Entry euk:NRPB2_ARATH

ID   NRPB2_ARATH             Reviewed;        1188 AA.
AC   P38420; Q9SVS6;
DT   01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT   20-JUN-2002, sequence version 2.
DT   12-APR-2017, entry version 139.
DE   RecName: Full=DNA-directed RNA polymerase II subunit 2;
DE   AltName: Full=DNA-directed RNA polymerase II 135 kDa polypeptide;
DE   AltName: Full=DNA-directed RNA polymerase II subunit RPB2;
DE            Short=RNA polymerase II subunit 2;
DE            Short=RNA polymerase II subunit B2;
DE            EC=2.7.7.6;
DE   AltName: Full=Protein EMBRYO DEFECTIVE 1989;
GN   Name=NRPB2; Synonyms=EMB1989, RP140, RPB135, RPB2;
GN   OrderedLocusNames=At4g21710; ORFNames=F17L22.170;
OS   Arabidopsis thaliana (Mouse-ear cress).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
OC   Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
OC   Arabidopsis.
OX   NCBI_TaxID=3702;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=8451172; DOI=10.1093/nar/21.4.1038;
RA   Larkin R., Guilfoyle T.J.;
RT   "The second largest subunit of RNA polymerase II from Arabidopsis
RT   thaliana.";
RL   Nucleic Acids Res. 21:1038-1038(1993).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=10617198; DOI=10.1038/47134;
RA   Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G.,
RA   Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N.,
RA   Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M.,
RA   Weichselgartner M., de Simone V., Obermaier B., Mache R., Mueller M.,
RA   Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T.,
RA   Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I.,
RA   Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P.,
RA   Langham S.-A., McCullagh B., Bilham L., Robben J.,
RA   van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F.,
RA   Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E.,
RA   Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA   Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W.,
RA   Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P.,
RA   Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H.,
RA   De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R.,
RA   van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S.,
RA   Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R.,
RA   Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S.,
RA   Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H.,
RA   Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S.,
RA   Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A.,
RA   Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA   Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R.,
RA   Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S.,
RA   Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E.,
RA   Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A.,
RA   Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T.,
RA   Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C.,
RA   Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S.,
RA   Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K.,
RA   Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L.,
RA   Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J.,
RA   Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J.,
RA   Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D.,
RA   Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA   Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA   Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D.,
RA   Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C.,
RA   Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C.,
RA   Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R.,
RA   Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S.,
RA   Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A.,
RA   Chen E., Marra M.A., Martienssen R., McCombie W.R.;
RT   "Sequence and analysis of chromosome 4 of the plant Arabidopsis
RT   thaliana.";
RL   Nature 402:769-777(1999).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RG   The Arabidopsis Information Portal (Araport);
RL   Submitted (MAY-2016) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   STRAIN=cv. Landsberg erecta;
RX   PubMed=17272265; DOI=10.1074/mcp.M600408-MCP200;
RA   Maor R., Jones A., Nuehse T.S., Studholme D.J., Peck S.C., Shirasu K.;
RT   "Multidimensional protein identification technology (MudPIT) analysis
RT   of ubiquitinated proteins in plants.";
RL   Mol. Cell. Proteomics 6:601-610(2007).
RN   [5]
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RX   PubMed=18723889; DOI=10.1534/genetics.108.090621;
RA   Onodera Y., Nakagawa K., Haag J.R., Pikaard D., Mikami T., Ream T.,
RA   Ito Y., Pikaard C.S.;
RT   "Sex-biased lethality or transmission of defective transcription
RT   machinery in Arabidopsis.";
RL   Genetics 180:207-218(2008).
RN   [6]
RP   FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, SUBUNIT, AND
RP   NOMENCLATURE.
RX   PubMed=19110459; DOI=10.1016/j.molcel.2008.12.015;
RA   Ream T.S., Haag J.R., Wierzbicki A.T., Nicora C.D., Norbeck A.D.,
RA   Zhu J.K., Hagen G., Guilfoyle T.J., Pasa-Tolic L., Pikaard C.S.;
RT   "Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V
RT   reveal their origins as specialized forms of RNA polymerase II.";
RL   Mol. Cell 33:192-203(2009).
