ID   RPD5B_ARATH             Reviewed;         218 AA.
AC   Q9ZVB9;
DT   18-SEP-2013, integrated into UniProtKB/Swiss-Prot.
DT   01-MAY-1999, sequence version 1.
DT   03-AUG-2022, entry version 129.
DE   RecName: Full=DNA-directed RNA polymerases IV and V subunit 5B;
DE   AltName: Full=DNA-directed RNA polymerase 23kD subunit;
GN   Name=NRPD5B; Synonyms=NRPE5B, RPB5B; OrderedLocusNames=At2g41340;
GN   ORFNames=F13H10.11;
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=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   [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   TISSUE SPECIFICITY.
RX   PubMed=19141635; DOI=10.1073/pnas.0810310106;
RA   Lahmy S., Pontier D., Cavel E., Vega D., El-Shami M., Kanno T.,
RA   Lagrange T.;
RT   "PolV(PolIVb) function in RNA-directed DNA methylation requires the
RT   conserved active site and an additional plant-specific subunit.";
RL   Proc. Natl. Acad. Sci. U.S.A. 106:941-946(2009).
RN   [5]
RP   IDENTIFICATION BY MASS SPECTROMETRY, INTERACTION WITH NRPD1, SUBUNIT, AND
RP   NOMENCLATURE.
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 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   -!- SUBUNIT: Component of the RNA polymerase IV and V complexes. Interacts
CC       with NRPD1. {ECO:0000269|PubMed:21811420}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC   -!- TISSUE SPECIFICITY: Expressed inleaves, flower buds, flowers and
CC       siliques. {ECO:0000269|PubMed:19141635}.
CC   -!- SIMILARITY: Belongs to the archaeal Rpo5/eukaryotic RPB5 RNA polymerase
CC       subunit family. {ECO:0000305}.
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DR   EMBL; AC005662; AAC78539.1; -; Genomic_DNA.
DR   EMBL; CP002685; AEC09961.1; -; Genomic_DNA.
DR   EMBL; AY078926; AAL84932.1; -; mRNA.
DR   PIR; E84840; E84840.
DR   RefSeq; NP_181665.1; NM_129697.3.
DR   AlphaFoldDB; Q9ZVB9; -.
DR   SMR; Q9ZVB9; -.
DR   BioGRID; 4069; 1.
DR   STRING; 3702.AT2G41340.1; -.
DR   PaxDb; Q9ZVB9; -.
DR   PRIDE; Q9ZVB9; -.
DR   ProteomicsDB; 227957; -.
DR   EnsemblPlants; AT2G41340.1; AT2G41340.1; AT2G41340.
DR   GeneID; 818732; -.
DR   Gramene; AT2G41340.1; AT2G41340.1; AT2G41340.
DR   KEGG; ath:AT2G41340; -.
DR   Araport; AT2G41340; -.
DR   TAIR; locus:2040257; AT2G41340.
DR   eggNOG; KOG3218; Eukaryota.
DR   HOGENOM; CLU_058320_0_0_1; -.
DR   InParanoid; Q9ZVB9; -.
DR   OMA; DPIVRYY; -.
DR   OrthoDB; 1255823at2759; -.
DR   PhylomeDB; Q9ZVB9; -.
DR   PRO; PR:Q9ZVB9; -.
DR   Proteomes; UP000006548; Chromosome 2.
DR   ExpressionAtlas; Q9ZVB9; baseline and differential.
DR   Genevisible; Q9ZVB9; AT.
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; 3.40.1340.10; -; 1.
DR   Gene3D; 3.90.940.20; -; 1.
DR   InterPro; IPR014381; Arch_Rpo5/euc_Rpb5.
DR   InterPro; IPR005571; RNA_pol_Rpb5_N.
DR   InterPro; IPR036710; RNA_pol_Rpb5_N_sf.
DR   InterPro; IPR000783; RNA_pol_subH/Rpb5_C.
DR   InterPro; IPR035913; RPB5-like_sf.
DR   PANTHER; PTHR10535; PTHR10535; 1.
DR   Pfam; PF01191; RNA_pol_Rpb5_C; 1.
DR   Pfam; PF03871; RNA_pol_Rpb5_N; 1.
DR   PIRSF; PIRSF000747; RPB5; 1.
DR   SUPFAM; SSF53036; SSF53036; 1.
DR   SUPFAM; SSF55287; SSF55287; 1.
PE   1: Evidence at protein level;
KW   DNA-directed RNA polymerase; Nucleus; Reference proteome; Transcription.
FT   CHAIN           1..218
FT                   /note="DNA-directed RNA polymerases IV and V subunit 5B"
FT                   /id="PRO_0000423328"
SQ   SEQUENCE   218 AA;  24901 MW;  C71F42D3F2DB8BB8 CRC64;
     MEGKGKEIVV GHSISKSSVE CHKYYLARRT TMEMLRDRGY DVSDEDINLS LQQFRALYGE
     HPDVDLLRIS AKHRFDSSKK ISVVFCGTGI VKVNAMRVIA ADVLSRENIT GLILVLQSHI
     TNQALKAVEL FSFKVELFEI TDLLVNVSKH VLRPKHQVLN DKEKESLLKK FSIEEKQLPR
     LSSKDPIVRY YGLETGQVMK VTYKDELSES HVTYRCVS