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Protein

DNA-directed RNA polymerase V subunit 1

Gene

NRPE1

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. Largest and catalytic component of RNA polymerase V involved in RNA-directed DNA methylation-dependent (RdDM) silencing of endogenous repeated sequences, including transposable elements. Also required for full erasure of methylation when the RNA trigger is withdrawn. Seems also involved in the synthesis of short-interfering RNAs (siRNA). Essential component of a self-reinforcing loop coupling de novo DNA methylation to siRNA production. Involved in the maintenance of post-transcriptional RNA silencing.12 Publications

Catalytic activityi

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi57Zinc 1By similarity1
Metal bindingi60Zinc 1By similarity1
Metal bindingi68Zinc 1By similarity1
Metal bindingi71Zinc 1; via tele nitrogenBy similarity1
Metal bindingi98Zinc 2By similarity1
Metal bindingi101Zinc 2By similarity1
Metal bindingi449Magnesium; catalyticBy similarity1
Metal bindingi451Magnesium; catalyticBy similarity1
Metal bindingi453Magnesium; catalyticBy similarity1

GO - Molecular functioni

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

GO - Biological processi

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

Keywordsi

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

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed RNA polymerase V subunit 1
Alternative name(s):
DNA-directed RNA polymerase D subunit 1b
Short name:
AtNRPD1b
Short name:
Nuclear RNA polymerase D 1b
DNA-directed RNA polymerase E subunit 1 (EC:2.7.7.6)
Short name:
Nuclear RNA polymerase E 1
Protein DEFECTIVE IN MERISTEM SILENCING 5
Protein DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 3
Protein RNA-DIRECTED DNA METHYLATION DEFECTIVE 1
RNA polymerase IV subunit 1
Short name:
POL IV 1
Gene namesi
Name:NRPE1
Synonyms:DMS5, DRD3, NRPD1b, RMD1, RPE1
Ordered Locus Names:At2g40030
ORF Names:T28M21.19
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 2

Organism-specific databases

AraportiAT2G40030.
TAIRilocus:2061151. AT2G40030.

Subcellular locationi

GO - Cellular componenti

  • DNA-directed RNA polymerase III complex Source: GO_Central
  • DNA-directed RNA polymerase V complex Source: UniProtKB
  • nuclear body Source: TAIR
  • nucleolus 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 accompanied by a reduction in 24-nt siRNAs. Reduction of heterochromatin association into chromocenters, coincident with losses in cytosine methylation at pericentromeric 5S gene clusters and AtSN1 retroelements. Impaired RNA-directed DNA methylation-dependent (RdDM) silencing. Defective in the maintenance of post-transcriptional RNA silencing.9 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi49G → R in nrpe1-12; decreased DNA methylation. 1 Publication1
Mutagenesisi451D → N in nrpe1-3/drd3-3; loss of CNN DNA methylation, but no effect on interaction with NRPE5A. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004079231 – 1976DNA-directed RNA polymerase V subunit 1Add BLAST1976

Proteomic databases

PaxDbiQ5D869.

PTM databases

iPTMnetiQ5D869.

Expressioni

Tissue specificityi

Mostly expressed in flowers, and, to a lower extent, in leaves. Present in sperm cells.3 Publications

Gene expression databases

GenevisibleiQ5D869. AT.

Interactioni

Subunit structurei

Component of the RNA polymerase V complex. Interacts with NRPD4, NRPD2A, and (via C-terminus) with AGO4. Interacts with SUVH2.6 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
AGO4Q9ZVD53EBI-2352263,EBI-2352199

Protein-protein interaction databases

BioGridi3929. 23 interactors.
DIPiDIP-48678N.
IntActiQ5D869. 2 interactors.
STRINGi3702.AT2G40030.1.

Structurei

3D structure databases

ProteinModelPortaliQ5D869.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati1215 – 121611 Publication2
Repeati1329 – 133021 Publication2
Repeati1378 – 137931 Publication2
Repeati1415 – 141641 Publication2
Repeati1430 – 143151 Publication2
Repeati1439 – 144061 Publication2
Repeati1447 – 144871 Publication2
Repeati1464 – 146581 Publication2
Repeati1498 – 149991 Publication2
Repeati1528 – 1529101 Publication2
Repeati1545 – 1546111 Publication2
Repeati1562 – 1563111 Publication2
Repeati1596 – 1597121 Publication2
Repeati1604 – 1605131 Publication2
Repeati1621 – 1622141 Publication2
Repeati1638 – 1639151 Publication2
Repeati1641 – 1642161 Publication2
Repeati1680 – 1681171 Publication2
Repeati1692 – 1693181 Publication2

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni751 – 763Bridging helixBy similarityAdd BLAST13
Regioni1215 – 169318 X 2 AA repeats of [WG]-[GW] repeatsAdd BLAST479

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi1870 – 1975Gln-richAdd BLAST106
Compositional biasi1891 – 1972Ser-richAdd BLAST82

Domaini

WG/GW repeats are involved in AGO4 binding.

