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Protein

DNA-directed RNA polymerases IV and V subunit 2

Gene

NRPD2

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerases IV and V which mediate short-interfering RNAs (siRNA) accumulation and subsequent RNA-directed DNA methylation-dependent (RdDM) transcriptional gene silencing (TGS) of endogenous repeated sequences, including transposable elements. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Also required for full erasure of methylation when the RNA trigger is withdrawn. Required for intercellular RNA interference (RNAi) leading to systemic post-transcriptional gene silencing. Involved in the maintenance of post-transcriptional RNA silencing. During interphase, mediates siRNA-independent heterochromatin association and methylation into chromocenters and condensation and cytosine methylation at pericentromeric major repeats. Required for complete maintenance of the 35S promoter homology-dependent TGS in transgenic plants and for the initial establishment of DNA methylation.12 Publications

Catalytic activityi

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi786Magnesium; shared with RPB1By similarity1
Metal bindingi1108ZincBy similarity1
Metal bindingi1111ZincBy similarity1
Metal bindingi1133ZincBy similarity1
Metal bindingi1136ZincBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri1108 – 1136C4-typeBy similarityAdd BLAST29

GO - Molecular functioni

  • DNA binding Source: InterPro
  • DNA-directed 5'-3' RNA polymerase activity Source: TAIR
  • metal ion binding Source: UniProtKB-KW
  • ribonucleoside binding Source: InterPro

GO - Biological processi

  • defense response to fungus Source: TAIR
  • DNA methylation Source: TAIR
  • gene silencing by RNA Source: TAIR
  • posttranscriptional gene silencing by RNA Source: TAIR
  • production of siRNA involved in RNA interference Source: TAIR
  • regulation of immune response Source: TAIR
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • transcription from RNA polymerase I promoter Source: GOC

Keywordsi

Molecular functionNucleotidyltransferase, Transferase
Biological processTranscription, Transcription regulation
LigandMagnesium, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed RNA polymerases IV and V subunit 2 (EC:2.7.7.6)
Alternative name(s):
DNA-directed RNA polymerase D subunit 2a
Short name:
AtNRPD2a
Short name:
Nuclear RNA polymerase D 2a
Nuclear RNA polymerase E 2
Protein DEFECTIVE IN MERISTEM SILENCING 2
Protein DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 2
RNA polymerase IV subunit 2a
Short name:
POL IV 2a
Gene namesi
Name:NRPD2
Synonyms:DMS2, DRD2, NRPD2a, NRPE2, RPD2a
Ordered Locus Names:At3g23780
ORF Names:MYM9.13
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 3

Organism-specific databases

AraportiAT3G23780.
TAIRilocus:2095233. AT3G23780.

Subcellular locationi

GO - Cellular componenti

  • DNA-directed RNA polymerase I complex Source: GO_Central
  • DNA-directed RNA polymerase IV complex Source: UniProtKB
  • DNA-directed RNA polymerase V complex Source: UniProtKB
  • nuclear heterochromatin Source: TAIR
  • nucleus Source: UniProtKB

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

Pathology & Biotechi

Disruption phenotypei

Blocked in the perpetuation of CNN, CG and CNG methylation in repeated endogenous DNA. Reduction of heterochromatin association and methylation into chromocenters, coincident with decondensation and losses in cytosine methylation at pericentromeric major repeats such as 5S gene clusters and AtSN1 retroelements during interphase, independently of siRNA accumulation. Altered cell-to-cell movement of siRNA beyond the vasculature. Reduced 35S promoter homology-dependent transcriptional gene silencing (TGS) in transgenic plants.10 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi629R → Q in nrpd/e2-19; decreased DNA methylation. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004079241 – 1172DNA-directed RNA polymerases IV and V subunit 2Add BLAST1172

Proteomic databases

PaxDbiQ9LK40.
PRIDEiQ9LK40.

Expressioni

Tissue specificityi

Mostly expressed in seedlings, flowers and roots, present ubiquitously, except in sperm cells.2 Publications

Gene expression databases

ExpressionAtlasiQ9LK40. baseline and differential.
GenevisibleiQ9LK40. AT.

Interactioni

Subunit structurei

Component of the RNA polymerase IV and V complexes. Interacts with SSH1, NRPD1 and NRPE1.5 Publications

Protein-protein interaction databases

BioGridi7292. 6 interactors.
STRINGi3702.AT3G23780.1.

Structurei

3D structure databases

ProteinModelPortaliQ9LK40.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RNA polymerase beta chain family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri1108 – 1136C4-typeBy similarityAdd BLAST29

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG0214. Eukaryota.
COG0085. LUCA.
HOGENOMiHOG000222962.
InParanoidiQ9LK40.
KOiK16252.
OMAiTRQWVAY.
OrthoDBiEOG093600LD.
PhylomeDBiQ9LK40.

