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Protein

Endoribonuclease dcr-1

Gene

dcr-1

Organism
Caenorhabditis elegans
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Involved in cleaving double-stranded RNA in the RNA interference (RNAi) pathway (PubMed:11641272, PubMed:20223951). It produces 21 to 23 bp dsRNAs (siRNAs) which target the selective destruction of homologous RNAs (PubMed:11641272, PubMed:20223951). Seems to process the precursor of the small temporal RNA let-7 which is involved in developmental timing (PubMed:11641272).2 Publications
tDCR-1 acts as a deoxyribonuclease (DNase) initiating DNA fragmentation during apoptosis, upstream of nucleases cps-6, crn-2 and nuc-1.1 Publication

Cofactori

Mg2+1 Publication, Mn2+By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi1682Magnesium or manganese1 Publication1
Sitei1787Important for activityBy similarity1
Metal bindingi1791Magnesium or manganeseBy similarity1
Metal bindingi1794Magnesium or manganese1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi33 – 40ATPPROSITE-ProRule annotation8

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • deoxyribonuclease I activity Source: WormBase
  • DNA binding Source: InterPro
  • helicase activity Source: UniProtKB-KW
  • metal ion binding Source: UniProtKB-KW
  • ribonuclease III activity Source: WormBase
  • RNA binding Source: GO_Central

GO - Biological processi

  • apoptotic DNA fragmentation Source: WormBase
  • DNA catabolic process, endonucleolytic Source: WormBase
  • dsRNA fragmentation Source: WormBase
  • gonad morphogenesis Source: WormBase
  • nematode larval development Source: WormBase
  • olfactory learning Source: WormBase
  • positive regulation of primary miRNA processing Source: WormBase
  • pre-miRNA processing Source: WormBase
  • production of siRNA involved in RNA interference Source: WormBase
  • regulation of development, heterochronic Source: WormBase
  • reproduction Source: WormBase
  • RNA catabolic process Source: WormBase
  • rRNA catabolic process Source: InterPro

Keywordsi

Molecular functionEndonuclease, Helicase, Hydrolase, Nuclease, RNA-binding
Biological processApoptosis, RNA-mediated gene silencing
LigandATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Endoribonuclease dcr-1 (EC:3.1.26.-2 Publications)
Cleaved into the following chain:
Death-promoting deoxyribonuclease1 Publication (EC:3.1.21.-1 Publication)
Short name:
tDCR-11 Publication
Gene namesi
Name:dcr-11 Publication
ORF Names:K12H4.8Imported
OrganismiCaenorhabditis elegans
Taxonomic identifieri6239 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
Proteomesi
  • UP000001940 Componenti: Chromosome III

Organism-specific databases

WormBaseiK12H4.8 ; CE47418 ; WBGene00000939 ; dcr-1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Pathology & Biotechi

Disruption phenotypei

RNAi-mediated knockdown in a cps-6 mutant background reduces the number of DNA breaks in embryonic cells undergoing apoptosis.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi1537D → E: Loss of cleavage by ced-3. Loss of deoxyribonuclease (DNase) activity. Reduced number of cell corpses in embryos. 1 Publication1
Mutagenesisi1682E → A: Severe reduction in both dsRNA dicing and DNase activities; when associated with A-1794. Loss of dsRNA dicing and DNase activities, bursting and protruding vulva and reduction in the number of cell corpses in embryos; when associated with A-1794 and A-1686. 1 Publication1
Mutagenesisi1686D → A: Loss of dsRNA dicing and DNase activities, bursting and protruding vulva and reduction in the number of cell corpses in embryos; when associated with A-1794 and A-1682. 1 Publication1
Mutagenesisi1794E → A: Severe reduction in both dsRNA dicing and DNase activities; when associated with A-1682. Loss of dsRNA dicing and DNase activities, bursting and protruding vulva and reduction in the number of cell corpses in embryos; when associated with A-1682 and A-1686. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001804731 – 1910Endoribonuclease dcr-1Add BLAST1910
ChainiPRO_00004411211538 – 1910Death-promoting deoxyribonucleaseCuratedAdd BLAST373

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei1537 – 1538Cleavage; by ced-31 Publication2

Proteomic databases

EPDiP34529
PaxDbiP34529
PeptideAtlasiP34529
PRIDEiP34529

Expressioni

Gene expression databases

BgeeiWBGene00000939

Interactioni

Subunit structurei

May interact with pir-1.1 Publication

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi41344, 2 interactors
DIPiDIP-25340N
IntActiP34529, 88 interactors
STRINGi6239.K12H4.8