Sequence similaritiesi

Belongs to the RNA polymerase beta' chain family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0260. Eukaryota.
KOG2992. Eukaryota.
COG0086. LUCA.
HOGENOMiHOG000082864.
InParanoidiQ5D869.
KOiK16251.
OMAiDCSFTQK.
OrthoDBiEOG09360038.
PhylomeDBiQ5D869.

Family and domain databases

InterProiView protein in InterPro
IPR000722. RNA_pol_asu.
IPR006592. RNA_pol_N.
IPR007080. RNA_pol_Rpb1_1.
IPR007066. RNA_pol_Rpb1_3.
IPR007081. RNA_pol_Rpb1_5.
PfamiView protein in Pfam
PF04997. RNA_pol_Rpb1_1. 1 hit.
PF00623. RNA_pol_Rpb1_2. 1 hit.
PF04983. RNA_pol_Rpb1_3. 1 hit.
PF04998. RNA_pol_Rpb1_5. 1 hit.
SMARTiView protein in SMART
SM00663. RPOLA_N. 1 hit.

Sequencei

Sequence statusi: Complete.

Q5D869-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEEESTSEIL DGEIVGITFA LASHHEICIQ SISESAINHP SQLTNAFLGL
60 70 80 90 100
PLEFGKCESC GATEPDKCEG HFGYIQLPVP IYHPAHVNEL KQMLSLLCLK
110 120 130 140 150
CLKIKKAKGT SGGLADRLLG VCCEEASQIS IKDRASDGAS YLELKLPSRS
160 170 180 190 200
RLQPGCWNFL ERYGYRYGSD YTRPLLAREV KEILRRIPEE SRKKLTAKGH
210 220 230 240 250
IPQEGYILEY LPVPPNCLSV PEASDGFSTM SVDPSRIELK DVLKKVIAIK
260 270 280 290 300
SSRSGETNFE SHKAEASEMF RVVDTYLQVR GTAKAARNID MRYGVSKISD
310 320 330 340 350
SSSSKAWTEK MRTLFIRKGS GFSSRSVITG DAYRHVNEVG IPIEIAQRIT
360 370 380 390 400
FEERVSVHNR GYLQKLVDDK LCLSYTQGST TYSLRDGSKG HTELKPGQVV
410 420 430 440 450
HRRVMDGDVV FINRPPTTHK HSLQALRVYV HEDNTVKINP LMCSPLSADF
460 470 480 490 500
DGDCVHLFYP QSLSAKAEVM ELFSVEKQLL SSHTGQLILQ MGSDSLLSLR
510 520 530 540 550
VMLERVFLDK ATAQQLAMYG SLSLPPPALR KSSKSGPAWT VFQILQLAFP
560 570 580 590 600
ERLSCKGDRF LVDGSDLLKF DFGVDAMGSI INEIVTSIFL EKGPKETLGF
610 620 630 640 650
FDSLQPLLME SLFAEGFSLS LEDLSMSRAD MDVIHNLIIR EISPMVSRLR
660 670 680 690 700
LSYRDELQLE NSIHKVKEVA ANFMLKSYSI RNLIDIKSNS AITKLVQQTG
710 720 730 740 750
FLGLQLSDKK KFYTKTLVED MAIFCKRKYG RISSSGDFGI VKGCFFHGLD
760 770 780 790 800
PYEEMAHSIA AREVIVRSSR GLAEPGTLFK NLMAVLRDIV ITNDGTVRNT
810 820 830 840 850
CSNSVIQFKY GVDSERGHQG LFEAGEPVGV LAATAMSNPA YKAVLDSSPN
860 870 880 890 900
SNSSWELMKE VLLCKVNFQN TTNDRRVILY LNECHCGKRF CQENAACTVR
910 920 930 940 950
NKLNKVSLKD TAVEFLVEYR KQPTISEIFG IDSCLHGHIH LNKTLLQDWN
960 970 980 990 1000
ISMQDIHQKC EDVINSLGQK KKKKATDDFK RTSLSVSECC SFRDPCGSKG
1010 1020 1030 1040 1050
SDMPCLTFSY NATDPDLERT LDVLCNTVYP VLLEIVIKGD SRICSANIIW
1060 1070 1080 1090 1100
NSSDMTTWIR NRHASRRGEW VLDVTVEKSA VKQSGDAWRV VIDSCLSVLH
1110 1120 1130 1140 1150
LIDTKRSIPY SVKQVQELLG LSCAFEQAVQ RLSASVRMVS KGVLKEHIIL
1160 1170 1180 1190 1200