Family and domain databases

CDDicd00653. RNA_pol_B_RPB2. 1 hit.
Gene3Di2.40.270.10. 1 hit.
InterProiView protein in InterPro
IPR015712. DNA-dir_RNA_pol_su2.
IPR007120. DNA-dir_RNA_pol_su2_6.
IPR007121. RNA_pol_bsu_CS.
IPR007644. RNA_pol_bsu_protrusion.
IPR007642. RNA_pol_Rpb2_2.
IPR007645. RNA_pol_Rpb2_3.
IPR007646. RNA_pol_Rpb2_4.
IPR007647. RNA_pol_Rpb2_5.
IPR007641. RNA_pol_Rpb2_7.
PANTHERiPTHR20856. PTHR20856. 1 hit.
PfamiView protein in Pfam
PF04563. RNA_pol_Rpb2_1. 1 hit.
PF04561. RNA_pol_Rpb2_2. 1 hit.
PF04565. RNA_pol_Rpb2_3. 1 hit.
PF04566. RNA_pol_Rpb2_4. 1 hit.
PF04567. RNA_pol_Rpb2_5. 1 hit.
PF00562. RNA_pol_Rpb2_6. 1 hit.
PF04560. RNA_pol_Rpb2_7. 1 hit.
PROSITEiView protein in PROSITE
PS01166. RNA_POL_BETA. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9LK40-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPDMDIDVKD LEEFEATTGE INLSELGEGF LQSFCKKAAT SFFDKYGLIS
60 70 80 90 100
HQLNSYNYFI EHGLQNVFQS FGEMLVEPSF DVVKKKDNDW RYATVKFGEV
110 120 130 140 150
TVEKPTFFSD DKELEFLPWH ARLQNMTYSA RIKVNVQVEV FKNTVVKSDK
160 170 180 190 200
FKTGQDNYVE KKILDVKKQD ILIGSIPVMV KSILCKTSEK GKENCKKGDC
210 220 230 240 250
AFDQGGYFVI KGAEKVFIAQ EQMCTKRLWI SNSPWTVSFR SENKRNRFIV
260 270 280 290 300
RLSENEKAED YKRREKVLTV YFLSTEIPVW LLFFALGVSS DKEAMDLIAF
310 320 330 340 350
DGDDASITNS LIASIHVADA VCEAFRCGNN ALTYVEQQIK STKFPPAESV
360 370 380 390 400
DECLHLYLFP GLQSLKKKAR FLGYMVKCLL NSYAGKRKCE NRDSFRNKRI
410 420 430 440 450
ELAGELLERE IRVHLAHARR KMTRAMQKHL SGDGDLKPIE HYLDASVITN
460 470 480 490 500
GLSRAFSTGA WSHPFRKMER VSGVVANLGR ANPLQTLIDL RRTRQQVLYT
510 520 530 540 550
GKVGDARYPH PSHWGRVCFL STPDGENCGL VKNMSLLGLV STQSLESVVE
560 570 580 590 600
KLFACGMEEL MDDTCTPLFG KHKVLLNGDW VGLCADSESF VAELKSRRRQ
610 620 630 640 650
SELPREMEIK RDKDDNEVRI FTDAGRLLRP LLVVENLQKL KQEKPSQYPF
660 670 680 690 700
DHLLDHGILE LIGIEEEEDC NTAWGIKQLL KEPKIYTHCE LDLSFLLGVS
710 720 730 740 750
CAVVPFANHD HGRRVLYQSQ KHCQQAIGFS STNPNIRCDT LSQQLFYPQK
760 770 780 790 800
PLFKTLASEC LKKEVLFNGQ NAIVAVNVHL GYNQEDSIVM NKASLERGMF
810 820 830 840 850
RSEQIRSYKA EVDAKDSEKR KKMDELVQFG KTHSKIGKVD SLEDDGFPFI
860 870 880 890 900
GANMSTGDIV IGRCTESGAD HSIKLKHTER GIVQKVVLSS NDEGKNFAAV
910 920 930 940 950
SLRQVRSPCL GDKFSSMHGQ KGVLGYLEEQ QNFPFTIQGI VPDIVINPHA
960 970 980 990 1000
FPSRQTPGQL LEAALSKGIA CPIQKEGSSA AYTKLTRHAT PFSTPGVTEI
1010 1020 1030 1040 1050
TEQLHRAGFS RWGNERVYNG RSGEMMRSMI FMGPTFYQRL VHMSEDKVKF
1060 1070 1080 1090 1100
RNTGPVHPLT RQPVADRKRF GGIKFGEMER DCLIAHGASA NLHERLFTLS
1110 1120 1130 1140 1150
DSSQMHICRK CKTYANVIER TPSSGRKIRG PYCRVCVSSD HVVRVYVPYG
1160 1170
AKLLCQELFS MGITLNFDTK LC
Length:1,172
Mass (Da):132,654
Last modified:October 1, 2000 - v1
Checksum:iF007A39F04D19365
GO

Sequence cautioni

The sequence BAD43874 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti1170K → E in BAD43874 (Ref. 5) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY862891 mRNA. Translation: AAW56422.1.
AY935711 mRNA. Translation: AAX73261.1.
AP000377 Genomic DNA. Translation: BAB01854.1.
CP002686 Genomic DNA. Translation: AEE76812.1.
CP002686 Genomic DNA. Translation: AEE76813.1.
AK176111 mRNA. Translation: BAD43874.1. Different initiation.
RefSeqiNP_001189957.1. NM_001203028.2.
NP_189020.2. NM_113282.3.
UniGeneiAt.37653.

Genome annotation databases

EnsemblPlantsiAT3G23780.1; AT3G23780.1; AT3G23780.
AT3G23780.2; AT3G23780.2; AT3G23780.
GeneIDi821960.
GrameneiAT3G23780.1; AT3G23780.1; AT3G23780.
AT3G23780.2; AT3G23780.2; AT3G23780.
KEGGiath:AT3G23780.

Similar proteinsi

Entry informationi

Entry nameiNRPD2_ARATH
AccessioniPrimary (citable) accession number: Q9LK40
Secondary accession number(s): Q67ZK6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 3, 2011
Last sequence update: October 1, 2000
Last modified: June 7, 2017
This is version 127 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families