000305}.
CC   -!- PTM: The tandem 7 residues repeats in the C-terminal domain (CTD)
CC       can be highly phosphorylated. The phosphorylation activates Pol
CC       II. Phosphorylation occurs mainly at residues 'Ser-2' and 'Ser-5'
CC       of the heptapeptide repeat. The phosphorylation state is believed
CC       to result from the balanced action of site-specific CTD kinases
CC       and phosphatase, and a 'CTD code' that specifies the position of
CC       Pol II within the transcription cycle has been proposed.
CC       {ECO:0000269|PubMed:18257517}.
CC   -!- MISCELLANEOUS: The binding of ribonucleoside triphosphate to the
CC       RNA polymerase II transcribing complex probably involves a two-
CC       step mechanism. The initial binding seems to occur at the entry
CC       (E) site and involves a magnesium ion temporarily coordinated by
CC       three conserved aspartate residues of the two largest RNA Pol II
CC       subunits. The ribonucleoside triphosphate is transferred by a
CC       rotation to the nucleotide addition (A) site for pairing with the
CC       template DNA. The catalytic A site involves three conserved
CC       aspartate residues of the RNA Pol II largest subunit which
CC       permanently coordinate a second magnesium ion.
CC   -!- SIMILARITY: Belongs to the RNA polymerase beta' chain family.
CC       {ECO:0000305}.
DR   EMBL; X56564; CAA39916.1; -; Genomic_DNA.
DR   EMBL; CU329671; CAB57941.1; -; Genomic_DNA.
DR   PIR; S26849; S26849.
DR   RefSeq; NP_595673.1; NM_001021568.2.
DR   PDB; 3H0G; X-ray; 3.65 A; A/M=1-1752.
DR   PDB; 4PZ6; X-ray; 2.41 A; P/Q=1704-1724.
DR   PDB; 5U0S; EM; 7.80 A; a=1-1752.
DR   PDBsum; 3H0G; -.
DR   PDBsum; 4PZ6; -.
DR   PDBsum; 5U0S; -.
DR   ProteinModelPortal; P36594; -.
DR   SMR; P36594; -.
DR   BioGrid; 276823; 34.
DR   IntAct; P36594; 9.
DR   MINT; MINT-1214221; -.
DR   STRING; 4896.SPBC28F2.12.1; -.
DR   iPTMnet; P36594; -.
DR   MaxQB; P36594; -.
DR   PRIDE; P36594; -.
DR   EnsemblFungi; SPBC28F2.12.1; SPBC28F2.12.1:pep; SPBC28F2.12.
DR   GeneID; 2540292; -.
DR   KEGG; spo:SPBC28F2.12; -.
DR   EuPathDB; FungiDB:SPBC28F2.12; -.
DR   PomBase; SPBC28F2.12; rpb1.
DR   HOGENOM; HOG000222975; -.
DR   InParanoid; P36594; -.
DR   KO; K03006; -.
DR   OMA; MPDFDPT; -.
DR   OrthoDB; EOG092C01XQ; -.
DR   PhylomeDB; P36594; -.
DR   BRENDA; 2.7.7.6; 5613.
DR   Reactome; R-SPO-113418; Formation of the Early Elongation Complex.
DR   Reactome; R-SPO-5578749; Transcriptional regulation by small RNAs.
DR   Reactome; R-SPO-674695; RNA Polymerase II Pre-transcription Events.
DR   Reactome; R-SPO-6781823; Formation of TC-NER Pre-Incision Complex.
DR   Reactome; R-SPO-6782135; Dual incision in TC-NER.
DR   Reactome; R-SPO-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
DR   Reactome; R-SPO-6796648; TP53 Regulates Transcription of DNA Repair Genes.
DR   Reactome; R-SPO-72086; mRNA Capping.
DR   Reactome; R-SPO-72165; mRNA Splicing - Minor Pathway.
DR   Reactome; R-SPO-73776; RNA Polymerase II Promoter Escape.
DR   Reactome; R-SPO-73779; RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
DR   Reactome; R-SPO-75953; RNA Polymerase II Transcription Initiation.
DR   Reactome; R-SPO-76042; RNA Polymerase II Transcription Initiation And Promoter Clearance.
DR   Reactome; R-SPO-77075; RNA Pol II CTD phosphorylation and interaction with CE.
DR   EvolutionaryTrace; P36594; -.
