ID   RPB9A_ARATH             Reviewed;         114 AA.
AC   Q6NLH0;
DT   18-SEP-2013, integrated into UniProtKB/Swiss-Prot.
DT   05-JUL-2004, sequence version 1.
DT   03-AUG-2022, entry version 125.
DE   RecName: Full=DNA-directed RNA polymerases II, IV and V subunit 9A;
GN   Name=NRPB9A; Synonyms=NRPE9A; OrderedLocusNames=At3g16980; ORFNames=K14A17;
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=10819329; DOI=10.1093/dnares/7.2.131;
RA   Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT   "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT   features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT   clones.";
RL   DNA Res. 7:131-135(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].
RA   Shinn P., Chen H., Cheuk R., Kim C.J., Ecker J.R.;
RT   "Arabidopsis ORF clones.";
RL   Submitted (APR-2004) to the EMBL/GenBank/DDBJ databases.
RN   [4]
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   [5]
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   [6]
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RX   PubMed=22550619; DOI=10.1016/j.celrep.2012.01.004;
RA   Tan E.H., Blevins T., Ream T.S., Pikaard C.S.;
RT   "Functional consequences of subunit diversity in RNA polymerases II and
RT   V.";
RL   Cell Rep. 1:208-214(2012).
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. Required for RNA silencing.
CC       {ECO:0000269|PubMed:19110459, ECO:0000269|PubMed:22550619}.
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       Q6NLH0; Q84MB2: TIFY8; NbExp=4; IntAct=EBI-2130783, EBI-4426557;
CC   -!- SUBCELLULAR LOCATION: Nucleus, nucleolus
CC       {ECO:0000250|UniProtKB:P32529}.
CC   -!- DISRUPTION PHENOTYPE: No visible phenotype; due to the redundancy with
CC       NRPB9B. No effect on methylation at RdDM target sites. Nrpb9a and
CC       nrpb9b double mutants are embryo lethal. {ECO:0000269|PubMed:22550619}.
CC   -!- MISCELLANEOUS: Pol IV and V functions are not impaired in nrpb9a
CC       mutants and Pol II functions are complemented by NRPB9B.
CC       {ECO:0000305|PubMed:22550619}.
CC   -!- SIMILARITY: Belongs to the archaeal RpoM/eukaryotic RPA12/RPB9/RPC11
CC       RNA polymerase 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; AB026636; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; CP002686; AEE75891.1; -; Genomic_DNA.
DR   EMBL; BT012109; AAS76204.1; -; mRNA.
DR   EMBL; BT012363; AAS88753.1; -; mRNA.
DR   RefSeq; NP_188323.1; NM_112574.3.
DR   PDB; 7EU0; EM; 3.16 A; I=1-114.
DR   PDB; 7EU1; EM; 3.86 A; I=1-114.
DR   PDBsum; 7EU0; -.
DR   PDBsum; 7EU1; -.
DR   AlphaFoldDB; Q6NLH0; -.
DR   SMR; Q6NLH0; -.
DR   BioGRID; 6287; 40.
DR   IntAct; Q6NLH0; 16.
DR   STRING; 3702.AT3G16980.1; -.
DR   PaxDb; Q6NLH0; -.
DR   PRIDE; Q6NLH0; -.
DR   ProteomicsDB; 227964; -.
DR   EnsemblPlants; AT3G16980.1; AT3G16980.1; AT3G16980.
DR   GeneID; 820954; -.
DR   Gramene; AT3G16980.1; AT3G16980.1; AT3G16980.
DR   KEGG; ath:AT3G16980; -.
DR   Araport; AT3G16980; -.
DR   TAIR; locus:2086042; AT3G16980.
DR   eggNOG; KOG2691; Eukaryota.
DR   HOGENOM; CLU_093932_0_1_1; -.
DR   InParanoid; Q6NLH0; -.
DR   OMA; EVADNSC; -.
DR   OrthoDB; 1421187at2759; -.
DR   PhylomeDB; Q6NLH0; -.
DR   PRO; PR:Q6NLH0; -.
DR   Proteomes; UP000006548; Chromosome 3.
