(data stored in ACNUC11299 zone)

HOGENOM: CAEELIV_PE952

ID   CAEELIV_PE952                        STANDARD;      PRT;   1852 AA.
AC   CAEELIV_PE952; P16356; Q20090;
DT   00-JAN-0000 (Rel. 1, Created)
DT   00-JAN-0000 (Rel. 2, Last sequence update)
DT   00-JAN-0000 (Rel. 3, Last annotation update)
DE   RecName: Full=DNA-directed RNA polymerase II subunit RPB1; Short=RNA
DE   polymerase II subunit B1; EC=2.7.7 6;AltName: Full=DNA-directed RNA
DE   polymerase III largest subunit; (CAEELIV.PE952).
GN   Name=ama-1; Synonyms=rpb-1; ORFNames=F36A4.7;
OS   CAENORHABDITIS ELEGANS.
OC   Eukaryota; Metazoa; Eumetazoa; Bilateria; Pseudocoelomata; Nematoda;
OC   Chromadorea; Rhabditida; Rhabditoidea; Rhabditidae; Peloderinae;
OC   Caenorhabditis.
OX   NCBI_TaxID=6239;
RN   [0]
RP   -.;
RG   -.;
RL   -.;
CC   -!- SEQ. DATA ORIGIN: Translated from the HOGENOM CDS CAEELIV.PE952.
CC       Caenorhabditis elegans chromosome IV WS210  sequence 1..17493784
CC       annotated by Ensembl
CC   -!- ANNOTATIONS ORIGIN:RPB1_CAEEL
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   -!- 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 (By similarity).
CC   -!- INTERACTION:
CC       Q9N337:mdt-6; NbExp=2; IntAct=EBI-1533906, EBI-1533827;
CC   -!- SUBCELLULAR LOCATION: Nucleus (By similarity).
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 heptapepdtide repeat. The phosphorylation state is believed
CC       to result from the balanced action of site-specific CTD kinases
CC       and phosphataes, and a "CTD code" that specifies the position of
CC       Pol II within the transcription cycle has been proposed.
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 nucelotide 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   -!- GENE_FAMILY: HOG000222975 [ FAMILY / ALN / TREE ]
DR   HOGENOM:Caenorhabditis_elegans;F36A4.7;F36A4.7;F36A4.7.
DR   EMBL; M29235; - ;
DR   EMBL; U53333; - ;
DR   UniProtKB/Swiss-Prot; P16356; Q20090; -.
DR   EMBL; M29235; AAA28126.1; -; mRNA.
DR   EMBL; U53333; AAA96158.2; -; Genomic_DNA.
DR   PIR; A34092; A34092.
DR   PIR; T29959; T29959.
DR   RefSeq; NP_500523.3; NM_068122.5.
DR   UniGene; Cel.13014; -.
DR   ProteinModelPortal; P16356; -.
DR   SMR; P16356; 13-895, 1035-1465.
DR   IntAct; P16356; 4.
DR   STRING; P16356; -.
DR   EnsemblMetazoa; F36A4.7.1; F36A4.7.1; F36A4.7.
DR   EnsemblMetazoa; F36A4.7.2; F36A4.7.2; F36A4.7.
DR   GeneID; 177190; -.
DR   KEGG; cel:F36A4.7; -.
DR   NMPDR; fig|6239.3.peg.13066; -.
DR   UCSC; F36A4.7; c. elegans.
DR   CTD; 247749; -.
DR   WormBase; F36A4.7; CE28300; WBGene00000123; ama-1.
DR   eggNOG; meNOG04682; -.
DR   GeneTree; EMGT00050000000220; -.
DR   InParanoid; P16356; -.
DR   OMA; SPTSPHY; -.
DR   PhylomeDB; P16356; -.
DR   NextBio; 895720; -.
DR   ArrayExpress; P16356; -.
DR   GO; GO:0005665; C:DNA-directed RNA polymerase II, core complex; IEA:InterPro.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0003899; F:DNA-directed RNA polymerase activity; IEA:UniProtKB-KW.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0005515; F:protein binding; IPI:IntAct.
DR   GO; GO:0008356; P:asymmetric cell division; IMP:WormBase.
DR   GO; GO:0009792; P:embryo development ending in birth or egg hatching; IMP:WormBase.
