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DNA-directed RNA polymerase D subunit 2b (AtNRPD2b) (Nuclear RNA polymerase D 2b) (EC 2.7.7.6) (RNA polymerase IV subunit 2b) (POL IV 2b)

 RPD2B_ARATH             Reviewed;        1119 AA.
Q9LV32; Q1ANE6;
03-MAY-2011, integrated into UniProtKB/Swiss-Prot.
01-OCT-2000, sequence version 1.
10-OCT-2018, entry version 123.
RecName: Full=DNA-directed RNA polymerase D subunit 2b;
Short=AtNRPD2b;
Short=Nuclear RNA polymerase D 2b;
EC=2.7.7.6;
AltName: Full=RNA polymerase IV subunit 2b;
Short=POL IV 2b;
Name=NRPD2b; Synonyms=RPD2b; OrderedLocusNames=At3g18090;
ORFNames=MRC8.7;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
PubMed=16140984; DOI=10.1101/gad.348405;
Pontier D., Yahubyan G., Vega D., Bulski A., Saez-Vasquez J.,
Hakimi M.-A., Lerbs-Mache S., Colot V., Lagrange T.;
"Reinforcement of silencing at transposons and highly repeated
sequences requires the concerted action of two distinct RNA
polymerases IV in Arabidopsis.";
Genes Dev. 19:2030-2040(2005).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10907853; DOI=10.1093/dnares/7.3.217;
Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.;
"Structural analysis of Arabidopsis thaliana chromosome 3. II.
Sequence features of the 4,251,695 bp regions covered by 90 P1, TAC
and BAC clones.";
DNA Res. 7:217-221(2000).
[3]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[4]
NUCLEOTIDE SEQUENCE [MRNA] OF 787-1119 (ISOFORM 1/2).
PubMed=17160640; DOI=10.1007/s00239-006-0093-z;
Luo J., Hall B.D.;
"A multistep process gave rise to RNA polymerase IV of land plants.";
J. Mol. Evol. 64:101-112(2007).
[5]
FUNCTION.
STRAIN=cv. Columbia;
PubMed=17360559; DOI=10.1073/pnas.0611456104;
Zhang X., Henderson I.R., Lu C., Green P.J., Jacobsen S.E.;
"Role of RNA polymerase IV in plant small RNA metabolism.";
Proc. Natl. Acad. Sci. U.S.A. 104:4536-4541(2007).
-!- FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription
of DNA into RNA using the four ribonucleoside triphosphates as
substrates. Second largest component of RNA polymerase IVa and IVb
which mediate short-interfering RNAs (siRNA) accumulation and
subsequent RNA-directed DNA methylation-dependent (RdDM) silencing
of endogenous repeated sequences, including transposable largest
subunit. Also required for full erasure of methylation elements.
Required for intercellular RNA interference (RNAi) leading to
systemic post-transcriptional gene silencing (Probable).
{ECO:0000305|PubMed:17360559}.
-!- CATALYTIC ACTIVITY: Nucleoside triphosphate + RNA(n) = diphosphate
+ RNA(n+1).
-!- SUBUNIT: Component of the RNA polymerase IVa and IVb (Pol IV)
complexes. {ECO:0000250}.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q9LV32-1; Sequence=Displayed;
Note=Constructed according to the conserved gene model. No
experimental confirmation available.;
Name=2;
IsoId=Q9LV32-2; Sequence=VSP_040974;
Note=No experimental confirmation available.;
-!- SIMILARITY: Belongs to the RNA polymerase beta chain family.
{ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AY935712; -; NOT_ANNOTATED_CDS; mRNA.
EMBL; AB020749; BAB02021.1; -; Genomic_DNA.
EMBL; CP002686; AEE76045.1; -; Genomic_DNA.
EMBL; DQ029109; AAY82004.1; -; mRNA.
RefSeq; NP_188437.2; NM_112691.4. [Q9LV32-2]
UniGene; At.22852; -.
UniGene; At.53365; -.
ProteinModelPortal; Q9LV32; -.
SMR; Q9LV32; -.
STRING; 3702.AT3G18090.1; -.
PaxDb; Q9LV32; -.
PRIDE; Q9LV32; -.
EnsemblPlants; AT3G18090.1; AT3G18090.1; AT3G18090. [Q9LV32-2]
GeneID; 821334; -.
