RPD2B_ARATH
ID RPD2B_ARATH Reviewed; 1119 AA.
AC Q9LV32; Q1ANE6;
DT 03-MAY-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=DNA-directed RNA polymerase D subunit 2b;
DE Short=AtNRPD2b;
DE Short=Nuclear RNA polymerase D 2b;
DE EC=2.7.7.6;
DE AltName: Full=RNA polymerase IV subunit 2b;
DE Short=POL IV 2b;
GN Name=NRPD2b; Synonyms=RPD2b; OrderedLocusNames=At3g18090; ORFNames=MRC8.7;
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] (ISOFORM 2).
RX PubMed=16140984; DOI=10.1101/gad.348405;
RA Pontier D., Yahubyan G., Vega D., Bulski A., Saez-Vasquez J., Hakimi M.-A.,
RA Lerbs-Mache S., Colot V., Lagrange T.;
RT "Reinforcement of silencing at transposons and highly repeated sequences
RT requires the concerted action of two distinct RNA polymerases IV in
RT Arabidopsis.";
RL Genes Dev. 19:2030-2040(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10907853; DOI=10.1093/dnares/7.3.217;
RA Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence
RT features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC
RT clones.";
RL DNA Res. 7:217-221(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 [MRNA] OF 787-1119 (ISOFORM 1/2).
RX PubMed=17160640; DOI=10.1007/s00239-006-0093-z;
RA Luo J., Hall B.D.;
RT "A multistep process gave rise to RNA polymerase IV of land plants.";
RL J. Mol. Evol. 64:101-112(2007).
RN [5]
RP FUNCTION.
RC STRAIN=cv. Columbia;
RX PubMed=17360559; DOI=10.1073/pnas.0611456104;
RA Zhang X., Henderson I.R., Lu C., Green P.J., Jacobsen S.E.;
RT "Role of RNA polymerase IV in plant small RNA metabolism.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:4536-4541(2007).
CC -!- FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription of
CC DNA into RNA using the four ribonucleoside triphosphates as substrates.
CC Second largest component of RNA polymerase IVa and IVb which mediate
CC short-interfering RNAs (siRNA) accumulation and subsequent RNA-directed
CC DNA methylation-dependent (RdDM) silencing of endogenous repeated
CC sequences, including transposable largest subunit. Also required for
CC full erasure of methylation elements. Required for intercellular RNA
CC interference (RNAi) leading to systemic post-transcriptional gene
CC silencing (Probable). {ECO:0000305|PubMed:17360559}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate +
CC RNA(n+1); Xref=Rhea:RHEA:21248, Rhea:RHEA-COMP:14527, Rhea:RHEA-
CC COMP:17342, ChEBI:CHEBI:33019, ChEBI:CHEBI:61557, ChEBI:CHEBI:140395;
CC EC=2.7.7.6;
CC -!- SUBUNIT: Component of the RNA polymerase IVa and IVb (Pol IV)
CC complexes. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9LV32-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9LV32-2; Sequence=VSP_040974;
CC -!- SIMILARITY: Belongs to the RNA polymerase beta chain family.
CC {ECO:0000305}.
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DR EMBL; AY935712; -; NOT_ANNOTATED_CDS; mRNA.
DR EMBL; AB020749; BAB02021.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE76045.1; -; Genomic_DNA.
DR EMBL; DQ029109; AAY82004.1; -; mRNA.
DR RefSeq; NP_188437.2; NM_112691.4. [Q9LV32-2]
DR AlphaFoldDB; Q9LV32; -.
DR SMR; Q9LV32; -.
DR BioGRID; 6667; 35.
DR PaxDb; Q9LV32; -.
DR PeptideAtlas; Q9LV32; -.
DR PRIDE; Q9LV32; -.
DR ProteomicsDB; 226919; -. [Q9LV32-1]
DR EnsemblPlants; AT3G18090.1; AT3G18090.1; AT3G18090. [Q9LV32-2]
DR GeneID; 821334; -.
DR Gramene; AT3G18090.1; AT3G18090.1; AT3G18090. [Q9LV32-2]
DR KEGG; ath:AT3G18090; -.
DR Araport; AT3G18090; -.
DR TAIR; locus:2092682; AT3G18090.
DR eggNOG; KOG0214; Eukaryota.
DR HOGENOM; CLU_000524_5_2_1; -.
DR InParanoid; Q9LV32; -.
DR OMA; MPIWLMF; -.
DR OrthoDB; 42570at2759; -.
DR PhylomeDB; Q9LV32; -.
DR PRO; PR:Q9LV32; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LV32; baseline and differential.
DR Genevisible; Q9LV32; AT.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0005665; C:RNA polymerase II, core complex; IBA:GO_Central.
DR GO; GO:0000418; C:RNA polymerase IV complex; ISS:UniProtKB.
DR GO; GO:0000419; C:RNA polymerase V complex; ISS:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0003899; F:DNA-directed 5'-3' RNA polymerase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0032549; F:ribonucleoside binding; IEA:InterPro.
DR GO; GO:0006351; P:transcription, DNA-templated; IEA:InterPro.
DR CDD; cd00653; RNA_pol_B_RPB2; 1.
DR Gene3D; 2.40.270.10; -; 1.
DR Gene3D; 2.40.50.150; -; 1.
DR Gene3D; 3.90.1110.10; -; 1.