DR   GO; GO:0010458; P:exit from mitosis; IMP:WormBase.
DR   GO; GO:0007369; P:gastrulation; IMP:WormBase.
DR   GO; GO:0007052; P:mitotic spindle organization; IMP:WormBase.
DR   GO; GO:0040010; P:positive regulation of growth rate; IMP:WormBase.
DR   GO; GO:0000003; P:reproduction; IMP:WormBase.
DR   GO; GO:0006366; P:transcription from RNA polymerase II promoter; IEA:InterPro.
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; 28.
DR   SMART; SM00663; RPOLA_N; 1.
DR   PROSITE; PS00115; RNA_POL_II_REPEAT; 26.
DR   HOGENOMDNA; CAEELIV.PE952; -.
KW   F36A4.711610200367fold_1320000031; F36A4.712141210.62fold_1320000031;
KW   M29235; U53333;
KW   Complete proteome; DNA-binding; DNA-directed RNA polymerase;
KW   Magnesium; Metal-binding; Nucleotidyltransferase; Nucleus;
KW   Phosphoprotein; Reference proteome; Repeat; Transcription;
KW   Transferase; Zinc.
SQ   SEQUENCE   1852 AA;  UNKNOWN MW;  UNKNOWN CRC64;
     MALVGVDFQA PLRIVSRVQF GILGPEEIKR MSVAHVEFPE VYENGKPKLG GLMDPRQGVI
     DRRGRCMTCA GNLTDCPGHF GHLELAKPVF HIGFLTKTLK ILRCVCFYCG RLLIDKSAPR
     VLEILKKTGT NSKKRLTMIY DLCKAKSVCE GAAEKEEGMP DDPDDPMNDG KKVAGGCGRY
     QPSYRRVGID INAEWKKNVN EDTQERKIML TAERVLEVFQ QITDEDILVI GMDPQFARPE
     WMICTVLPVP PLAVRPAVVT FGSAKNQDDL THKLSDIIKT NQQLQRNEAN GAAAHVLTDD
     VRLLQFHVAT LVDNCIPGLP TATQKGGRPL KSIKQRLKGK EGRIRGNLMG KRVDFSARTV
     ITADPNLPID TVGVPRTIAQ NLTFPEIVTP FNVDKLQELV NRGDTQYPGA KENGARVDLR
     YHPRAADLHL QPGYRVERHM KDGDIIVFNR QPTLHKMSMM GHRVKILPWS TFRMNLSVTS
     PYNADFDGDE MNLHLPQSLE TRAEIEEIAM VPRQLITPQA NKPVMGIVQD TLCAVRMMTK
     RDVFIDWPFM MDLLMYLPTW DGKVPQPAIL KPKPLWTGKQ VFSLIIPGNV NVLRTHSTHP
     DSEDSGPYKW ISPGDTKVII EHGELLSGIV CSKTVGKSAG NLLHVVTLEL GYEIAANFYS
     HIQTVINAWL IREGHTIGIG DTIADQATYL DIQNTIRKAK QDVVDVIEKA HNDDLEPTPG
     NTLRQTFENK VNQILNDARD RTGSSAQKSL SEFNNFKSMV VSGSKGSKIN ISQVIACVGQ
     QNVEGKRIPF GFRHRTLPHF IKDDYGPESK GFVENSYLAG LTPSEFFFHA MGGREGLIDT
     AVKTAETGYI QRRLIKAMES VMVNYDGTVR NSLAQMVQLR YGEDGLDGMW VENQNMPTMK
     PNNAVFERDF RMDLTDNKFL RKNYSEDVVR EIQESEDGIS LVESEWSQLE EDRRLLRKIF
     PRGDAKIVLP CNLQRLIWNA QKIFKVDLRK PVNLSPLHVI SGVRELSKKL IIVSGNDEIS
     KQAQYNATLL MNILLRSTLC TKNMCTKSKL NSEAFDWLLG EIESRFQQAI AQPGEMVGAL
     AAQSLGEPAT QMTLNTFHYA GVSAKNVTLG VPRLKEIINV SKTLKTPSLT VFLTGAAAKD
     PEKAKDVLCK LEHTTLKKVT CNTAIYYDPD PKNTVIAEDE EWVSIFYEMP DHDLSRTSPW
     LLRIELDRKR MVDKKLTMEM IADRIHGGFG NDVHTIYTDD NAEKLVFRLR IAGEDKGEAQ
     EEQVDKMEDD VFLRCIEANM LSDLTLQGIP AISKVYMNQP NTDDKKRIII TPEGGFKSVA
     DWILETDGTA LLRVLSERQI DPVRTTSNDI CEIFEVLGIE AVRKAIEREM DNVISFDGSY
     VNYRHLALLC DVMTAKGHLM AITRHGINRQ EVGALMRCSF EETVDILMEA AVHAEEDPVK
     GVSENIMLGQ LARCGTGCFD LVLDVEKCKY GMEIPQNVVM GGGFYGSFAG SPSNREFSPA
     HSPWNSGVTP TYAGAAWSPT TGGMSPGAGF SPAGNTDGGA SPFNEGGWSP ASPGDPLGAL
     SPRTPSYGGM SPGVYSPSSP QFSMTSPHYS PTSPSYSPTS PAAGQSPVSP SYSPTSPSYS
     PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPSSPS YSPSSPSYSP SSPRYSPTSP
     TYSPTSPTYS PTSPTYSPTS PTYSPTSPSY ESGGGYSPSS PKYSPSSPTY SPTSPSYSPT
     SPQYSPTSPQ YSPSSPTYTP SSPTYNPTSP RGFSSPQYSP TSPTYSPTSP SYTPSSPQYS
     PTSPTYTPSP SEQPGTSAQY SPTSPTYSPS SPTYSPASPS YSPSSPTYDP NS
//

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