RDE12_CAEEL
ID RDE12_CAEEL Reviewed; 959 AA.
AC P90897; G3MU56; G3MU57;
DT 09-DEC-2015, integrated into UniProtKB/Swiss-Prot.
DT 13-JUL-2010, sequence version 4.
DT 03-AUG-2022, entry version 164.
DE RecName: Full=DEAD-box ATP-dependent RNA helicase rde-12 {ECO:0000305};
DE EC=3.6.4.13 {ECO:0000250|UniProtKB:P09052};
DE AltName: Full=RNA interference defective protein 12 {ECO:0000312|WormBase:F58G11.2a};
GN Name=rde-12 {ECO:0000312|WormBase:F58G11.2a};
GN ORFNames=F58G11.2 {ECO:0000312|WormBase:F58G11.2a};
OS Caenorhabditis elegans.
OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
OC Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae;
OC Caenorhabditis.
OX NCBI_TaxID=6239 {ECO:0000312|Proteomes:UP000001940};
RN [1] {ECO:0000312|Proteomes:UP000001940}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Bristol N2 {ECO:0000312|Proteomes:UP000001940};
RX PubMed=9851916; DOI=10.1126/science.282.5396.2012;
RG The C. elegans sequencing consortium;
RT "Genome sequence of the nematode C. elegans: a platform for investigating
RT biology.";
RL Science 282:2012-2018(1998).
RN [2] {ECO:0000305}
RP FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, DOMAIN, AND MUTAGENESIS
RP OF 540-GLU--THR-580.
RX PubMed=24684930; DOI=10.1016/j.cub.2014.01.008;
RA Yang H., Vallandingham J., Shiu P., Li H., Hunter C.P., Mak H.Y.;
RT "The DEAD box helicase RDE-12 promotes amplification of RNAi in cytoplasmic
RT foci in C. elegans.";
RL Curr. Biol. 24:832-838(2014).
RN [3] {ECO:0000305}
RP IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, INTERACTION WITH WAGO-1;
RP ERGO-1 AND RDE-1, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE, AND
RP MUTAGENESIS OF LYS-430.
RX PubMed=24684931; DOI=10.1016/j.cub.2014.03.008;
RA Shirayama M., Stanney W., Gu W., Seth M., Mello C.C.;
RT "The vasa homolog rde-12 engages target mRNA and multiple argonaute
RT proteins to promote RNAi in C. elegans.";
RL Curr. Biol. 24:845-851(2014).
CC -!- FUNCTION: Probable ATP-dependent RNA helicase involved in RNAi-mediated
CC gene silencing (PubMed:24684930, PubMed:24684931). Specifically
CC required in the endogenous siRNA pathway for biogenesis of secondary
CC endogenous small interfering RNA (siRNA) intermediates called 22G-RNAs
CC (PubMed:24684930, PubMed:24684931). May associate with and recruit rde-
CC 10 to primary siRNA-targeted mRNA for secondary siRNA synthesis
CC (PubMed:24684930). May be recruited to target mRNAs by rde-1 and/or
CC ergo-1 (PubMed:24684930, PubMed:24684931).
CC {ECO:0000269|PubMed:24684930, ECO:0000269|PubMed:24684931}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;
CC Evidence={ECO:0000250|UniProtKB:P09052};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:P09052};
CC -!- SUBUNIT: Interacts with wago-1, ergo-1 and rde-1.
CC {ECO:0000269|PubMed:24684931}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm, perinuclear region
CC {ECO:0000269|PubMed:24684931}. Cytoplasmic granule
CC {ECO:0000269|PubMed:24684930, ECO:0000269|PubMed:24684931}. Cytoplasm
CC {ECO:0000269|PubMed:24684931}. Cytoplasm, P-body
CC {ECO:0000269|PubMed:24684930}. Note=Colocalizes with pgl-1 in
CC perinuclear P granules. Colocalizes with rsd-6 in a subset of germline
CC and embryonic foci. {ECO:0000269|PubMed:24684930}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=a {ECO:0000312|WormBase:F58G11.2a};
CC IsoId=P90897-1; Sequence=Displayed;
CC Name=b {ECO:0000312|WormBase:F58G11.2b};
CC IsoId=P90897-2; Sequence=VSP_057997;
CC Name=c {ECO:0000312|WormBase:F58G11.2c};
CC IsoId=P90897-3; Sequence=VSP_057996;
CC -!- TISSUE SPECIFICITY: Expressed in the soma and germline.