DR   PRO; PR:P36594; -.
DR   Proteomes; UP000002485; Chromosome II.
DR   GO; GO:0005829; C:cytosol; IDA:PomBase.
DR   GO; GO:0005665; C:DNA-directed RNA polymerase II, core complex; ISO:PomBase.
DR   GO; GO:0000790; C:nuclear chromatin; IDA:PomBase.
DR   GO; GO:0005634; C:nucleus; IDA:PomBase.
DR   GO; GO:0003677; F:DNA binding; IDA:PomBase.
DR   GO; GO:0003899; F:DNA-directed 5'-3' RNA polymerase activity; IEA:UniProtKB-KW.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0006366; P:transcription from RNA polymerase II promoter; IC:PomBase.
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   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; 19.
DR   SMART; SM00663; RPOLA_N; 1.
DR   PROSITE; PS00115; RNA_POL_II_REPEAT; 24.
PE   1: Evidence at protein level;
DR   PRODOM; P36594.
DR   SWISS-2DPAGE; P36594.
KW   3D-structure; Complete proteome; DNA-binding;
KW   DNA-directed RNA polymerase; Magnesium; Metal-binding;
KW   Nucleotidyltransferase; Nucleus; Phosphoprotein; Reference proteome;
KW   Repeat; Transcription; Transferase; Zinc.
FT   CHAIN         1   1752       DNA-directed RNA polymerase II subunit
FT                                rpb1.
FT                                /FTId=PRO_0000073945.
FT   REPEAT     1558   1564       1.
FT   REPEAT     1578   1584       2.
FT   REPEAT     1585   1591       3.
FT   REPEAT     1592   1598       4.
FT   REPEAT     1599   1605       5.
FT   REPEAT     1606   1612       6; approximate.
FT   REPEAT     1613   1619       7.
FT   REPEAT     1620   1626       8.
FT   REPEAT     1627   1633       9.
FT   REPEAT     1634   1640       10.
FT   REPEAT     1641   1647       11.
FT   REPEAT     1648   1654       12.
FT   REPEAT     1655   1661       13.
FT   REPEAT     1662   1668       14.
FT   REPEAT     1669   1675       15.
FT   REPEAT     1676   1682       16.
FT   REPEAT     1683   1689       17.
FT   REPEAT     1690   1696       18.
FT   REPEAT     1697   1703       19.
FT   REPEAT     1704   1710       20.
FT   REPEAT     1711   1717       21.
FT   REPEAT     1718   1724       22.
FT   REPEAT     1725   1731       23.
FT   REPEAT     1732   1738       24.
FT   REPEAT     1739   1745       25.
FT   REPEAT     1746   1752       26.
FT   REGION      816    828       Bridging helix.
FT   REGION     1558   1752       C-terminal domain (CTD); 26 X 7 AA
FT                                approximate tandem repeats of Y-S-P-[TS]-
FT                                S-P-S.
FT   METAL        69     69       Zinc 1. {ECO:0000250}.
FT   METAL        72     72       Zinc 1. {ECO:0000250}.
FT   METAL        79     79       Zinc 1. {ECO:0000250}.
FT   METAL        82     82       Zinc 1. {ECO:0000250}.
FT   METAL       109    109       Zinc 2. {ECO:0000250}.
FT   METAL       112    112       Zinc 2. {ECO:0000250}.
FT   METAL       150    150       Zinc 2. {ECO:0000250}.
FT   METAL       175    175       Zinc 2. {ECO:0000250}.
FT   METAL       487    487       Magnesium 1; catalytic. {ECO:0000250}.
FT   METAL       487    487       Magnesium 2; shared with RPB2.
FT                                {ECO:0000250}.
FT   METAL       489    489       Magnesium 1; catalytic. {ECO:0000250}.
FT   METAL       489    489       Magnesium 2; shared with RPB2.
FT                                {ECO:0000250}.
FT   METAL       491    491       Magnesium 1; catalytic. {ECO:0000250}.
FT   MOD_RES    1489   1489       Phosphoserine.
FT                                {ECO:0000269|PubMed:18257517}.
FT   MOD_RES    1499   1499       Phosphoserine.
FT                                {ECO:0000269|PubMed:18257517}.
FT   MOD_RES    1506   1506       Phosphoserine.
FT                                {ECO:0000269|PubMed:18257517}.
FT   MOD_RES    1529   1529       Phosphoserine.