Structurei

3D structure databases

ProteinModelPortaliP34529
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini20 – 201Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST182
Domaini371 – 542Helicase C-terminalPROSITE-ProRule annotationAdd BLAST172
Domaini571 – 667Dicer dsRNA-binding foldPROSITE-ProRule annotationAdd BLAST97
Domaini847 – 1003PAZPROSITE-ProRule annotationAdd BLAST157
Domaini1381 – 1589RNase III 1PROSITE-ProRule annotationAdd BLAST209
Domaini1643 – 1805RNase III 2PROSITE-ProRule annotationAdd BLAST163
Domaini1833 – 1896DRBMPROSITE-ProRule annotationAdd BLAST64

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili1245 – 1280Sequence analysisAdd BLAST36

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi145 – 148DEAH boxPROSITE-ProRule annotation4

Sequence similaritiesi

Belongs to the helicase family. Dicer subfamily.Curated

Keywords - Domaini

Coiled coil, Repeat

Phylogenomic databases

eggNOGiKOG0701 Eukaryota
COG0571 LUCA
COG1111 LUCA
GeneTreeiENSGT00510000046789
HOGENOMiHOG000022395
InParanoidiP34529
KOiK11592
OMAiCYPKAIP
OrthoDBiEOG091G00M8

Family and domain databases

CDDicd00079 HELICc, 1 hit
cd00593 RIBOc, 2 hits
Gene3Di1.10.1520.10, 1 hit
3.30.160.380, 1 hit
HAMAPiMF_00104 RNase_III, 1 hit
InterProiView protein in InterPro
IPR038248 Dicer_dimer_sf
IPR005034 Dicer_dimerisation_dom
IPR014720 dsRBD_dom
IPR006935 Helicase/UvrB_N
IPR014001 Helicase_ATP-bd
IPR001650 Helicase_C
IPR027417 P-loop_NTPase
IPR003100 PAZ_dom
IPR036085 PAZ_dom_sf
IPR011907 RNase_III
IPR000999 RNase_III_dom
IPR036389 RNase_III_sf
PfamiView protein in Pfam
PF03368 Dicer_dimer, 1 hit
PF00271 Helicase_C, 1 hit
PF02170 PAZ, 1 hit
PF04851 ResIII, 1 hit
PF00636 Ribonuclease_3, 2 hits
SMARTiView protein in SMART
SM00487 DEXDc, 1 hit
SM00490 HELICc, 1 hit
SM00949 PAZ, 1 hit
SM00535 RIBOc, 2 hits
SUPFAMiSSF101690 SSF101690, 1 hit
SSF52540 SSF52540, 2 hits
SSF69065 SSF69065, 4 hits
PROSITEiView protein in PROSITE
PS51327 DICER_DSRBF, 1 hit
PS50137 DS_RBD, 1 hit
PS51192 HELICASE_ATP_BIND_1, 1 hit
PS51194 HELICASE_CTER, 1 hit
PS50821 PAZ, 1 hit
PS00517 RNASE_3_1, 1 hit
PS50142 RNASE_3_2, 2 hits