LANNMTCSGT MLGFNSGGYK ALTRSLNIKA PFTEATLIAP RKCFEKAAEK
1210 1220 1230 1240 1250
CHTDSLSTVV GSCSWGKRVD VGTGSQFELL WNQKETGLDD KEETDVYSFL
1260 1270 1280 1290 1300
QMVISTTNAD AFVSSPGFDV TEEEMAEWAE SPERDSALGE PKFEDSADFQ
1310 1320 1330 1340 1350
NLHDEGKPSG ANWEKSSSWD NGCSGGSEWG VSKSTGGEAN PESNWEKTTN
1360 1370 1380 1390 1400
VEKEDAWSSW NTRKDAQESS KSDSGGAWGI KTKDADADTT PNWETSPAPK
1410 1420 1430 1440 1450
DSIVPENNEP TSDVWGHKSV SDKSWDKKNW GTESAPAAWG STDAAVWGSS
1460 1470 1480 1490 1500
DKKNSETESD AAAWGSRDKN NSDVGSGAGV LGPWNKKSSE TESNGATWGS
1510 1520 1530 1540 1550
SDKTKSGAAA WNSWDKKNIE TDSEPAAWGS QGKKNSETES GPAAWGAWDK
1560 1570 1580 1590 1600
KKSETEPGPA GWGMGDKKNS ETELGPAAMG NWDKKKSDTK SGPAAWGSTD
1610 1620 1630 1640 1650
AAAWGSSDKN NSETESDAAA WGSRNKKTSE IESGAGAWGS WGQPSPTAED
1660 1670 1680 1690 1700
KDTNEDDRNP WVSLKETKSR EKDDKERSQW GNPAKKFPSS GGWSNGGGAD
1710 1720 1730 1740 1750
WKGNRNHTPR PPRSEDNLAP MFTATRQRLD SFTSEEQELL SDVEPVMRTL
1760 1770 1780 1790 1800
RKIMHPSAYP DGDPISDDDK TFVLEKILNF HPQKETKLGS GVDFITVDKH
1810 1820 1830 1840 1850
TIFSDSRCFF VVSTDGAKQD FSYRKSLNNY LMKKYPDRAE EFIDKYFTKP
1860 1870 1880 1890 1900
RPSGNRDRNN QDATPPGEEQ SQPPNQSIGN GGDDFQTQTQ SQSPSQTRAQ
1910 1920 1930 1940 1950
SPSQAQAQSP SQTQSQSQSQ SQSQSQSQSQ SQSQSQSQSQ SQSQSQSPSQ
1960 1970
TQTQSPSQTQ AQAQSPSSQS PSQTQT
Length:1,976
Mass (Da):218,228
Last modified:March 29, 2005 - v1
Checksum:iC16F6B0BBDC40617
GO

Sequence cautioni

The sequence AAB95288 differs from that shown. Reason: Erroneous gene model prediction.Curated
The sequence AAB95289 differs from that shown. Reason: Erroneous gene model prediction.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY826516 mRNA. Translation: AAX12373.1.
AY927744 mRNA. Translation: AAY15198.1.
DQ020656 mRNA. Translation: AAY89362.1.
AF002109 Genomic DNA. Translation: AAB95288.1. Sequence problems.
AF002109 Genomic DNA. Translation: AAB95289.1. Sequence problems.
CP002685 Genomic DNA. Translation: AEC09767.1.
PIRiD84824.
E84824.
RefSeqiNP_181532.2. NM_129561.4.
UniGeneiAt.37106.

Genome annotation databases

EnsemblPlantsiAT2G40030.1; AT2G40030.1; AT2G40030.
GeneIDi818591.
GrameneiAT2G40030.1; AT2G40030.1; AT2G40030.
KEGGiath:AT2G40030.

Similar proteinsi

Entry informationi

Entry nameiNRPE1_ARATH
AccessioniPrimary (citable) accession number: Q5D869
Secondary accession number(s): O04206, O04207, Q1L5X4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 3, 2011
Last sequence update: March 29, 2005
Last modified: July 5, 2017
This is version 101 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