CC {ECO:0000269|PubMed:24684930}.
CC -!- DOMAIN: The C-terminal region is necessary for localization to P
CC granules. {ECO:0000269|PubMed:24684930}.
CC -!- DISRUPTION PHENOTYPE: Viable with no obvious developmental defects.
CC Insensitive to RNAi-mediated gene silencing. Increased sensitivity to
CC viral infection. {ECO:0000269|PubMed:24684931}.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DDX3/DED1
CC subfamily. {ECO:0000305}.
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DR EMBL; BX284605; CAB03153.4; -; Genomic_DNA.
DR EMBL; BX284605; CCD31087.1; -; Genomic_DNA.
DR EMBL; BX284605; CCD31088.1; -; Genomic_DNA.
DR RefSeq; NP_001256533.1; NM_001269604.1. [P90897-1]
DR RefSeq; NP_001256534.1; NM_001269605.1. [P90897-2]
DR RefSeq; NP_001256535.1; NM_001269606.1. [P90897-3]
DR AlphaFoldDB; P90897; -.
DR SMR; P90897; -.
DR STRING; 6239.F58G11.2a; -.
DR EPD; P90897; -.
DR PaxDb; P90897; -.
DR PeptideAtlas; P90897; -.
DR EnsemblMetazoa; F58G11.2a.1; F58G11.2a.1; WBGene00010280. [P90897-1]
DR EnsemblMetazoa; F58G11.2b.1; F58G11.2b.1; WBGene00010280. [P90897-2]
DR EnsemblMetazoa; F58G11.2c.1; F58G11.2c.1; WBGene00010280. [P90897-3]
DR GeneID; 179855; -.
DR KEGG; cel:CELE_F58G11.2; -.
DR UCSC; F58G11.2; c. elegans. [P90897-1]
DR CTD; 179855; -.
DR WormBase; F58G11.2a; CE44827; WBGene00010280; rde-12. [P90897-1]
DR WormBase; F58G11.2b; CE46130; WBGene00010280; rde-12. [P90897-2]
DR WormBase; F58G11.2c; CE46471; WBGene00010280; rde-12. [P90897-3]
DR eggNOG; KOG0334; Eukaryota.
DR HOGENOM; CLU_007063_0_0_1; -.
DR InParanoid; P90897; -.
DR OMA; KTAWANR; -.
DR OrthoDB; 973872at2759; -.
DR PRO; PR:P90897; -.
DR Proteomes; UP000001940; Chromosome V.
DR Bgee; WBGene00010280; Expressed in larva and 4 other tissues.
DR GO; GO:0005737; C:cytoplasm; IDA:WormBase.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0043186; C:P granule; IDA:WormBase.
DR GO; GO:0000932; C:P-body; IEA:UniProtKB-SubCell.
DR GO; GO:0048471; C:perinuclear region of cytoplasm; IDA:WormBase.
DR GO; GO:0031332; C:RNAi effector complex; IDA:WormBase.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0019899; F:enzyme binding; IPI:WormBase.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0003724; F:RNA helicase activity; IBA:GO_Central.
DR GO; GO:0030154; P:cell differentiation; IBA:GO_Central.
DR GO; GO:0007276; P:gamete generation; IBA:GO_Central.
DR GO; GO:0006417; P:regulation of translation; IEA:UniProtKB-KW.
DR GO; GO:0043330; P:response to exogenous dsRNA; IMP:WormBase.
DR GO; GO:0030422; P:siRNA processing; IMP:WormBase.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR000629; RNA-helicase_DEAD-box_CS.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR PROSITE; PS00039; DEAD_ATP_HELICASE; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS51195; Q_MOTIF; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; ATP-binding; Cytoplasm; Helicase; Hydrolase;
KW Nucleotide-binding; Reference proteome; Repressor;
KW RNA-mediated gene silencing; Translation regulation.
