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DNA-directed RNA polymerase II subunit 2 (DNA-directed RNA polymerase II 135 kDa polypeptide) (DNA-directed RNA polymerase II subunit RPB2) (RNA polymerase II subunit 2) (RNA polymerase II subunit B2) (EC 2.7.7.6) (Protein EMBRYO DEFECTIVE 1989)

 NRPB2_ARATH             Reviewed;        1188 AA.
P38420; Q9SVS6;
01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
20-JUN-2002, sequence version 2.
05-DEC-2018, entry version 150.
RecName: Full=DNA-directed RNA polymerase II subunit 2;
AltName: Full=DNA-directed RNA polymerase II 135 kDa polypeptide;
AltName: Full=DNA-directed RNA polymerase II subunit RPB2;
Short=RNA polymerase II subunit 2;
Short=RNA polymerase II subunit B2;
EC=2.7.7.6;
AltName: Full=Protein EMBRYO DEFECTIVE 1989;
Name=NRPB2; Synonyms=EMB1989, RP140, RPB135, RPB2;
OrderedLocusNames=At4g21710; ORFNames=F17L22.170;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [MRNA].
STRAIN=cv. Columbia;
PubMed=8451172; DOI=10.1093/nar/21.4.1038;
Larkin R., Guilfoyle T.J.;
"The second largest subunit of RNA polymerase II from Arabidopsis
thaliana.";
Nucleic Acids Res. 21:1038-1038(1993).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10617198; DOI=10.1038/47134;
Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G.,
Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N.,
Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M.,
Weichselgartner M., de Simone V., Obermaier B., Mache R., Mueller M.,
Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T.,
Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I.,
Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P.,
Langham S.-A., McCullagh B., Bilham L., Robben J.,
van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F.,
Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E.,
Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W.,
Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P.,
Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H.,
De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R.,
van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S.,
Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R.,
Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S.,
Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H.,
Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S.,
Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A.,
Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R.,
Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S.,
Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E.,
Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A.,
Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T.,
Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C.,
Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S.,
Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K.,
Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L.,
Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J.,
Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J.,
Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D.,
Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D.,
Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C.,
Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C.,
Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R.,
Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S.,
Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A.,
Chen E., Marra M.A., Martienssen R., McCombie W.R.;
"Sequence and analysis of chromosome 4 of the plant Arabidopsis
thaliana.";
Nature 402:769-777(1999).
[3]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[4]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=cv. Landsberg erecta;
PubMed=17272265; DOI=10.1074/mcp.M600408-MCP200;
Maor R., Jones A., Nuehse T.S., Studholme D.J., Peck S.C., Shirasu K.;
"Multidimensional protein identification technology (MudPIT) analysis
of ubiquitinated proteins in plants.";
Mol. Cell. Proteomics 6:601-610(2007).
[5]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=18723889; DOI=10.1534/genetics.108.090621;
Onodera Y., Nakagawa K., Haag J.R., Pikaard D., Mikami T., Ream T.,
Ito Y., Pikaard C.S.;
"Sex-biased lethality or transmission of defective transcription
machinery in Arabidopsis.";
Genetics 180:207-218(2008).
[6]
FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, SUBUNIT, AND
NOMENCLATURE.
PubMed=19110459; DOI=10.1016/j.molcel.2008.12.015;
Ream T.S., Haag J.R., Wierzbicki A.T., Nicora C.D., Norbeck A.D.,
Zhu J.K., Hagen G., Guilfoyle T.J., Pasa-Tolic L., Pikaard C.S.;
"Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V
reveal their origins as specialized forms of RNA polymerase II.";
Mol. Cell 33:192-203(2009).
-!- FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription
of DNA into RNA using the four ribonucleoside triphosphates as
substrates. Second largest component of RNA polymerase II which
synthesizes mRNA precursors and many functional non-coding RNAs.