CC   -!- FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription
CC       of DNA into RNA using the four ribonucleoside triphosphates as
CC       substrates. Second largest component of RNA polymerase II which
CC       synthesizes mRNA precursors and many functional non-coding RNAs.
CC       Proposed to contribute to the polymerase catalytic activity and
CC       forms the polymerase active center together with the largest
CC       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. NRPB2 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 (By similarity). {ECO:0000250}.
CC   -!- FUNCTION: Essential for the completion of the three rounds of
CC       mitosis in female megaspores required for the development of
CC       mature gametophytes (PubMed:18723889).
CC       {ECO:0000269|PubMed:18723889}.
CC   -!- CATALYTIC ACTIVITY: Nucleoside triphosphate + RNA(n) = diphosphate
CC       + RNA(n+1).
CC   -!- SUBUNIT: Component of the RNA polymerase II complex consisting of
CC       at least 12 subunits. {ECO:0000269|PubMed:19110459}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC   -!- DISRUPTION PHENOTYPE: Defect in seed production due to female
CC       gametophyte developmental arrest. {ECO:0000269|PubMed:18723889}.
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 coordinated by three
CC       conserved aspartate residues of the two largest RNA Pol II
CC       subunits (By similarity). {ECO:0000250}.
CC   -!- SIMILARITY: Belongs to the RNA polymerase beta chain family.
CC       {ECO:0000305}.
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DR   EMBL; Z19120; CAA79527.1; -; mRNA.
DR   EMBL; Z19121; CAA79528.1; -; Genomic_DNA.
DR   EMBL; AL035527; CAB36815.1; -; Genomic_DNA.
DR   EMBL; AL161555; CAB81278.1; -; Genomic_DNA.
DR   EMBL; CP002687; AEE84493.1; -; Genomic_DNA.
DR   PIR; T05846; T05846.
DR   RefSeq; NP_193902.1; NM_118291.4.
DR   UniGene; At.112; -.
DR   ProteinModelPortal; P38420; -.
DR   SMR; P38420; -.
DR   BioGrid; 13548; 4.
DR   STRING; 3702.AT4G21710.1; -.
DR   iPTMnet; P38420; -.
DR   PaxDb; P38420; -.
DR   PRIDE; P38420; -.
DR   EnsemblPlants; AT4G21710.1; AT4G21710.1; AT4G21710.
DR   GeneID; 828259; -.
DR   Gramene; AT4G21710.1; AT4G21710.1; AT4G21710.
DR   KEGG; ath:AT4G21710; -.
DR   Araport; AT4G21710; -.
DR   TAIR; locus:2119013; AT4G21710.
DR   eggNOG; KOG0214; Eukaryota.
DR   eggNOG; COG0085; LUCA.
DR   HOGENOM; HOG000218612; -.
DR   InParanoid; P38420; -.
DR   KO; K03010; -.
DR   OMA; RTQPHFE; -.
DR   OrthoDB; EOG093600IR; -.
DR   PhylomeDB; P38420; -.
DR   Reactome; R-ATH-113418; Formation of the Early Elongation Complex.
DR   Reactome; R-ATH-5578749; Transcriptional regulation by small RNAs.
DR   Reactome; R-ATH-674695; RNA Polymerase II Pre-transcription Events.
DR   Reactome; R-ATH-6781823; Formation of TC-NER Pre-Incision Complex.
DR   Reactome; R-ATH-6782135; Dual incision in TC-NER.
DR   Reactome; R-ATH-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
DR   Reactome; R-ATH-6796648; TP53 Regulates Transcription of DNA Repair Genes.
DR   Reactome; R-ATH-72086; mRNA Capping.
DR   Reactome; R-ATH-72163; mRNA Splicing - Major Pathway.
DR   Reactome; R-ATH-72165; mRNA Splicing - Minor Pathway.
DR   Reactome; R-ATH-72203; Processing of Capped Intron-Containing Pre-mRNA.
