NRPB3_ARATH
ID NRPB3_ARATH Reviewed; 319 AA.
AC Q39211;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 170.
DE RecName: Full=DNA-directed RNA polymerases II, IV and V subunit 3;
DE AltName: Full=DNA-directed RNA polymerase II 36 kDa polypeptide A;
DE AltName: Full=DNA-directed RNA polymerase II subunit RPB3-A;
DE Short=RNA polymerase II subunit 3-A;
DE Short=RNA polymerase II subunit B3-A;
GN Name=NRPB3; Synonyms=NRPD3, NRPE3A, RPB36A; OrderedLocusNames=At2g15430;
GN ORFNames=F26H6.5;
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 [GENOMIC DNA], AND INTERACTION WITH NRPB11.
RC STRAIN=cv. Columbia;
RX PubMed=8617787; DOI=10.1074/jbc.271.9.5085;
RA Ulmasov T., Larkin R.M., Guilfoyle T.J.;
RT "Association between 36- and 13.6-kDa alpha-like subunits of Arabidopsis
RT thaliana RNA polymerase II.";
RL J. Biol. Chem. 271:5085-5094(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
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).
RN [6]
RP INTERACTION WITH IYO.
RX PubMed=21620701; DOI=10.1016/j.cub.2011.04.041;
RA Sanmartin M., Sauer M., Munoz A., Zouhar J., Ordonez A., van de Ven W.T.,
RA Caro E., de la Paz Sanchez M., Raikhel N.V., Gutierrez C.,
RA Sanchez-Serrano J.J., Rojo E.;
RT "A molecular switch for initiating cell differentiation in Arabidopsis.";
RL Curr. Biol. 21:999-1008(2011).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY, INTERACTION WITH NRPD1, AND SUBUNIT.
RX PubMed=21811420; DOI=10.1371/journal.pgen.1002195;
RA Law J.A., Vashisht A.A., Wohlschlegel J.A., Jacobsen S.E.;
RT "SHH1, a homeodomain protein required for DNA methylation, as well as RDR2,
RT RDM4, and chromatin remodeling factors, associate with RNA polymerase IV.";
RL PLoS Genet. 7:E1002195-E1002195(2011).
RN [8]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
RN [9]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND INTERACTION WITH SHH1 AND CLSY1.
RX PubMed=23637343; DOI=10.1073/pnas.1300585110;
RA Zhang H., Ma Z.Y., Zeng L., Tanaka K., Zhang C.J., Ma J., Bai G., Wang P.,
RA Zhang S.W., Liu Z.W., Cai T., Tang K., Liu R., Shi X., He X.J., Zhu J.K.;
RT "DTF1 is a core component of RNA-directed DNA methylation and may assist in
RT the recruitment of Pol IV.";
RL Proc. Natl. Acad. Sci. U.S.A. 110:8290-8295(2013).
CC -!- FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription of
CC DNA into RNA using the four ribonucleoside triphosphates as substrates.
CC Component of RNA polymerase II which synthesizes mRNA precursors and
CC many functional non-coding RNAs. Pol II is the central component of the
CC basal RNA polymerase II transcription machinery. It is composed of
CC mobile elements that move relative to each other. NRPB3 is part of the
CC core element with the central large cleft and the clamp element that
CC moves to open and close the cleft. Component of RNA polymerases IV and
CC V which mediate short-interfering RNAs (siRNA) accumulation and
CC subsequent RNA-directed DNA methylation-dependent (RdDM)
CC transcriptional gene silencing (TGS) of endogenous repeated sequences,
CC including transposable elements. {ECO:0000269|PubMed:19110459}.
CC -!- SUBUNIT: Component of the RNA polymerase II complex consisting of at
CC least 12 subunits. Interacts with SHH1, CLSY1, NRPB11 and NRPD1
CC (PubMed:19110459, PubMed:21811420, PubMed:23637343, PubMed:8617787).
CC Interacts with IYO (PubMed:21620701). {ECO:0000269|PubMed:19110459,
CC ECO:0000269|PubMed:21620701, ECO:0000269|PubMed:21811420,
CC ECO:0000269|PubMed:23637343, ECO:0000269|PubMed:8617787}.
CC -!- SUBCELLULAR LOCATION: Nucleus.
CC -!- SIMILARITY: Belongs to the archaeal Rpo3/eukaryotic RPB3 RNA polymerase
CC subunit family. {ECO:0000305}.
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DR EMBL; L34770; AAB03741.1; -; Genomic_DNA.
DR EMBL; AC006920; AAD22281.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC06400.1; -; Genomic_DNA.
DR EMBL; AY063965; AAL36321.1; -; mRNA.
DR EMBL; AY096406; AAM20046.1; -; mRNA.
DR PIR; S71176; S71176.
DR RefSeq; NP_179145.1; NM_127103.3.
DR PDB; 7EU0; EM; 3.16 A; C=1-319.
DR PDB; 7EU1; EM; 3.86 A; C=1-319.
DR PDBsum; 7EU0; -.
DR PDBsum; 7EU1; -.
DR AlphaFoldDB; Q39211; -.
