RPB5A_ARATH
ID RPB5A_ARATH Reviewed; 205 AA.
AC O81098;
DT 18-SEP-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1998, sequence version 1.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=DNA-directed RNA polymerases II and IV subunit 5A;
DE Short=RPB5a;
DE AltName: Full=DNA-directed RNA polymerase II subunit E;
DE AltName: Full=RNA polymerase I, II and III 24.3 kDa subunit;
DE Short=AtRPB24.3;
GN Name=NRPB5A; Synonyms=NRPD5A, RPABC24.3; OrderedLocusNames=At3g22320;
GN ORFNames=MCB17.4, MCB17_5;
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 [MRNA], AND SUBCELLULAR LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=10231567; DOI=10.1016/s0378-1119(99)00090-6;
RA Larkin R.M., Hagen G., Guilfoyle T.J.;
RT "Arabidopsis thaliana RNA polymerase II subunits related to yeast and human
RT RPB5.";
RL Gene 231:41-47(1999).
RN [2]
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 [3]
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 [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 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 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 [8]
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 polymerase IV which mediates short-interfering RNAs (siRNA)
CC accumulation and subsequent RNA-directed DNA methylation-dependent
CC (RdDM) transcriptional gene silencing (TGS) of target sequences.
CC {ECO:0000269|PubMed:19110459}.
CC -!- SUBUNIT: Component of the RNA polymerases II and IV complexes.
CC Interacts with NRPD1. {ECO:0000269|PubMed:19110459,
CC ECO:0000269|PubMed:21811420}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:10231567}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, leaves and seeds, and to a
CC lower level, in flower buds, flowers and siliques.
CC {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; AF019248; AAC28253.1; -; mRNA.
DR EMBL; AB022215; BAB01769.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE76621.1; -; Genomic_DNA.
DR EMBL; AF370551; AAK48978.1; -; mRNA.
DR EMBL; AF412101; AAL06554.1; -; mRNA.
DR EMBL; AY086150; AAM63355.1; -; mRNA.
DR EMBL; BT002130; AAN72141.1; -; mRNA.
DR PIR; T51950; T51950.
DR RefSeq; NP_188871.1; NM_113130.4.
DR PDB; 7EU0; EM; 3.16 A; E=1-205.
DR PDB; 7EU1; EM; 3.86 A; E=1-205.
DR PDBsum; 7EU0; -.
DR PDBsum; 7EU1; -.
DR AlphaFoldDB; O81098; -.
DR SMR; O81098; -.
DR BioGRID; 7133; 58.
DR DIP; DIP-48677N; -.
DR IntAct; O81098; 3.
DR STRING; 3702.AT3G22320.1; -.
DR PaxDb; O81098; -.
DR PRIDE; O81098; -.
DR ProteomicsDB; 227958; -.
DR EnsemblPlants; AT3G22320.1; AT3G22320.1; AT3G22320.
DR GeneID; 821801; -.
DR Gramene; AT3G22320.1; AT3G22320.1; AT3G22320.
DR KEGG; ath:AT3G22320; -.
DR Araport; AT3G22320; -.
DR TAIR; locus:2087842; AT3G22320.
DR eggNOG; KOG3218; Eukaryota.
DR HOGENOM; CLU_058320_0_1_1; -.
DR InParanoid; O81098; -.
DR OMA; CYFADES; -.
DR OrthoDB; 1255823at2759; -.
DR PhylomeDB; O81098; -.
DR PRO; PR:O81098; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; O81098; baseline and differential.
DR Genevisible; O81098; 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:0006351; P:transcription, DNA-templated; IEA:InterPro.
DR Gene3D; 3.40.1340.10; -; 1.
DR Gene3D; 3.90.940.20; -; 1.
DR HAMAP; MF_00025; RNApol_Rpo5_RPB5; 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; IPR020608; RNA_pol_subH/Rpb5_CS.
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.
DR PROSITE; PS01110; RNA_POL_H_23KD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA-directed RNA polymerase; Nucleus; Reference proteome;
KW Transcription.
FT CHAIN 1..205
FT /note="DNA-directed RNA polymerases II and IV subunit 5A"
FT /id="PRO_0000423326"
FT HELIX 4..24
FT /evidence="ECO:0007829|PDB:7EU0"
FT HELIX 30..33
FT /evidence="ECO:0007829|PDB:7EU0"
FT HELIX 37..41
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 55..58
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 63..70
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 73..76
FT /evidence="ECO:0007829|PDB:7EU0"
FT HELIX 79..91
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 96..103
FT /evidence="ECO:0007829|PDB:7EU0"
FT TURN 107..109
FT /evidence="ECO:0007829|PDB:7EU0"
FT HELIX 112..115
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 121..126
FT /evidence="ECO:0007829|PDB:7EU0"
FT TURN 127..130
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 134..140
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 142..145
FT /evidence="ECO:0007829|PDB:7EU0"
FT HELIX 148..158
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 162..165
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 167..169
FT /evidence="ECO:0007829|PDB:7EU0"
FT HELIX 173..177
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 185..190
FT /evidence="ECO:0007829|PDB:7EU0"
FT STRAND 198..205
FT /evidence="ECO:0007829|PDB:7EU0"
SQ SEQUENCE 205 AA; 24301 MW; 97933DEA098076C3 CRC64;
MLTEEELKRL YRIQKTLMQM LRDRGYFIAD SELTMTKQQF IRKHGDNMKR EDLVTLKAKR
NDNSDQLYIF FPDEAKVGVK TMKMYTNRMK SENVFRAILV VQQNLTPFAR TCISEISSKF
HLEVFQEAEM LVNIKEHVLV PEHQVLTTEE KKTLLERYTV KETQLPRIQV TDPIARYFGL
KRGQVVKIIR PSETAGRYVT YRYVV