FT CHAIN 1..959
FT /note="DEAD-box ATP-dependent RNA helicase rde-12"
FT /evidence="ECO:0000305"
FT /id="PRO_0000435004"
FT DOMAIN 411..599
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 632..792
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 1..336
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 793..834
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 858..959
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 380..408
FT /note="Q motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00552"
FT MOTIF 539..542
FT /note="DEAD box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT COMPBIAS 12..47
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 68..100
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 101..119
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 120..137
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 138..161
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 165..199
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 200..214
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 216..235
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 236..258
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 268..283
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 293..328
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 927..947
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 424..431
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT VAR_SEQ 60..79
FT /note="GGHQGNHGNSYGRREDDRSH -> D (in isoform c)"
FT /evidence="ECO:0000305"
FT /id="VSP_057996"
FT VAR_SEQ 73..78
FT /note="Missing (in isoform b)"
FT /evidence="ECO:0000305"
FT /id="VSP_057997"
FT MUTAGEN 430
FT /note="K->A: RNAi gene targeting defect."
FT /evidence="ECO:0000269|PubMed:24684931"
FT MUTAGEN 540
FT /note="E->Q: Results in accumulation in cytoplasm."
FT /evidence="ECO:0000269|PubMed:24684930"
FT MUTAGEN 578..580
FT /note="SAT->AAA: Results in accumulation in cytoplasm."
FT /evidence="ECO:0000269|PubMed:24684930"
SQ SEQUENCE 959 AA; 103832 MW; 750445097404D350 CRC64;
MSSFGNNAGG GGREYHDDRS NRDHRHGNGG SDAGQRRRED HNSSYQSYRR PDGRQDSYGG
GHQGNHGNSY GRREDDRSHS RDNHGGSRYG ERDDRGNNGR SADNRYSQSN YNYDSNRGGQ
HYQRDNHGSK DDRGPMNQYN DHGSNHNSNS RNDQYRQGSY QGDGHSGYRR DDDRRRNDND
QARPYQSNRD SDRNSPRDHH NYNSQSSPRS HQGGQDRYSA PKEDNQRRYD NHQGGHDSYR
GQNSGGYSGN NSGEYRNDYR SQQDSRDHRS GGNNSSSGFK NDGGFGGNDN RGFGNNGGGS
FGNPNNSYRG NSNNIGGFHR SDGSNSEGVN APVRAPRDWV PVTRDIDELV RETADRLADC
DVGQDRAVEI RNAEKDVRLT SWTNSGLHPT ILETLKRIKY NNVRTIQGAM IPQVLDGHDV
LGQAETSAGK TAAFGLPIID KILRMDEETR NKARQDDGPL ALILAPTREL AAQIHEALRT
YCQNTDIIVL LSYGQSDRAR SLNEIRNGCD ILIGTCGRIM DFTVKSHISL LHLRFLVFDE
ADRLLQDMKK DPLGHLGAII KDAGFMESAA TRQTIMTSAT FNASVMTVAN ELMKRLPGQD
EMIKIVLANG RLSKRVNLEF FECKGLAEKN AKLREILKQN VNGKTLKTII FVQKKDQCDA
CAAKLTSGGM LAQTLHGDRS QDMREKLIND FKSNRVNLLV TTDLLSRGID VSDLDRVINF
DLPDGDPDQG ADTFIHRAGR TGRTGRKENG LCVSFVDPQS DRDSLLAPKL VELIISQNLP
DLKVPDFLDA MAKSSRGKSG TSGFGQRGGY GGRGGGFGGT GRGRGGGVFG GGGRGGDFGG
SGNFGGSGGG GSFGGSGGGG GFGGVKPSGF GGSRNNAEPT SSGGGFGAPK APTGFPSDNN
DASEDAPAAG GFGFSTKAAQ DAKKAEESAT LGSSTFGTAN NADEEPTETG ADGNDDDEW