DR   Reactome; R-ATH-73776; RNA Polymerase II Promoter Escape.
DR   Reactome; R-ATH-73779; RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
DR   Reactome; R-ATH-75953; RNA Polymerase II Transcription Initiation.
DR   Reactome; R-ATH-76042; RNA Polymerase II Transcription Initiation And Promoter Clearance.
DR   Reactome; R-ATH-77075; RNA Pol II CTD phosphorylation and interaction with CE.
DR   PRO; PR:P38420; -.
DR   Proteomes; UP000006548; Chromosome 4.
DR   ExpressionAtlas; P38420; baseline and differential.
DR   Genevisible; P38420; AT.
DR   GO; GO:0005829; C:cytosol; IDA:TAIR.
DR   GO; GO:0005665; C:DNA-directed RNA polymerase II, core complex; IDA:UniProtKB.
DR   GO; GO:0016591; C:DNA-directed RNA polymerase II, holoenzyme; ISS:TAIR.
DR   GO; GO:0009506; C:plasmodesma; IDA:TAIR.
DR   GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR   GO; GO:0003899; F:DNA-directed 5'-3' RNA polymerase activity; ISS:TAIR.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0032549; F:ribonucleoside binding; IEA:InterPro.
DR   GO; GO:0006366; P:transcription from RNA polymerase II promoter; IEA:GOC.
DR   CDD; cd00653; RNA_pol_B_RPB2; 1.
DR   Gene3D; 2.40.270.10; -; 2.
DR   Gene3D; 3.90.1110.10; -; 1.
DR   InterPro; IPR015712; DNA-dir_RNA_pol_su2.
DR   InterPro; IPR007120; DNA-dir_RNA_pol_su2_6.
DR   InterPro; IPR007121; RNA_pol_bsu_CS.
DR   InterPro; IPR007644; RNA_pol_bsu_protrusion.
DR   InterPro; IPR007642; RNA_pol_Rpb2_2.
DR   InterPro; IPR007645; RNA_pol_Rpb2_3.
DR   InterPro; IPR007646; RNA_pol_Rpb2_4.
DR   InterPro; IPR007647; RNA_pol_Rpb2_5.
DR   InterPro; IPR007641; RNA_pol_Rpb2_7.
DR   PANTHER; PTHR20856; PTHR20856; 1.
DR   Pfam; PF04563; RNA_pol_Rpb2_1; 1.
DR   Pfam; PF04561; RNA_pol_Rpb2_2; 1.
DR   Pfam; PF04565; RNA_pol_Rpb2_3; 1.
DR   Pfam; PF04566; RNA_pol_Rpb2_4; 1.
DR   Pfam; PF04567; RNA_pol_Rpb2_5; 1.
DR   Pfam; PF00562; RNA_pol_Rpb2_6; 1.
DR   Pfam; PF04560; RNA_pol_Rpb2_7; 1.
DR   PROSITE; PS01166; RNA_POL_BETA; 1.
PE   1: Evidence at protein level;
KW   Complete proteome; DNA-directed RNA polymerase; Magnesium;
KW   Metal-binding; Nucleotidyltransferase; Nucleus; Reference proteome;
KW   Transcription; Transferase; Zinc; Zinc-finger.
FT   CHAIN         1   1188       DNA-directed RNA polymerase II subunit 2.
FT                                /FTId=PRO_0000048081.
FT   ZN_FING    1124   1145       C4-type.
FT   COMPBIAS     14     20       Asp/Glu-rich (acidic).
FT   METAL       800    800       Magnesium; shared with RPB1.
FT                                {ECO:0000250}.
FT   METAL      1124   1124       Zinc. {ECO:0000250}.
FT   METAL      1127   1127       Zinc. {ECO:0000250}.
FT   METAL      1142   1142       Zinc. {ECO:0000250}.
FT   METAL      1145   1145       Zinc. {ECO:0000250}.
FT   VARIANT     787    787       I -> N.
FT   CONFLICT    354    355       PH -> LY (in Ref. 1; CAA79527/CAA79528).