Gramene; AT3G18090.1; AT3G18090.1; AT3G18090. [Q9LV32-2]
KEGG; ath:AT3G18090; -.
Araport; AT3G18090; -.
TAIR; locus:2092682; AT3G18090.
eggNOG; KOG0214; Eukaryota.
eggNOG; COG0085; LUCA.
HOGENOM; HOG000222962; -.
InParanoid; Q9LV32; -.
KO; K16252; -.
OMA; IWLMFFA; -.
OrthoDB; EOG093600LD; -.
PhylomeDB; Q9LV32; -.
PRO; PR:Q9LV32; -.
Proteomes; UP000006548; Chromosome 3.
ExpressionAtlas; Q9LV32; baseline and differential.
Genevisible; Q9LV32; AT.
GO; GO:0016020; C:membrane; IDA:TAIR.
GO; GO:0005634; C:nucleus; ISS:UniProtKB.
GO; GO:0005736; C:RNA polymerase I complex; IBA:GO_Central.
GO; GO:0000418; C:RNA polymerase IV complex; ISS:UniProtKB.
GO; GO:0000419; C:RNA polymerase V complex; ISS:UniProtKB.
GO; GO:0003677; F:DNA binding; IEA:InterPro.
GO; GO:0003899; F:DNA-directed 5'-3' RNA polymerase activity; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0032549; F:ribonucleoside binding; IEA:InterPro.
GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:UniProtKB-KW.
GO; GO:0006360; P:transcription by RNA polymerase I; IEA:GOC.
CDD; cd00653; RNA_pol_B_RPB2; 1.
Gene3D; 2.40.270.10; -; 3.
Gene3D; 2.40.50.150; -; 2.
Gene3D; 3.90.1110.10; -; 1.
InterPro; IPR015712; DNA-dir_RNA_pol_su2.
InterPro; IPR007120; DNA-dir_RNAP_su2_dom.
InterPro; IPR037033; DNA-dir_RNAP_su2_hyb_sf.
InterPro; IPR007121; RNA_pol_bsu_CS.
InterPro; IPR007644; RNA_pol_bsu_protrusion.
InterPro; IPR007642; RNA_pol_Rpb2_2.
InterPro; IPR037034; RNA_pol_Rpb2_2_sf.
InterPro; IPR007645; RNA_pol_Rpb2_3.
InterPro; IPR007646; RNA_pol_Rpb2_4.
InterPro; IPR007647; RNA_pol_Rpb2_5.
InterPro; IPR007641; RNA_pol_Rpb2_7.
InterPro; IPR014724; RNA_pol_RPB2_OB-fold.
PANTHER; PTHR20856; PTHR20856; 1.
Pfam; PF04563; RNA_pol_Rpb2_1; 1.
Pfam; PF04561; RNA_pol_Rpb2_2; 1.
Pfam; PF04565; RNA_pol_Rpb2_3; 1.
Pfam; PF04566; RNA_pol_Rpb2_4; 1.
Pfam; PF04567; RNA_pol_Rpb2_5; 1.
Pfam; PF00562; RNA_pol_Rpb2_6; 1.
Pfam; PF04560; RNA_pol_Rpb2_7; 1.
PROSITE; PS01166; RNA_POL_BETA; 1.
2: Evidence at transcript level;
Alternative splicing; Complete proteome; DNA-directed RNA polymerase;
Magnesium; Metal-binding; Nucleotidyltransferase; Nucleus;
Reference proteome; Transcription; Transcription regulation;
Transferase; Zinc; Zinc-finger.
CHAIN 1 1119 DNA-directed RNA polymerase D subunit 2b.
/FTId=PRO_0000407925.
ZN_FING 1055 1083 C4-type. {ECO:0000250}.
METAL 732 732 Magnesium; shared with RPB1.
{ECO:0000250}.
METAL 1055 1055 Zinc. {ECO:0000250}.
METAL 1058 1058 Zinc. {ECO:0000250}.
METAL 1080 1080 Zinc. {ECO:0000250}.
METAL 1083 1083 Zinc. {ECO:0000250}.
VAR_SEQ 1 85 MDVDEIESAGQINISELGESFLQTFCKKAATSFFEEFGLIS
HQLNSYNFFIEHGLQNVFESFGDILVEPSFDVIKKKDGDWR
YAT -> MACRLQNMTYSARIKVNAQVE (in isoform
2). {ECO:0000303|PubMed:16140984}.
/FTId=VSP_040974.
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


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