RPB8B_ARATH
ID RPB8B_ARATH Reviewed; 146 AA.
AC Q9M1A8;
DT 18-SEP-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=DNA-directed RNA polymerases II, IV and V subunit 8B;
DE AltName: Full=RNA polymerase Rpb8;
GN Name=NRPB8B; Synonyms=NRPD8B, NRPE8B; OrderedLocusNames=At3g59600;
GN ORFNames=T16L24.150;
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 [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 [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND INTERACTION WITH THE MEDIATOR
RP COMPLEX.
RX PubMed=17560376; DOI=10.1016/j.molcel.2007.05.007;
RA Baeckstroem S., Elfving N., Nilsson R., Wingsle G., Bjoerklund S.;
RT "Purification of a plant mediator from Arabidopsis thaliana identifies PFT1
RT as the Med25 subunit.";
RL Mol. Cell 26:717-729(2007).
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 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. Component of RNA
CC polymerases IV and V which mediate short-interfering RNAs (siRNA)
CC accumulation and subsequent RNA-directed DNA methylation-dependent
CC (RdDM) transcriptional gene silencing (TGS) of endogenous repeated
CC sequences, including transposable elements.
CC {ECO:0000269|PubMed:19110459}.
CC -!- SUBUNIT: Component of the RNA polymerase II, IV and V complexes.
CC Associates with the mediator complex. {ECO:0000269|PubMed:19110459}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the eukaryotic RPB8 RNA polymerase subunit
CC family. {ECO:0000305}.
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DR EMBL; AL138659; CAB75457.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE79944.1; -; Genomic_DNA.
DR EMBL; AK119016; BAC43592.1; -; mRNA.
DR EMBL; BT008531; AAP40358.1; -; mRNA.
DR EMBL; AY086002; AAM63211.1; -; mRNA.
DR PIR; T49301; T49301.
DR RefSeq; NP_191519.1; NM_115822.4.
DR PDB; 7EU0; EM; 3.16 A; H=1-146.
DR PDB; 7EU1; EM; 3.86 A; H=1-146.
DR PDBsum; 7EU0; -.
DR PDBsum; 7EU1; -.
DR AlphaFoldDB; Q9M1A8; -.
DR SMR; Q9M1A8; -.
DR BioGRID; 10443; 25.
DR IntAct; Q9M1A8; 1.
DR STRING; 3702.AT3G59600.1; -.
DR PaxDb; Q9M1A8; -.
DR PRIDE; Q9M1A8; -.
DR ProteomicsDB; 228223; -.
DR EnsemblPlants; AT3G59600.1; AT3G59600.1; AT3G59600.
DR GeneID; 825129; -.
DR Gramene; AT3G59600.1; AT3G59600.1; AT3G59600.
DR KEGG; ath:AT3G59600; -.
DR Araport; AT3G59600; -.
DR TAIR; locus:2097468; AT3G59600.
DR eggNOG; KOG3400; Eukaryota.
DR HOGENOM; CLU_103864_1_1_1; -.
DR InParanoid; Q9M1A8; -.
DR OMA; TINAYVS; -.
DR OrthoDB; 1504067at2759; -.
DR PhylomeDB; Q9M1A8; -.
DR PRO; PR:Q9M1A8; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9M1A8; baseline and differential.
DR Genevisible; Q9M1A8; AT.
DR GO; GO:0005736; C:RNA polymerase I complex; IBA:GO_Central.
DR GO; GO:0005665; C:RNA polymerase II, core complex; IDA:UniProtKB.
DR GO; GO:0005666; C:RNA polymerase III 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:0006351; P:transcription, DNA-templated; IEA:InterPro.
DR Gene3D; 2.40.50.140; -; 1.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR005570; RNA_pol_Rpb8.
DR PANTHER; PTHR10917; PTHR10917; 1.
DR Pfam; PF03870; RNA_pol_Rpb8; 1.
DR PIRSF; PIRSF000779; RNA_pol_Rpb8; 1.
DR SMART; SM00658; RPOL8c; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Nucleus; Reference proteome.
FT CHAIN 1..146
FT /note="DNA-directed RNA polymerases II, IV and V subunit
FT 8B"
FT /id="PRO_0000423325"
FT STRAND 9..19
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 28..34
FT /evidence="ECO:0007829|PDB:7EU0"
FT TURN 35..37
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 40..45
FT /evidence="ECO:0007829|PDB:7EU0"
FT TURN 47..49
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 57..61
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 66..70
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 93..99
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 113..118
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 120..124
FT /evidence="ECO:0007829|PDB:7EU0"
FT TURN 127..129
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 135..144
FT /evidence="ECO:0007829|PDB:7EU0"
SQ SEQUENCE 146 AA; 16603 MW; 230F6E9995E368B7 CRC64;
MASNIIMFED IFVVDKLDPD GKKFDKVTRV EARSHNLEMF MHLDVNTEVY PLAVGDKFTL
AMAPTLNLDG TPDTGYFTPG AKKTLADKYE YIMHGKLYKI SERDGKTPKA ELYVSFGGLL
MLLQGDPAHI SHFELDQRLF LLMRKL