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P34529-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVRVRADLQC FNPRDYQVEL LDKATKKNTI VQLGTGSGKT FIAVLLLKEY
60 70 80 90 100
GVQLFAPLDQ GGKRAFFVVE KVNLVEQQAI HIEVHTSFKV GQVHGQTSSG
110 120 130 140 150
LWDSKEQCDQ FMKRHHVVVI TAQCLLDLIR HAYLKIEDMC VLIFDECHHA
160 170 180 190 200
LGSQHPYRSI MVDYKLLKKD KPVPRVLGLT ASLIKAKVAP EKLMEQLKKL
210 220 230 240 250
ESAMDSVIET ASDLVSLSKY GAKPYEVVII CKDFEIGCLG IPNFDTVIEI
260 270 280 290 300
FDETVAFVNT TTEFHPDLDL DPRRPIKDSL KTTRAVFRQL GPWAAWRTAQ
310 320 330 340 350
VWEKELGKII KSQVLPDKTL RFLNMAKTSM ITIKRLLEPE MKKIKSIEAL
360 370 380 390 400
RPYVPQRVIR LFEILETFNP EFQKERMKLE KAEHLSAIIF VDQRYIAYSL
410 420 430 440 450
LLMMRHIKSW EPKFKFVNPD YVVGASGRNL ASSDSQGLHK RQTEVLRRFH
460 470 480 490 500
RNEINCLIAT SVLEEGVDVK QCNLVIKFDR PLDMRSYVQS KGRARRAGSR
510 520 530 540 550
YVITVEEKDT AACDSDLKDF QQIEKILLSR HRTVNNPIED DSDRFEEFDV
560 570 580 590 600
DSQMEPYVVE KTGATLKMST AIALINRYCS KLPSDIFTRL VPHNQIIPIE
610 620 630 640 650
ENGVTKYCAE LLLPINSPIK HAIVLKNPMP NKKTAQMAVA LEACRQLHLE
660 670 680 690 700
GELDDNLLPK GRESIAKLLE HIDEEPDEYA PGIAAKVGSS KRKQLYDKKI
710 720 730 740 750
ARALNESFVE ADKECFIYAF ELERFREAEL TLNPKRRKFE DPFNYEYCFG
760 770 780 790 800
FLSAKEIPKI PPFPVFLRQG NMKVRLIVAP KKTTVTAAQL QEIQLFHNYL
810 820 830 840 850
FTQVLQMCKT GNLEFDGTSN APLNTLIVPL NKRKDDMSYT INMKYVSEVV
860 870 880 890 900
ANMENMPRIP KDEVRRQYKF NAEDYKDAIV MPWYRNLEQP VFYYVAEILP
910 920 930 940 950
EWRPSSKFPD THFETFNEYF IKKYKLEIYD QNQSLLDVDF TSTRLNLLQP
960 970 980 990 1000
RIQNQPRRSR TVSNSSTSNI PQASASDSKE SNTSVPHSSQ RQILVPELMD
1010 1020 1030 1040 1050
IHPISATLWN VIAALPSIFY RVNQLLLTDE LRETILVKAF GKEKTKLDDN
1060 1070 1080 1090 1100
VEWNSLAYAT EYEEKQTIIV KKIQQLRDLN QKSIEDQERE TRENDKIDDG
1110 1120 1130 1140 1150
EELFNIGVWD PEEAVRIGVE ISSRDDRMDG EDQDTVGLTQ GLHDGNISDE
1160 1170 1180 1190 1200
DDELPFVMHD YTARLTSNRN GIGAWSGSES IVPSGWGDWD GPEPDNSPMP
1210 1220 1230 1240 1250
FQILGGPGGL NVQALMADVG RVFDPSTASS SLSQTVQEST VSPPKQLTKE
1260 1270 1280 1290 1300
EEQFKKLQND LLKQAKERLE ALEMSEDMEK PRRLEDTVNL EDYGDDQENQ
1310 1320 1330 1340 1350
EDENTPTNFP KTIDEEIEEL SIGARKKQEI DDNAAKTDVL ERENCEVLPV
1360 1370 1380 1390 1400
AINEKSRSFS FEKESKAING RLIRQRSEEY VSHIDSDIGL GVSPCLLLTA
1410 1420 1430 1440 1450
LTTSNAADGM SLERFETIGD SFLKFATTDY LYHTLLDQHE GKLSFARSKE
1460 1470 1480 1490 1500
VSNCNLYRLG KKLGIPQLIV ANKFDAHDSW LPPCYIPTCD FKAPNTDDAE
1510 1520 1530 1540 1550
EKDNEIERIL DGQVIEEKPE NKTGWDIGGD VSKSTTDGIE TITFPKQARV
1560 1570 1580 1590 1600
GNDDISPLPY NLLTQQHISD KSIADAVEAL IGVHLLTLGP NPTLKVMNWM
1610 1620 1630 1640 1650
GLKVIQKDQK SDVPSPLLRF IDTPTNPNAS LNFLNNLWQQ FQFTQLEEKI
1660 1670 1680 1690 1700
GYRFKERAYL VQAFTHASYI NNRVTGCYQR LEFLGDAVLD YMITRYLFED
1710 1720 1730 1740 1750
SRQYSPGVLT DLRSALVNNT IFASLAVKFE FQKHFIAMCP GLYHMIEKFV
1760 1770 1780 1790 1800
KLCSERNFDT NFNAEMYMVT TEEEIDEGQE EDIEVPKAMG DIFESVAGAI
1810 1820 1830 1840 1850
YLDSGRNLDT TWQVIFHMMR GTIELCCANP PRSPIRELME FEQSKVRFSK
1860 1870 1880 1890 1900
MERILESGKV RVTVEVVNNM RFTGMGRNYR IAKATAAKRA LKYLHQIEQQ
1910
RRQSPSLTTV
Length:1,910
Mass (Da):218,423
Last modified:October 3, 2012 - v3
Checksum:iB49D19D7B3730F80
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FO081380 Genomic DNA Translation: CCD71200.2
PIRiS44849
RefSeqiNP_498761.2, NM_066360.3
UniGeneiCel.38691

Genome annotation databases

EnsemblMetazoaiK12H4.8.1; K12H4.8.1; WBGene00000939
K12H4.8.2; K12H4.8.2; WBGene00000939
GeneIDi176138
KEGGicel:CELE_K12H4.8
UCSCiK12H4.8 c. elegans

Similar proteinsi

Entry informationi

Entry nameiDCR1_CAEEL
AccessioniPrimary (citable) accession number: P34529
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: October 3, 2012
Last modified: May 23, 2018
This is version 160 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis annotation project

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
  2. SIMILARITY comments
    Index of protein domains and families

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