FT                                {ECO:0000269|PubMed:18257517}.
FT   MOD_RES    1531   1531       Phosphotyrosine.
FT                                {ECO:0000269|PubMed:18257517}.
SQ   SEQUENCE   1752 AA;  194163 MW;  15A4F0B59E60E570 CRC64;
     MSGIQFSPSS VPLRRVEEVQ FGILSPEEIR SMSVAKIEFP ETMDESGQRP RVGGLLDPRL
     GTIDRQFKCQ TCGETMADCP GHFGHIELAK PVFHIGFLSK IKKILECVCW NCGKLKIDSS
     NPKFNDTQRY RDPKNRLNAV WNVCKTKMVC DTGLSAGSDN FDLSNPSANM GHGGCGAAQP
     TIRKDGLRLW GSWKRGKDES DLPEKRLLSP LEVHTIFTHI SSEDLAHLGL NEQYARPDWM
     IITVLPVPPP SVRPSISVDG TSRGEDDLTH KLSDIIKANA NVRRCEQEGA PAHIVSEYEQ
     LLQFHVATYM DNEIAGQPQA LQKSGRPLKS IRARLKGKEG RLRGNLMGKR VDFSARTVIT
     GDPNLSLDEL GVPRSIAKTL TYPETVTPYN IYQLQELVRN GPDEHPGAKY IIRDTGERID
     LRYHKRAGDI PLRYGWRVER HIRDGDVVIF NRQPSLHKMS MMGHRIRVMP YSTFRLNLSV
     TSPYNADFDG DEMNMHVPQS EETRAEIQEI TMVPKQIVSP QSNKPVMGIV QDTLAGVRKF
     SLRDNFLTRN AVMNIMLWVP DWDGILPPPV ILKPKVLWTG KQILSLIIPK GINLIRDDDK
     QSLSNPTDSG MLIENGEIIY GVVDKKTVGA SQGGLVHTIW KEKGPEICKG FFNGIQRVVN
     YWLLHNGFSI GIGDTIADAD TMKEVTRTVK EARRQVAECI QDAQHNRLKP EPGMTLRESF
     EAKVSRILNQ ARDNAGRSAE HSLKDSNNVK QMVAAGSKGS FINISQMSAC VGQQIVEGKR
     IPFGFKYRTL PHFPKDDDSP ESRGFIENSY LRGLTPQEFF FHAMAGREGL IDTAVKTAET
     GYIQRRLVKA MEDVMVRYDG TVRNAMGDII QFAYGEDGLD ATLVEYQVFD SLRLSTKQFE
     KKYRIDLMED RSLSLYMENS IENDSSVQDL LDEEYTQLVA DRELLCKFIF PKGDARWPLP
     VNVQRIIQNA LQIFHLEAKK PTDLLPSDII NGLNELIAKL TIFRGSDRIT RDVQNNATLL
     FQILLRSKFA VKRVIMEYRL NKVAFEWIMG EVEARFQQAV VSPGEMVGTL AAQSIGEPAT
     QMTLNTFHYA GVSSKNVTLG VPRLKEILNV AKNIKTPSLT IYLMPWIAAN MDLAKNVQTQ
     IEHTTLSTVT SATEIHYDPD PQDTVIEEDK DFVEAFFAIP DEEVEENLYK QSPWLLRLEL
     DRAKMLDKKL SMSDVAGKIA ESFERDLFTI WSEDNADKLI IRCRIIRDDD RKAEDDDNMI
     EEDVFLKTIE GHMLESISLR GVPNITRVYM MEHKIVRQIE DGTFERADEW VLETDGINLT
     EAMTVEGVDA TRTYSNSFVE ILQILGIEAT RSALLKELRN VIEFDGSYVN YRHLALLCDV
     MTSRGHLMAI TRHGINRAET GALMRCSFEE TVEILMDAAA SGEKDDCKGI SENIMLGQLA
     PMGTGAFDIY LDQDMLMNYS LGTAVPTLAG SGMGTSQLPE GAGTPYERSP MVDSGFVGSP
     DAAAFSPLVQ GGSEGREGFG DYGLLGAASP YKGVQSPGYT SPFSSAMSPG YGLTSPSYSP
     SSPGYSTSPA YMPSSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPSYSATS PSYSPTSPSY
     SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS
     PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS
     PTSPSYSPTS PS
//

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