RPD3B_ARATH
ID RPD3B_ARATH Reviewed; 319 AA.
AC Q39212; Q9SJP1;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2000, sequence version 2.
DT 03-AUG-2022, entry version 172.
DE RecName: Full=DNA-directed RNA polymerases IV and V subunit 3B;
DE AltName: Full=DNA-directed RNA polymerase II 36 kDa polypeptide B;
DE AltName: Full=DNA-directed RNA polymerase II subunit RPB3-B;
DE Short=RNA polymerase II subunit 3-B;
DE Short=RNA polymerase II subunit B3-B;
GN Name=NRPD3B; Synonyms=NRPE3B, RPB36B; OrderedLocusNames=At2g15400;
GN ORFNames=F26H6.8;
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 INTERACTION WITH GRP23.
RX PubMed=16489121; DOI=10.1105/tpc.105.039495;
RA Ding Y.-H., Liu N.-Y., Tang Z.-S., Liu J., Yang W.-C.;
RT "Arabidopsis GLUTAMINE-RICH PROTEIN23 is essential for early embryogenesis
RT and encodes a novel nuclear PPR motif protein that interacts with RNA
RT polymerase II subunit III.";
RL Plant Cell 18:815-830(2006).
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).
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 IDENTIFICATION BY MASS SPECTROMETRY, AND INTERACTION WITH SHH1.
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 polymerases IV and V which mediate short-interfering
CC RNAs (siRNA) accumulation and subsequent RNA-directed DNA methylation-
CC dependent (RdDM) transcriptional gene silencing (TGS) of endogenous
CC repeated sequences, including transposable elements.
CC {ECO:0000269|PubMed:19110459}.
CC -!- SUBUNIT: Component of the RNA polymerase IV and V complexes. Interacts
CC with NRPB11, SHH1, GRP23 and NRPD1. {ECO:0000269|PubMed:16489121,
CC ECO:0000269|PubMed:19110459, ECO:0000269|PubMed:21811420,
CC ECO:0000269|PubMed:23637343, ECO:0000269|PubMed:8617787}.
CC -!- INTERACTION:
CC Q39212; Q9SY69: GRP23; NbExp=3; IntAct=EBI-1769627, EBI-1769617;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q39212-1; Sequence=Displayed;
CC -!- SIMILARITY: Belongs to the archaeal Rpo3/eukaryotic RPB3 RNA polymerase
CC subunit family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; L34771; AAB03740.1; -; Genomic_DNA.
DR EMBL; AC006920; AAD22284.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC06397.1; -; Genomic_DNA.
DR EMBL; BT005715; AAO64135.1; -; mRNA.
DR EMBL; BT006072; AAP04057.1; -; mRNA.
DR PIR; E84528; E84528.
DR PIR; S71177; S71177.
DR RefSeq; NP_179142.1; NM_127100.4. [Q39212-1]
DR AlphaFoldDB; Q39212; -.
DR SMR; Q39212; -.
DR BioGRID; 1391; 81.
DR IntAct; Q39212; 1.
DR STRING; 3702.AT2G15400.1; -.
DR PaxDb; Q39212; -.
DR PRIDE; Q39212; -.
DR ProteomicsDB; 228231; -. [Q39212-1]
DR EnsemblPlants; AT2G15400.1; AT2G15400.1; AT2G15400. [Q39212-1]
DR GeneID; 816032; -.
DR Gramene; AT2G15400.1; AT2G15400.1; AT2G15400. [Q39212-1]
DR KEGG; ath:AT2G15400; -.
DR Araport; AT2G15400; -.
DR TAIR; locus:2047198; AT2G15400.
DR eggNOG; KOG1522; Eukaryota.
DR HOGENOM; CLU_038421_3_0_1; -.
DR InParanoid; Q39212; -.
DR OMA; HDSFVFT; -.
DR PhylomeDB; Q39212; -.
DR PRO; PR:Q39212; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q39212; baseline and differential.
DR Genevisible; Q39212; AT.
DR GO; GO:0005665; C:RNA polymerase II, core complex; IBA:GO_Central.
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: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 Acetylation; Alternative splicing; DNA-directed RNA polymerase; Nucleus;
KW Reference proteome; Transcription.
FT CHAIN 1..319
FT /note="DNA-directed RNA polymerases IV and V subunit 3B"
FT /id="PRO_0000132746"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0000250|UniProtKB:Q39211"
FT CONFLICT 268..271
FT /note="FTVE -> LSVH (in Ref. 1; AAB03740)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 319 AA; 35575 MW; 68C898B882BD130A CRC64;
MDGVTYQRFP TVKIRELKDD YAKFELRETD VSMANALRRV MISEVPTMAI HLVKIEVNSS
VLNDEFIAQR LSLIPLTSER AMSMRFCQDC EDCNGDEHCE FCSVEFPLSA KCVTDQTLDV
TSRDLYSADP TVTPVDFTSN SSTSDSSEHK GIIIAKLRRG QELKLKALAR KGIGKDHAKW
SPAATVTYMY EPDIIINEEM MNTLTDEEKI DLIESSPTKV FGIDPVTGQV VVVDPEAYTY
DEEVIKKAEA MGKPGLIEIH PKHDSFVFTV ESTGALKASQ LVLNAIDILK QKLDAIRLSD
NTVEADDQFG ELGAHMREG