Proposed to contribute to the polymerase catalytic activity and
forms the polymerase active center together with the largest
subunit. Pol II is the central component of the basal RNA
polymerase II transcription machinery. It is composed of mobile
elements that move relative to each other. NRPB2 is part of the
core element with the central large cleft, the clamp element that
moves to open and close the cleft and the jaws that are thought to
grab the incoming DNA template (By similarity). {ECO:0000250}.
-!- FUNCTION: Essential for the completion of the three rounds of
mitosis in female megaspores required for the development of
mature gametophytes (PubMed:18723889).
{ECO:0000269|PubMed:18723889}.
-!- CATALYTIC ACTIVITY:
Reaction=a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate +
RNA(n+1); Xref=Rhea:RHEA:21248, Rhea:RHEA-COMP:11128, Rhea:RHEA-
COMP:11129, ChEBI:CHEBI:33019, ChEBI:CHEBI:61557,
ChEBI:CHEBI:83400; EC=2.7.7.6;
-!- SUBUNIT: Component of the RNA polymerase II complex consisting of
at least 12 subunits. {ECO:0000269|PubMed:19110459}.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
-!- DISRUPTION PHENOTYPE: Defect in seed production due to female
gametophyte developmental arrest. {ECO:0000269|PubMed:18723889}.
-!- MISCELLANEOUS: The binding of ribonucleoside triphosphate to the
RNA polymerase II transcribing complex probably involves a two-
step mechanism. The initial binding seems to occur at the entry
(E) site and involves a magnesium ion coordinated by three
conserved aspartate residues of the two largest RNA Pol II
subunits (By similarity). {ECO:0000250}.
-!- SIMILARITY: Belongs to the RNA polymerase beta chain family.
{ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; Z19120; CAA79527.1; -; mRNA.
EMBL; Z19121; CAA79528.1; -; Genomic_DNA.
EMBL; AL035527; CAB36815.1; -; Genomic_DNA.
EMBL; AL161555; CAB81278.1; -; Genomic_DNA.
EMBL; CP002687; AEE84493.1; -; Genomic_DNA.
PIR; T05846; T05846.
RefSeq; NP_193902.1; NM_118291.4.
UniGene; At.112; -.
ProteinModelPortal; P38420; -.
SMR; P38420; -.
BioGrid; 13548; 4.
STRING; 3702.AT4G21710.1; -.
iPTMnet; P38420; -.
PaxDb; P38420; -.
PRIDE; P38420; -.
EnsemblPlants; AT4G21710.1; AT4G21710.1; AT4G21710.
GeneID; 828259; -.
Gramene; AT4G21710.1; AT4G21710.1; AT4G21710.
KEGG; ath:AT4G21710; -.
Araport; AT4G21710; -.
TAIR; locus:2119013; AT4G21710.
eggNOG; KOG0214; Eukaryota.
eggNOG; COG0085; LUCA.
HOGENOM; HOG000218612; -.
InParanoid; P38420; -.
KO; K03010; -.
OMA; RTQPHFE; -.
OrthoDB; EOG093600IR; -.
PhylomeDB; P38420; -.
Reactome; R-ATH-113418; Formation of the Early Elongation Complex.
Reactome; R-ATH-5578749; Transcriptional regulation by small RNAs.
Reactome; R-ATH-674695; RNA Polymerase II Pre-transcription Events.
Reactome; R-ATH-6781823; Formation of TC-NER Pre-Incision Complex.
Reactome; R-ATH-6782135; Dual incision in TC-NER.
Reactome; R-ATH-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
Reactome; R-ATH-6796648; TP53 Regulates Transcription of DNA Repair Genes.
Reactome; R-ATH-72086; mRNA Capping.
Reactome; R-ATH-72163; mRNA Splicing - Major Pathway.
Reactome; R-ATH-72165; mRNA Splicing - Minor Pathway.
Reactome; R-ATH-72203; Processing of Capped Intron-Containing Pre-mRNA.
Reactome; R-ATH-73776; RNA Polymerase II Promoter Escape.
Reactome; R-ATH-73779; RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
Reactome; R-ATH-75953; RNA Polymerase II Transcription Initiation.
