NRPBB_ARATH
ID NRPBB_ARATH Reviewed; 116 AA.
AC Q38859;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 148.
DE RecName: Full=DNA-directed RNA polymerases II, IV and V subunit 11;
DE AltName: Full=DNA-directed RNA polymerase II 13.6 kDa polypeptide;
DE AltName: Full=DNA-directed RNA polymerase II subunit J;
DE AltName: Full=DNA-directed RNA polymerase II subunit RPB11;
DE Short=RNA polymerase II subunit B11;
GN Name=NRPB11; Synonyms=NRPD11, NRPE11, RPB13.6; OrderedLocusNames=At3g52090;
GN ORFNames=F4F15.200;
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], AND INTERACTION WITH NRPB3 AND NRPE3B.
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=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
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 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).
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. NRPB11 is part of the
CC core element with the central large cleft. Component of RNA polymerases
CC IV and 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, IV and V complexes.
CC Interacts with NRPD1, NRPB3 and NRPE3B. {ECO:0000269|PubMed:19110459,
CC ECO:0000269|PubMed:21811420, ECO:0000269|PubMed:8617787}.
CC -!- SUBCELLULAR LOCATION: Nucleus.
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=Q38859-1; Sequence=Displayed;
CC -!- SIMILARITY: Belongs to the archaeal Rpo11/eukaryotic RPB11/RPC19 RNA
CC polymerase subunit family. {ECO:0000305}.
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DR EMBL; U28048; AAB02849.1; -; mRNA.
DR EMBL; AL049711; CAB41329.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE78889.1; -; Genomic_DNA.
DR EMBL; BT005984; AAO64919.1; -; mRNA.
DR PIR; S71204; S71204.
DR RefSeq; NP_190777.1; NM_115068.5. [Q38859-1]
DR PDB; 7EU0; EM; 3.16 A; K=1-116.
DR PDB; 7EU1; EM; 3.86 A; K=1-116.
DR PDBsum; 7EU0; -.
DR PDBsum; 7EU1; -.
DR AlphaFoldDB; Q38859; -.
DR SMR; Q38859; -.
DR BioGRID; 9690; 28.
DR IntAct; Q38859; 2.
DR PRIDE; Q38859; -.
DR ProteomicsDB; 249449; -. [Q38859-1]
DR EnsemblPlants; AT3G52090.1; AT3G52090.1; AT3G52090. [Q38859-1]
DR GeneID; 824372; -.
DR Gramene; AT3G52090.1; AT3G52090.1; AT3G52090. [Q38859-1]
DR KEGG; ath:AT3G52090; -.
DR Araport; AT3G52090; -.
DR HOGENOM; CLU_090381_2_2_1; -.
DR InParanoid; Q38859; -.
DR OMA; LEQACTK; -.
DR PhylomeDB; Q38859; -.
DR PRO; PR:Q38859; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q38859; baseline and differential.
DR Genevisible; Q38859; AT.
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:0046983; F:protein dimerization activity; IEA:InterPro.
DR GO; GO:0001055; F:RNA polymerase II activity; IEA:InterPro.
DR CDD; cd06926; RNAP_II_RPB11; 1.
DR Gene3D; 3.30.1360.10; -; 1.
DR HAMAP; MF_00261; RNApol_arch_Rpo11; 1.
DR InterPro; IPR037685; RBP11.
DR InterPro; IPR036603; RBP11-like.
DR InterPro; IPR009025; RBP11-like_dimer.
DR InterPro; IPR008193; RNA_pol_Rpb11_13-16kDa_CS.
DR Pfam; PF13656; RNA_pol_L_2; 1.
DR SUPFAM; SSF55257; SSF55257; 1.
DR PROSITE; PS01154; RNA_POL_L_13KD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; DNA-directed RNA polymerase; Nucleus;
KW Reference proteome; Transcription.
FT CHAIN 1..116
FT /note="DNA-directed RNA polymerases II, IV and V subunit
FT 11"
FT /id="PRO_0000149313"
FT STRAND 25..27
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 30..36
FT /evidence="ECO:0007829|PDB:7EU0"
FT HELIX 40..50
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 56..62
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 66..68
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 70..77
FT /evidence="ECO:0007829|PDB:7EU0"
FT HELIX 83..109
FT /evidence="ECO:0007829|PDB:7EU0"
SQ SEQUENCE 116 AA; 13563 MW; DCFC8609E0F5CDEB CRC64;
MNAPERYERF VVPEGTKKVS YDRDTKIINA ASFTVEREDH TIGNIVRMQL HRDENVLFAG
YQLPHPLKYK IIVRIHTTSQ SSPMQAYNQA INDLDKELDY LKNQFEAEVA KFSNQF