DR InterPro; IPR015712; DNA-dir_RNA_pol_su2.
DR InterPro; IPR007120; DNA-dir_RNAP_su2_dom.
DR InterPro; IPR037033; DNA-dir_RNAP_su2_hyb_sf.
DR InterPro; IPR007121; RNA_pol_bsu_CS.
DR InterPro; IPR007644; RNA_pol_bsu_protrusion.
DR InterPro; IPR007642; RNA_pol_Rpb2_2.
DR InterPro; IPR037034; RNA_pol_Rpb2_2_sf.
DR InterPro; IPR007645; RNA_pol_Rpb2_3.
DR InterPro; IPR007646; RNA_pol_Rpb2_4.
DR InterPro; IPR007647; RNA_pol_Rpb2_5.
DR InterPro; IPR007641; RNA_pol_Rpb2_7.
DR InterPro; IPR014724; RNA_pol_RPB2_OB-fold.
DR PANTHER; PTHR20856; PTHR20856; 2.
DR Pfam; PF04563; RNA_pol_Rpb2_1; 1.
DR Pfam; PF04561; RNA_pol_Rpb2_2; 1.
DR Pfam; PF04565; RNA_pol_Rpb2_3; 1.
DR Pfam; PF04566; RNA_pol_Rpb2_4; 1.
DR Pfam; PF04567; RNA_pol_Rpb2_5; 1.
DR Pfam; PF00562; RNA_pol_Rpb2_6; 1.
DR Pfam; PF04560; RNA_pol_Rpb2_7; 1.
DR PROSITE; PS01166; RNA_POL_BETA; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; DNA-directed RNA polymerase; Magnesium;
KW Metal-binding; Nucleotidyltransferase; Nucleus; Reference proteome;
KW Transcription; Transcription regulation; Transferase; Zinc; Zinc-finger.
FT CHAIN 1..1119
FT /note="DNA-directed RNA polymerase D subunit 2b"
FT /id="PRO_0000407925"
FT ZN_FING 1055..1083
FT /note="C4-type"
FT /evidence="ECO:0000250"
FT BINDING 732
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="ligand shared with RPB1"
FT /evidence="ECO:0000250"
FT BINDING 1055
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 1058
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 1080
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 1083
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT VAR_SEQ 1..85
FT /note="MDVDEIESAGQINISELGESFLQTFCKKAATSFFEEFGLISHQLNSYNFFIE
FT HGLQNVFESFGDILVEPSFDVIKKKDGDWRYAT -> MACRLQNMTYSARIKVNAQVE
FT (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:16140984"
FT /id="VSP_040974"
SQ SEQUENCE 1119 AA; 126262 MW; 101274921C4CC810 CRC64;
MDVDEIESAG QINISELGES FLQTFCKKAA TSFFEEFGLI SHQLNSYNFF IEHGLQNVFE
SFGDILVEPS FDVIKKKDGD WRYATVFKKI VIKHDKFKTG QDEYVEKEIL DVKKQDILIG
SIPVMVKSVL CKTSEKGKEN CKKGNCAFDQ GGYFVIKGAE KVFIAQEQMC TKRLWISNSP
WTVSFRSETK RNRFIVRLSE NEKAEDYKIM EKVLTVYFLS TEIPVWLLFF ALGVSSDKEA
MDLIAFDGDD ASITNSLIAS IHEADAVCEA FRCGNNALTY VEHQIKSTKF PPAESVDDCL
RLYLFPCLQG LKKKARFLGY MVKCLLSAYA GKRKCENRDS FRNKRIELAG ELLEREIRVH
LAHARRKMTR AMQKQLSGDG DLKPIEHYLD ASVITNGLNR AFSTGAWSHP FRKMERVSGV
VANLGRANPL QTLIDLRRTR QQVLYTGKVG DARHPHPSHW GRVCFLSTPD GENCGLVKNM
SLLGLVSTQG LESVVEMLFT CGMEELMNDT STPLCGKHKV LLNGDWVGLC ADSESFVGEL
KSRRRQSELP LEMEIKRDKD DNEVRIFTDA GRLLRPLLVV ENLHKLKQDK PTQYPFKHLL
DQGILELIGI EEEEDCTTAW GIKQLLKEPK NYTHCELDLS FLLGVSCAIV PFANHDHGKR
VLYQSQKHCQ QAIGFSSTNP NIRCDTLSQQ LFYPQKPLFK TLASECLEKE VLFNGQNAIV
AVNVHLGYNQ EDSIVMNKAS LERGMFRSEQ IRSYKAEVDT KDSEKRKKMD ELVQFGKTYS
KIGKVDSLED DGFPFIGANM STGDIVIGRC TESGADHSIK LKHTERGIVQ KVVLSSNDEG
KNFAAVSLRQ VRSPCLGDKF SSMHGQKGVL GYLEEQQNFP FTIQGIVPDI VINPHAFPSR
QTPGQLLEAA LSKGIACPIQ KKEGSSAAYT KLTRHATPFS TPGVTEITEQ LHRAGFSRWG
NERVYNGRSG EMMRSLIFMG PTFYQRLVHM SENKVKFRNT GPVHPLTRQP VADRKRFGGI
RFGEMERDCL IAHGASANLH ERLFTLSDSS QMHICRKCKT YANVIERTPS SGRKIRGPYC
RVCASSDHVV RVYVPYGAKL LCQELFSMGI TLNFDTKLC
