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 03-AUG-2022, entry version 166.
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; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; 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., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., 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., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
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 of
RT 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., Ito Y.,
RA Pikaard C.S.;
RT "Sex-biased lethality or transmission of defective transcription machinery
RT in Arabidopsis.";
RL Genetics 180:207-218(2008).
RN [6]
RP FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, SUBUNIT, AND 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., Zhu J.K.,
RA Hagen G., Guilfoyle T.J., Pasa-Tolic L., Pikaard C.S.;
RT "Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal
RT 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 of
CC DNA into RNA using the four ribonucleoside triphosphates as substrates.
CC Second largest component of RNA polymerase II which synthesizes mRNA
CC precursors and many functional non-coding RNAs. Proposed to contribute
CC to the polymerase catalytic activity and forms the polymerase active
CC center together with the largest subunit. Pol II is the central
CC component of the basal RNA polymerase II transcription machinery. It is
CC composed of mobile elements that move relative to each other. NRPB2 is
CC part of the core element with the central large cleft, the clamp
CC element that moves to open and close the cleft and the jaws that are
CC thought to grab the incoming DNA template (By similarity).
CC {ECO:0000250}.
CC -!- FUNCTION: Essential for the completion of the three rounds of mitosis
CC in female megaspores required for the development of mature
CC gametophytes (PubMed:18723889). {ECO:0000269|PubMed:18723889}.
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 complex consisting of at
CC 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 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 coordinated by three conserved aspartate
CC residues of the two largest RNA Pol II subunits (By similarity).
CC {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 AlphaFoldDB; P38420; -.
DR SMR; P38420; -.
DR BioGRID; 13548; 37.
DR STRING; 3702.AT4G21710.1; -.
DR iPTMnet; P38420; -.
DR PaxDb; P38420; -.
DR PRIDE; P38420; -.
DR ProteomicsDB; 250565; -.
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 HOGENOM; CLU_000524_5_2_1; -.
DR InParanoid; P38420; -.
DR OMA; RDLHGTH; -.
DR OrthoDB; 42570at2759; -.
DR PhylomeDB; P38420; -.
DR PRO; PR:P38420; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; P38420; baseline and differential.
DR Genevisible; P38420; AT.
DR GO; GO:0009506; C:plasmodesma; HDA:TAIR.
DR GO; GO:0005665; C:RNA polymerase II, core complex; IDA:UniProtKB.
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:0035196; P:miRNA processing; IMP:TAIR.
DR GO; GO:0006351; P:transcription, DNA-templated; IEA:InterPro.
DR CDD; cd00653; RNA_pol_B_RPB2; 1.
DR Gene3D; 2.40.270.10; -; 1.
DR Gene3D; 2.40.50.150; -; 1.
DR Gene3D; 3.90.1110.10; -; 1.
DR InterPro; IPR015712; DNA-dir_RNA_pol_su2.
DR InterPro; IPR007120; DNA-dir_RNAP_su2_dom.
DR InterPro; IPR037033; DNA-dir_RNAP_su2_hyb_sf.
DR InterPro; IPR007121; RNA_pol_bsu_CS.
DR InterPro; IPR007644; RNA_pol_bsu_protrusion.
DR InterPro; IPR007642; RNA_pol_Rpb2_2.
DR InterPro; IPR037034; RNA_pol_Rpb2_2_sf.
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 InterPro; IPR014724; RNA_pol_RPB2_OB-fold.
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 DNA-directed RNA polymerase; Magnesium; Metal-binding;
KW Nucleotidyltransferase; Nucleus; Reference proteome; Transcription;
KW Transferase; Zinc; Zinc-finger.
FT CHAIN 1..1188
FT /note="DNA-directed RNA polymerase II subunit 2"
FT /id="PRO_0000048081"
FT ZN_FING 1124..1145
FT /note="C4-type"
FT REGION 852..871
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 877..897
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 800
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="ligand shared with RPB1"
FT /evidence="ECO:0000250"
FT BINDING 1124
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 1127
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 1142
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 1145
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT VARIANT 787
FT /note="I -> N"
FT CONFLICT 354..355
FT /note="PH -> LY (in Ref. 1; CAA79527/CAA79528)"
FT /evidence="ECO:0000305"
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
