NRPBC_ARATH
ID NRPBC_ARATH Reviewed; 51 AA.
AC Q9FLM8;
DT 18-SEP-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 126.
DE RecName: Full=DNA-directed RNA polymerases II, IV and V subunit 12;
DE AltName: Full=DNA-directed RNA Polymerase II subunit K;
GN Name=NRPB12; Synonyms=NRPD12, NRPE12; OrderedLocusNames=At5g41010;
GN ORFNames=MEE6.8;
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=9628582; DOI=10.1093/dnares/5.1.41;
RA Sato S., Kaneko T., Kotani H., Nakamura Y., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. IV. Sequence
RT features of the regions of 1,456,315 bp covered by nineteen physically
RT assigned P1 and TAC clones.";
RL DNA Res. 5:41-54(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 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 [6]
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 [7]
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 Associates with the mediator complex. Interacts with NRPD1.
CC {ECO:0000269|PubMed:17560376, ECO:0000269|PubMed:19110459,
CC ECO:0000269|PubMed:21811420}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the archaeal Rpo12/eukaryotic RPC10 RNA
CC polymerase subunit family. {ECO:0000305}.
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DR EMBL; AB010072; BAB09703.1; -; Genomic_DNA.
DR EMBL; CP002688; AED94625.1; -; Genomic_DNA.
DR EMBL; AY045954; AAK76628.1; -; mRNA.
DR EMBL; AY079307; AAL85038.1; -; mRNA.
DR EMBL; AY084743; AAM67289.1; -; mRNA.
DR RefSeq; NP_198917.1; NM_123466.3.
DR PDB; 7EU0; EM; 3.16 A; L=1-51.
DR PDB; 7EU1; EM; 3.86 A; L=1-51.
DR PDBsum; 7EU0; -.
DR PDBsum; 7EU1; -.
DR AlphaFoldDB; Q9FLM8; -.
DR SMR; Q9FLM8; -.
DR BioGRID; 19354; 2.
DR IntAct; Q9FLM8; 1.
DR STRING; 3702.AT5G41010.1; -.
DR PaxDb; Q9FLM8; -.
DR PRIDE; Q9FLM8; -.
DR ProteomicsDB; 249450; -.
DR EnsemblPlants; AT5G41010.1; AT5G41010.1; AT5G41010.
DR GeneID; 834103; -.
DR Gramene; AT5G41010.1; AT5G41010.1; AT5G41010.
DR KEGG; ath:AT5G41010; -.
DR Araport; AT5G41010; -.
DR TAIR; locus:2163051; AT5G41010.
DR eggNOG; KOG3507; Eukaryota.
DR HOGENOM; CLU_179456_1_1_1; -.
DR InParanoid; Q9FLM8; -.
DR OMA; VIRCREC; -.
DR OrthoDB; 1620152at2759; -.
DR PhylomeDB; Q9FLM8; -.
DR PRO; PR:Q9FLM8; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FLM8; baseline and differential.
DR Genevisible; Q9FLM8; 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:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0003899; F:DNA-directed 5'-3' RNA polymerase activity; IEA:InterPro.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0006351; P:transcription, DNA-templated; IEA:InterPro.
DR InterPro; IPR006591; RNAP_P/RPABC4.
DR InterPro; IPR039747; RPABC4.
DR InterPro; IPR029040; RPABC4/Spt4.
DR PANTHER; PTHR12056; PTHR12056; 1.
DR Pfam; PF03604; DNA_RNApol_7kD; 1.
DR SMART; SM00659; RPOLCX; 1.
DR SUPFAM; SSF63393; SSF63393; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA-directed RNA polymerase; Metal-binding; Nucleus;
KW Reference proteome; Transcription; Zinc.
FT CHAIN 1..51
FT /note="DNA-directed RNA polymerases II, IV and V subunit
FT 12"
FT /id="PRO_0000423320"
FT BINDING 12
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 15
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 29
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 32
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT STRAND 10..15
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 36..39
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 46..49
FT /evidence="ECO:0007829|PDB:7EU0"
SQ SEQUENCE 51 AA; 5897 MW; B3B32CFFC943AE5A CRC64;
MDPAPEPVTY VCGDCGQENT LKSGDVIQCR ECGYRILYKK RTRRVVQYEA R
