RPD6A_ARATH
ID RPD6A_ARATH Reviewed; 144 AA.
AC Q9FJ98;
DT 18-SEP-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 139.
DE RecName: Full=DNA-directed RNA polymerases II, IV and V subunit 6A;
DE AltName: Full=RNA polymerase Rpb6;
GN Name=NRPB6A; Synonyms=NRPD6A, NRPE6A; OrderedLocusNames=At5g51940;
GN ORFNames=MSG15.2;
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=9872454; DOI=10.1093/dnares/5.5.297;
RA Nakamura Y., Sato S., Asamizu E., Kaneko T., Kotani H., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. VII. Sequence
RT features of the regions of 1,013,767 bp covered by sixteen physically
RT assigned P1 and TAC clones.";
RL DNA Res. 5:297-308(1998).
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=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 [4]
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 [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. 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 Interacts with NRPD1. {ECO:0000269|PubMed:19110459,
CC ECO:0000269|PubMed:21811420}.
CC -!- INTERACTION:
CC Q9FJ98; Q9LNC9: MYB13; NbExp=3; IntAct=EBI-25517907, EBI-25521688;
CC Q9FJ98; Q5CCK4: VAL2; NbExp=3; IntAct=EBI-25517907, EBI-15193683;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the archaeal Rpo6/eukaryotic RPB6 RNA polymerase
CC subunit family. {ECO:0000305}.
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DR EMBL; AB015478; BAB11042.1; -; Genomic_DNA.
DR EMBL; CP002688; AED96148.1; -; Genomic_DNA.
DR EMBL; AF370301; AAK44116.1; -; mRNA.
DR EMBL; AY063088; AAL34262.1; -; mRNA.
DR EMBL; AY088602; AAM66131.1; -; mRNA.
DR RefSeq; NP_200007.1; NM_124573.3.
DR PDB; 7EU0; EM; 3.16 A; F=1-144.
DR PDB; 7EU1; EM; 3.86 A; F=1-144.
DR PDBsum; 7EU0; -.
DR PDBsum; 7EU1; -.
DR AlphaFoldDB; Q9FJ98; -.
DR SMR; Q9FJ98; -.
DR BioGRID; 20514; 9.
DR IntAct; Q9FJ98; 2.
DR STRING; 3702.AT5G51940.1; -.
DR PaxDb; Q9FJ98; -.
DR PRIDE; Q9FJ98; -.
DR ProteomicsDB; 228244; -.
DR EnsemblPlants; AT5G51940.1; AT5G51940.1; AT5G51940.
DR GeneID; 835269; -.
DR Gramene; AT5G51940.1; AT5G51940.1; AT5G51940.
DR KEGG; ath:AT5G51940; -.
DR Araport; AT5G51940; -.
DR TAIR; locus:2173058; AT5G51940.
DR eggNOG; KOG3405; Eukaryota.
DR HOGENOM; CLU_112527_1_0_1; -.
DR InParanoid; Q9FJ98; -.
DR OMA; LIVEDTW; -.
DR OrthoDB; 1488436at2759; -.
DR PhylomeDB; Q9FJ98; -.
DR PRO; PR:Q9FJ98; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FJ98; baseline and differential.
DR Genevisible; Q9FJ98; 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:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0003899; F:DNA-directed 5'-3' RNA polymerase activity; IEA:InterPro.
DR GO; GO:0006351; P:transcription, DNA-templated; IEA:InterPro.
DR Gene3D; 3.90.940.10; -; 1.
DR HAMAP; MF_00192; RNApol_arch_Rpo6; 1.
DR InterPro; IPR020708; DNA-dir_RNA_polK_14-18kDa_CS.
DR InterPro; IPR006110; Pol_omega/Rpo6/RPB6.
DR InterPro; IPR028363; RPB6.
DR InterPro; IPR036161; RPB6/omega-like_sf.
DR InterPro; IPR006111; Rpo6/Rpb6.
DR Pfam; PF01192; RNA_pol_Rpb6; 1.
DR PIRSF; PIRSF500154; RPB6; 1.
DR PIRSF; PIRSF000778; RpoK/RPB6; 1.
DR SMART; SM01409; RNA_pol_Rpb6; 1.
DR SUPFAM; SSF63562; SSF63562; 1.
DR PROSITE; PS01111; RNA_POL_K_14KD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA-directed RNA polymerase; Nucleus; Reference proteome;
KW Transcription.
FT CHAIN 1..144
FT /note="DNA-directed RNA polymerases II, IV and V subunit
FT 6A"
FT /id="PRO_0000423322"
FT REGION 1..62
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..36
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 37..62
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT HELIX 67..82
FT /evidence="ECO:0007829|PDB:7EU0"
FT HELIX 97..107
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 113..117
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 123..127
FT /evidence="ECO:0007829|PDB:7EU0"
FT TURN 128..130
FT /evidence="ECO:0007829|PDB:7EU0"
SQ SEQUENCE 144 AA; 16652 MW; 6BCF2128F79A3734 CRC64;
MADEDYNDVD DLGYEDEPAE PEIEEGVEED VEMKENDDVN GEPIEAEDKV ETEPVQRPRK
TSKFMTKYER ARILGTRALQ ISMNAPVMVE LEGETDPLEI AMKELRQRKI PFTIRRYLPD
GSFEEWGVDE LIVEDSWKRQ VGGD