FT                                {ECO:0000305}.
CC   --------------------------------------------------------------------------
CC   The following FT lines are automated annotations from the MyHits database.
CC   --------------------------------------------------------------------------
FT   MYHIT       657    708       ipfam:RNA_pol_Rpb2_5 [T]
FT   MYHIT       472    536       ipfam:RNA_pol_Rpb2_3 [T]
FT   MYHIT        38    447       ipfam:RNA_pol_Rpb2_1 [T]
FT   MYHIT       715   1085       ipfam:RNA_pol_Rpb2_6 [T]
FT   MYHIT       938    950       ipat:RNA_POL_BETA [T]
FT   MYHIT       571    632       ipfam:RNA_pol_Rpb2_4 [T]
FT   MYHIT      1087   1178       ipfam:RNA_pol_Rpb2_7 [T]
FT   MYHIT       208    399       ipfam:RNA_pol_Rpb2_2 [T]
SQ   SEQUENCE   1188 AA;  135019 MW;  C304E43515C2C364 CRC64;
     MEYNEYEPEP QYVEDDDDEE ITQEDAWAVI SAYFEEKGLV RQQLDSFDEF IQNTMQEIVD
     ESADIEIRPE SQHNPGHQSD FAETIYKISF GQIYLSKPMM TESDGETATL FPKAARLRNL
     TYSAPLYVDV TKRVIKKGHD GEEVTETQDF TKVFIGKVPI MLRSSYCTLF QNSEKDLTEL
     GECPYDQGGY FIINGSEKVL IAQEKMSTNH VYVFKKRQPN KYAYVGEVRS MAENQNRPPS
     TMFVRMLARA SAKGGSSGQY IRCTLPYIRT EIPIIIVFRA LGFVADKDIL EHICYDFADT
     QMMELLRPSL EEAFVIQNQL VALDYIGKRG ATVGVTKEKR IKYARDILQK EMLPHVGIGE
     HCETKKAYYF GYIIHRLLLC ALGRRPEDDR DHYGNKRLDL AGPLLGGLFR MLFRKLTRDV
     RSYVQKCVDN GKEVNLQFAI KAKTITSGLK YSLATGNWGQ ANAAGTRAGV SQVLNRLTYA
     STLSHLRRLN SPIGREGKLA KPRQLHNSQW GMMCPAETPE GQACGLVKNL ALMVYITVGS
     AAYPILEFLE EWGTENFEEI SPSVIPQATK IFVNGMWVGV HRDPDMLVKT LRRLRRRVDV
     NTEVGVVRDI RLKELRIYTD YGRCSRPLFI VDNQKLLIKK RDIYALQQRE SAEEDGWHHL
     VAKGFIEYID TEEEETTMIS MTISDLVQAR LRPEEAYTEN YTHCEIHPSL ILGVCASIIP
     FPDHNQSPRN TYQSAMGKQA MGIYVTNYQF RMDTLAYVLY YPQKPLVTTR AMEHLHFRQL
     PAGINAIVAI SCYSGYNQED SVIMNQSSID RGFFRSLFFR SYRDEEKKMG TLVKEDFGRP
     DRGSTMGMRH GSYDKLDDDG LAPPGTRVSG EDVIIGKTTP ISQDEAQGQS SRYTRRDHSI
     SLRHSETGMV DQVLLTTNAD GLRFVKVRVR SVRIPQIGDK FSSRHGQKGT VGMTYTQEDM
     PWTIEGVTPD IIVNPHAIPS RMTIGQLIEC IMGKVAAHMG KEGDATPFTD VTVDNISKAL
     HKCGYQMRGF ERMYNGHTGR PLTAMIFLGP TYYQRLKHMV DDKIHSRGRG PVQILTRQPA
     EGRSRDGGLR FGEMERDCMI AHGAAHFLKE RLFDQSDAYR VHVCEVCGLI AIANLKKNSF
     ECRGCKNKTD IVQVYIPYAC KLLFQELMSM AIAPRMLTKH LKSAKGRQ
//