(data stored in ACNUC11299 zone)

SWISSPROT: 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   07-JUN-2017, entry version 100.
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   Rhabditoidea; Rhabditidae; Peloderinae; 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.,
RA   D'Eustachio P., Fitch D.H.A., Fulton L.A., Fulton R.E.,
RA   Griffiths-Jones S., Harris T.W., Hillier L.W., Kamath R.,
RA   Kuwabara P.E., Mardis E.R., Marra M.A., Miner T.L., Minx P.,
RA   Mullikin J.C., Plumb R.W., Rogers J., Schein J.E., Sohrmann M.,
RA   Spieth J., Stajich J.E., Wei C., Willey D., Wilson R.K., Durbin R.M.,
RA   Waterston R.H.;
RT   "The genome sequence of Caenorhabditis briggsae: a platform for
RT   comparative 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
RT   ama-1 gene.";
RL   Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases.
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 (By
CC       similarity). {ECO:0000250}.
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}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAA27891.1; Type=Frameshift; Positions=29; Evidence={ECO:0000305};
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   ProteinModelPortal; P35074; -.
DR   SMR; P35074; -.
DR   STRING; 6238.CBG05355; -.
DR   PRIDE; P35074; -.
DR   EnsemblMetazoa; CBG05355; CBG05355; WBGene00027817.
DR   GeneID; 8576752; -.
DR   KEGG; cbr:CBG05355; -.
DR   CTD; 8576752; -.
DR   WormBase; CBG05355a; CBP01350; WBGene00027817; Cbr-rpb-1.
DR   eggNOG; KOG0260; Eukaryota.
DR   eggNOG; COG0086; LUCA.
DR   HOGENOM; HOG000222975; -.
DR   InParanoid; P35074; -.
DR   KO; K03006; -.
DR   OMA; MPDFDPT; -.
DR   OrthoDB; EOG091G00CH; -.
DR   Proteomes; UP000008549; Chromosome IV.
DR   Proteomes; UP000008549; Unassembled WGS sequence.
DR   GO; GO:0005665; C:DNA-directed RNA polymerase II, core complex; IBA:GO_Central.
DR   GO; GO:0035327; C:transcriptionally active chromatin; IEA:EnsemblMetazoa.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0001055; F:RNA polymerase II activity; IEA:EnsemblMetazoa.
DR   GO; GO:0009792; P:embryo development ending in birth or egg hatching; IEA:EnsemblMetazoa.
DR   GO; GO:0007369; P:gastrulation; IEA:EnsemblMetazoa.
DR   GO; GO:0042789; P:mRNA transcription from RNA polymerase II promoter; IEA:EnsemblMetazoa.
DR   GO; GO:2000543; P:positive regulation of gastrulation; IEA:EnsemblMetazoa.
DR   GO; GO:0045893; P:positive regulation of transcription, DNA-templated; IEA:EnsemblMetazoa.
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; 23.
DR   SMART; SM00663; RPOLA_N; 1.
DR   PROSITE; PS00115; RNA_POL_II_REPEAT; 26.
PE   3: Inferred from homology;
DR   PRODOM; P35074.
DR   SWISS-2DPAGE; P35074.
KW   Complete proteome; DNA-binding; DNA-directed RNA polymerase;
KW   Magnesium; Metal-binding; Nucleotidyltransferase; Nucleus;
KW   Phosphoprotein; Reference proteome; Repeat; Transcription;
KW   Transferase; Zinc.
FT   CHAIN         1   1853       DNA-directed RNA polymerase II subunit
FT                                RPB1.
FT                                /FTId=PRO_0000073934.
FT   REPEAT     1592   1598       1.
FT   REPEAT     1599   1605       2.
FT   REPEAT     1616   1622       3.
FT   REPEAT     1623   1629       4.
FT   REPEAT     1630   1636       5.
FT   REPEAT     1637   1643       6.
FT   REPEAT     1644   1650       7.
FT   REPEAT     1651   1657       8.
FT   REPEAT     1658   1664       9.
FT   REPEAT     1665   1671       10.
FT   REPEAT     1679   1685       11.
FT   REPEAT     1686   1692       12.
FT   REPEAT     1693   1699       13.
FT   REPEAT     1700   1706       14.
FT   REPEAT     1707   1713       15.
FT   REPEAT     1717   1723       16.
FT   REPEAT     1724   1730       17.
FT   REPEAT     1731   1737       18.
FT   REPEAT     1752   1758       19.
FT   REPEAT     1759   1765       20.
FT   REPEAT     1779   1785       21.
FT   REPEAT     1786   1792       22.
FT   REPEAT     1800   1806       23.
FT   REPEAT     1821   1827       24.
FT   REPEAT     1828   1834       25.
FT   REPEAT     1842   1848       26.
FT   REGION      256    268       Lid loop. {ECO:0000250}.
FT   REGION      314    331       Rudder loop. {ECO:0000250}.
FT   REGION      827    839       Bridging helix.
FT   REGION     1592   1848       C-terminal domain (CTD); 26 X 7 AA
FT                                approximate tandem repeats of Y-[ST]-P-
FT                                [ST]-S-P-[AGKNQRST].
FT   METAL        66     66       Zinc 1. {ECO:0000250}.
FT   METAL        69     69       Zinc 1. {ECO:0000250}.
FT   METAL        76     76       Zinc 1. {ECO:0000250}.
FT   METAL        79     79       Zinc 1. {ECO:0000250}.
FT   METAL       106    106       Zinc 2. {ECO:0000250}.
FT   METAL       109    109       Zinc 2. {ECO:0000250}.
FT   METAL       149    149       Zinc 2. {ECO:0000250}.
FT   METAL       177    177       Zinc 2. {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   METAL       491    491       Magnesium 2; shared with RPB2.
FT                                {ECO:0000250}.
FT   METAL       493    493       Magnesium 1; catalytic. {ECO:0000250}.
FT   CONFLICT     22     22       I -> F (in Ref. 2; AAA27891).
FT                                {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
//

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