DR SMR; Q39211; -.
DR BioGRID; 1394; 92.
DR IntAct; Q39211; 2.
DR STRING; 3702.AT2G15430.1; -.
DR iPTMnet; Q39211; -.
DR PaxDb; Q39211; -.
DR PRIDE; Q39211; -.
DR ProteomicsDB; 250602; -.
DR EnsemblPlants; AT2G15430.1; AT2G15430.1; AT2G15430.
DR GeneID; 816035; -.
DR Gramene; AT2G15430.1; AT2G15430.1; AT2G15430.
DR KEGG; ath:AT2G15430; -.
DR Araport; AT2G15430; -.
DR TAIR; locus:2047168; AT2G15430.
DR eggNOG; KOG1522; Eukaryota.
DR HOGENOM; CLU_038421_3_0_1; -.
DR InParanoid; Q39211; -.
DR OMA; ENTSPFH; -.
DR OrthoDB; 834009at2759; -.
DR PhylomeDB; Q39211; -.
DR PRO; PR:Q39211; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q39211; baseline and differential.
DR Genevisible; Q39211; AT.
DR GO; GO:0005737; C:cytoplasm; IDA:TAIR.
DR GO; GO:0005730; C:nucleolus; HDA:TAIR.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0005665; C:RNA polymerase II, core complex; IDA:UniProtKB.
DR GO; GO:0000418; C:RNA polymerase IV complex; IDA:UniProtKB.
DR GO; GO:0000419; C:RNA polymerase V complex; IDA:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0003899; F:DNA-directed 5'-3' RNA polymerase activity; IEA:InterPro.
DR GO; GO:0046983; F:protein dimerization activity; IEA:InterPro.
DR GO; GO:0010374; P:stomatal complex development; IMP:TAIR.
DR GO; GO:0010375; P:stomatal complex patterning; IMP:TAIR.
DR GO; GO:0006351; P:transcription, DNA-templated; IEA:InterPro.
DR Gene3D; 2.170.120.12; -; 1.
DR Gene3D; 3.30.1360.10; -; 1.
DR HAMAP; MF_00320; RNApol_arch_Rpo3; 1.
DR InterPro; IPR001514; DNA-dir_RNA_pol_30-40kDasu_CS.
DR InterPro; IPR011262; DNA-dir_RNA_pol_insert.
DR InterPro; IPR011263; DNA-dir_RNA_pol_RpoA/D/Rpb3.
DR InterPro; IPR036603; RBP11-like.
DR InterPro; IPR022842; RNAP_Rpo3/Rpb3/RPAC1.
DR InterPro; IPR036643; RNApol_insert_sf.
DR Pfam; PF01000; RNA_pol_A_bac; 1.
DR Pfam; PF01193; RNA_pol_L; 1.
DR SMART; SM00662; RPOLD; 1.
DR SUPFAM; SSF55257; SSF55257; 1.
DR SUPFAM; SSF56553; SSF56553; 1.
DR PROSITE; PS00446; RNA_POL_D_30KD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; DNA-directed RNA polymerase; Nucleus;
KW Reference proteome; Transcription.
FT CHAIN 1..319
FT /note="DNA-directed RNA polymerases II, IV and V subunit 3"
FT /id="PRO_0000132745"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT STRAND 11..17
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 19..29
FT /evidence="ECO:0007829|PDB:7EU0"
FT HELIX 31..43
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 47..57
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 60..62
FT /evidence="ECO:0007829|PDB:7EU0"
FT HELIX 64..72
FT /evidence="ECO:0007829|PDB:7EU0"
FT TURN 81..83
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 87..89
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 96..98
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 100..112
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 114..116
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 118..120
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 122..124
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 126..129
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 155..157
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 159..172
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 187..196
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 198..200
FT /evidence="ECO:0007829|PDB:7EU0"
FT HELIX 208..214
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 217..219
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 221..223
FT /evidence="ECO:0007829|PDB:7EU0"
FT TURN 225..227
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 228..232
FT /evidence="ECO:0007829|PDB:7EU0"
FT HELIX 244..250
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 256..272
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 274..276
FT /evidence="ECO:0007829|PDB:7EU0"
FT HELIX 278..302
FT /evidence="ECO:0007829|PDB:7EU0"
SQ SEQUENCE 319 AA; 35461 MW; 6DD5CC747A1B1A57 CRC64;
MDGATYQRFP KIKIRELKDD YAKFELRETD VSMANALRRV MISEVPTVAI DLVEIEVNSS
VLNDEFIAHR LGLIPLTSER AMSMRFSRDC DACDGDGQCE FCSVEFRLSS KCVTDQTLDV
TSRDLYSADP TVTPVDFTID SSVSDSSEHK GIIIVKLRRG QELKLRAIAR KGIGKDHAKW
SPAATVTFMY EPDIIINEDM MDTLSDEEKI DLIESSPTKV FGMDPVTRQV VVVDPEAYTY
DEEVIKKAEA MGKPGLIEIS PKDDSFIFTV ESTGAVKASQ LVLNAIDLLK QKLDAVRLSD
DTVEADDQFG ELGAHMRGG
