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   02-SEP-2026, entry version 183.
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   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RG   The Arabidopsis Information Resource (TAIR);
RT   "Community-consensus reference genome of Arabidopsis thaliana Col-0.";
RL   Submitted (FEB-2026) to the EMBL/GenBank/DDBJ databases.
RN   [5]
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   [6]
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   [7]
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=RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) +
CC         diphosphate; 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   EMBL; OZ408686; CAO7048178.1; -; 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   FunCoup; P38420; 4763.
DR   STRING; 3702.P38420; -.
DR   GlyGen; P38420; 1 site.
DR   iPTMnet; P38420; -.
DR   PaxDb; 3702-P38420; -.
DR   ProteomicsDB; 250565; -.
DR   GeneID; 828259; -.
DR   KEGG; ath:AT4G21710; -.
DR   Araport; AT4G21710; -.
DR   TAIR; AT4G21710; NRPB2.
DR   eggNOG; KOG0214; Eukaryota.
DR   HOGENOM; CLU_000524_5_2_1; -.
DR   InParanoid; P38420; -.
DR   OMA; CYDRNDS; -.
DR   OrthoDB; 1038491at2759; -.
DR   PhylomeDB; P38420; -.
DR   CD-CODE; 4299E36E; Nucleolus.
DR   PRO; PR:P38420; -.
DR   Proteomes; UP000006548; Chromosome 4.
DR   ExpressionAtlas; P38420; baseline and differential.
DR   GO; GO:0005634; C:nucleus; ISM:TAIR.
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 RNA polymerase activity; ISS:TAIR.
DR   GO; GO:0032549; F:ribonucleoside binding; IEA:InterPro.
DR   GO; GO:0006354; P:DNA-templated transcription elongation; IBA:GO_Central.
DR   GO; GO:0035196; P:miRNA processing; IMP:TAIR.
DR   GO; GO:0006367; P:transcription initiation at RNA polymerase II promoter; IBA:GO_Central.
DR   CDD; cd00653; RNA_pol_B_RPB2; 1.
DR   FunFam; 2.40.270.10:FF:000011; DNA-directed RNA polymerase subunit beta; 1.
DR   FunFam; 2.40.50.150:FF:000002; DNA-directed RNA polymerase subunit beta; 1.
DR   FunFam; 3.90.1070.20:FF:000001; DNA-directed RNA polymerase subunit beta; 1.
DR   FunFam; 3.90.1100.10:FF:000003; DNA-directed RNA polymerase subunit beta; 1.
DR   FunFam; 3.90.1100.10:FF:000005; DNA-directed RNA polymerase subunit beta; 1.
DR   FunFam; 3.90.1110.10:FF:000005; DNA-directed RNA polymerase subunit beta; 1.
DR   FunFam; 3.90.1800.10:FF:000002; DNA-directed RNA polymerase subunit beta; 1.
DR   Gene3D; 2.40.50.150; -; 1.
DR   Gene3D; 3.90.1100.10; -; 1.
DR   Gene3D; 2.40.270.10; DNA-directed RNA polymerase, subunit 2, domain 6; 1.
DR   Gene3D; 3.90.1800.10; RNA polymerase alpha subunit dimerisation domain; 1.
DR   Gene3D; 3.90.1110.10; RNA polymerase Rpb2, domain 2; 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   NCBIfam; NF007175; PRK09606.1; 1.
DR   PANTHER; PTHR20856; DNA-DIRECTED RNA POLYMERASE I SUBUNIT 2; 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   SUPFAM; SSF64484; beta and beta-prime subunits of DNA dependent RNA-polymerase; 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   COMPBIAS        879..892
FT                   /note="Polar residues"
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
//