DR   ExpressionAtlas; Q6NLH0; baseline and differential.
DR   Genevisible; Q6NLH0; AT.
DR   GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
DR   GO; GO:0005665; C:RNA polymerase II, core complex; IDA:UniProtKB.
DR   GO; GO:0000419; C:RNA polymerase V complex; IDA:UniProtKB.
DR   GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
DR   GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR   GO; GO:0001193; P:maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter; IBA:GO_Central.
DR   GO; GO:0006379; P:mRNA cleavage; IEA:InterPro.
DR   GO; GO:0006367; P:transcription initiation from RNA polymerase II promoter; IBA:GO_Central.
DR   GO; GO:0006283; P:transcription-coupled nucleotide-excision repair; IBA:GO_Central.
DR   CDD; cd10508; Zn-ribbon_RPB9; 1.
DR   InterPro; IPR019761; DNA-dir_RNA_pol-M_15_CS.
DR   InterPro; IPR001529; DNA-dir_RNA_pol_M/15kDasu.
DR   InterPro; IPR012164; Rpa12/Rpb9/Rpc10/TFS.
DR   InterPro; IPR034012; Zn_ribbon_RPB9_C.
DR   InterPro; IPR001222; Znf_TFIIS.
DR   PANTHER; PTHR11239; PTHR11239; 1.
DR   Pfam; PF02150; RNA_POL_M_15KD; 1.
DR   Pfam; PF01096; TFIIS_C; 1.
DR   PIRSF; PIRSF005586; RNApol_RpoM; 1.
DR   SMART; SM00661; RPOL9; 1.
DR   SMART; SM00440; ZnF_C2C2; 1.
DR   PROSITE; PS01030; RNA_POL_M_15KD; 1.
DR   PROSITE; PS51133; ZF_TFIIS_2; 1.
PE   1: Evidence at protein level;
KW   3D-structure; DNA-directed RNA polymerase; Metal-binding; Nucleus;
KW   Reference proteome; Transcription; Zinc; Zinc-finger.
FT   CHAIN           1..114
FT                   /note="DNA-directed RNA polymerases II, IV and V subunit
FT                   9A"
FT                   /id="PRO_0000423336"
FT   ZN_FING         72..113
FT                   /note="TFIIS-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00472"
FT   BINDING         76
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00472"
FT   BINDING         79
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00472"
FT   BINDING         103
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00472"
FT   BINDING         108
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00472"
FT   STRAND          8..10
FT                   /evidence="ECO:0007829|PDB:7EU0"
FT   STRAND          12..19
FT                   /evidence="ECO:0007829|PDB:7EU0"
FT   TURN            20..23
FT                   /evidence="ECO:0007829|PDB:7EU0"
FT   STRAND          24..33
FT                   /evidence="ECO:0007829|PDB:7EU0"
FT   STRAND          35..37
FT                   /evidence="ECO:0007829|PDB:7EU0"
FT   STRAND          42..47
FT                   /evidence="ECO:0007829|PDB:7EU0"
FT   TURN            54..61
FT                   /evidence="ECO:0007829|PDB:7EU0"
FT   STRAND          77..79
FT                   /evidence="ECO:0007829|PDB:7EU0"
FT   STRAND          84..89
FT                   /evidence="ECO:0007829|PDB:7EU0"
FT   STRAND          92..96
FT                   /evidence="ECO:0007829|PDB:7EU0"
FT   STRAND          98..103
FT                   /evidence="ECO:0007829|PDB:7EU0"
FT   TURN            106..108
FT                   /evidence="ECO:0007829|PDB:7EU0"
FT   STRAND          111..113
FT                   /evidence="ECO:0007829|PDB:7EU0"
SQ   SEQUENCE   114 AA;  13276 MW;  B7A782CEA84B65A1 CRC64;
     MSTMKFCREC NNILYPKEDK EQKILLYACR NCDHQEVADN SCVYRNEVHH SVSERTQILT
     DVASDPTLPR TKAVRCSKCQ HREAVFFQAT ARGEEGMTLF FVCCNPNCGH RWRE