Reactome; R-ATH-76042; RNA Polymerase II Transcription Initiation And Promoter Clearance.
Reactome; R-ATH-77075; RNA Pol II CTD phosphorylation and interaction with CE.
Reactome; R-ATH-9018519; Estrogen-dependent gene expression.
PRO; PR:P38420; -.
Proteomes; UP000006548; Chromosome 4.
ExpressionAtlas; P38420; baseline and differential.
Genevisible; P38420; AT.
GO; GO:0005829; C:cytosol; IDA:TAIR.
GO; GO:0009506; C:plasmodesma; IDA:TAIR.
GO; GO:0005665; C:RNA polymerase II, core complex; IDA:UniProtKB.
GO; GO:0003677; F:DNA binding; IEA:InterPro.
GO; GO:0003899; F:DNA-directed 5'-3' RNA polymerase activity; ISS:TAIR.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0032549; F:ribonucleoside binding; IEA:InterPro.
GO; GO:0035196; P:production of miRNAs involved in gene silencing by miRNA; IMP:TAIR.
GO; GO:0006366; P:transcription by RNA polymerase II; IEA:GOC.
CDD; cd00653; RNA_pol_B_RPB2; 1.
Gene3D; 2.40.270.10; -; 1.
Gene3D; 2.40.50.150; -; 1.
Gene3D; 3.90.1110.10; -; 1.
InterPro; IPR015712; DNA-dir_RNA_pol_su2.
InterPro; IPR007120; DNA-dir_RNAP_su2_dom.
InterPro; IPR037033; DNA-dir_RNAP_su2_hyb_sf.
InterPro; IPR007121; RNA_pol_bsu_CS.
InterPro; IPR007644; RNA_pol_bsu_protrusion.
InterPro; IPR007642; RNA_pol_Rpb2_2.
InterPro; IPR037034; RNA_pol_Rpb2_2_sf.
InterPro; IPR007645; RNA_pol_Rpb2_3.
InterPro; IPR007646; RNA_pol_Rpb2_4.
InterPro; IPR007647; RNA_pol_Rpb2_5.
InterPro; IPR007641; RNA_pol_Rpb2_7.
InterPro; IPR014724; RNA_pol_RPB2_OB-fold.
PANTHER; PTHR20856; PTHR20856; 1.
Pfam; PF04563; RNA_pol_Rpb2_1; 1.
Pfam; PF04561; RNA_pol_Rpb2_2; 1.
Pfam; PF04565; RNA_pol_Rpb2_3; 1.
Pfam; PF04566; RNA_pol_Rpb2_4; 1.
Pfam; PF04567; RNA_pol_Rpb2_5; 1.
Pfam; PF00562; RNA_pol_Rpb2_6; 1.
Pfam; PF04560; RNA_pol_Rpb2_7; 1.
PROSITE; PS01166; RNA_POL_BETA; 1.
1: Evidence at protein level;
Complete proteome; DNA-directed RNA polymerase; Magnesium;
Metal-binding; Nucleotidyltransferase; Nucleus; Reference proteome;
Transcription; Transferase; Zinc; Zinc-finger.
CHAIN 1 1188 DNA-directed RNA polymerase II subunit 2.
/FTId=PRO_0000048081.
ZN_FING 1124 1145 C4-type.
COMPBIAS 14 20 Asp/Glu-rich (acidic).
METAL 800 800 Magnesium; shared with RPB1.
{ECO:0000250}.
METAL 1124 1124 Zinc. {ECO:0000250}.
METAL 1127 1127 Zinc. {ECO:0000250}.
METAL 1142 1142 Zinc. {ECO:0000250}.
METAL 1145 1145 Zinc. {ECO:0000250}.
VARIANT 787 787 I -> N.
CONFLICT 354 355 PH -> LY (in Ref. 1; CAA79527/CAA79528).
{ECO:0000305}.
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


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