GenomeNet

Database: UniProt
Entry: P90897
LinkDB: P90897
Original site: P90897 
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   16-OCT-2019, entry version 155.
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
RT   investigating biology.";
RL   Science 282:2012-2018(1998).
RN   [2] {ECO:0000305}
RP   FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, DOMAIN, AND
RP   MUTAGENESIS 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
RT   cytoplasmic foci in C. elegans.";
RL   Curr. Biol. 24:832-838(2014).
RN   [3] {ECO:0000305}
RP   IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, INTERACTION WITH
RP   WAGO-1; ERGO-1 AND RDE-1, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE,
RP   AND 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-
CC       mediated gene silencing (PubMed:24684930, PubMed:24684931).
CC       Specifically required in the endogenous siRNA pathway for
CC       biogenesis of secondary endogenous small interfering RNA (siRNA)
CC       intermediates called 22G-RNAs (PubMed:24684930, PubMed:24684931).
CC       May associate with and recruit rde-10 to primary siRNA-targeted
CC       mRNA for secondary siRNA synthesis (PubMed:24684930). May be
CC       recruited to target mRNAs by rde-1 and/or ergo-1 (PubMed:24684930,
CC       PubMed:24684931). {ECO:0000269|PubMed:24684930,
CC       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}.
CC       Cytoplasm {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
CC       germline 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         Note=No experimental confirmation available. {ECO:0000305};
CC       Name=b {ECO:0000312|WormBase:F58G11.2b};
CC         IsoId=P90897-2; Sequence=VSP_057997;
CC         Note=No experimental confirmation available. {ECO:0000305};
CC       Name=c {ECO:0000312|WormBase:F58G11.2c};
CC         IsoId=P90897-3; Sequence=VSP_057996;
CC         Note=No experimental confirmation available. {ECO:0000305};
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
CC       defects. Insensitive to RNAi-mediated gene silencing. Increased
CC       sensitivity to viral infection. {ECO:0000269|PubMed:24684931}.
CC   -!- SIMILARITY: Belongs to the DEAD box helicase family. DDX3/DED1
CC       subfamily. {ECO:0000305}.
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   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   eggNOG; ENOG410XSQV; LUCA.
DR   InParanoid; P90897; -.
DR   OMA; MRYTASA; -.
DR   OrthoDB; 973872at2759; -.
DR   PRO; PR:P90897; -.
DR   Proteomes; UP000001940; Chromosome V.
DR   Bgee; WBGene00010280; Expressed in 5 organ(s), highest expression level in multi-cellular organism.
DR   GO; GO:0005737; C:cytoplasm; IDA:WormBase.
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:0019899; F:enzyme binding; IPI:WormBase.
DR   GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR   GO; GO:0003724; F:RNA helicase activity; IEA:UniProtKB-EC.
DR   GO; GO:0030422; P:production of siRNA involved in RNA interference; IMP:WormBase.
DR   GO; GO:0006417; P:regulation of translation; IEA:UniProtKB-KW.
DR   GO; GO:0043330; P:response to exogenous dsRNA; IMP:WormBase.
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   InterPro; IPR014014; RNA_helicase_DEAD_Q_motif.
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; Complete proteome; Cytoplasm;
KW   Helicase; Hydrolase; Nucleotide-binding; Reference proteome;
KW   Repressor; RNA-mediated gene silencing; Translation regulation.
FT   CHAIN         1    959       DEAD-box ATP-dependent RNA helicase rde-
FT                                12. {ECO:0000305}.
FT                                /FTId=PRO_0000435004.
FT   DOMAIN      411    599       Helicase ATP-binding.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00541}.
FT   DOMAIN      632    792       Helicase C-terminal.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00542}.
FT   NP_BIND     424    431       ATP. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00541}.
FT   MOTIF       380    408       Q motif. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00552}.
FT   MOTIF       539    542       DEAD box. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00541}.
FT   COMPBIAS    797    887       Gly-rich. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00008}.
FT   VAR_SEQ      60     79       GGHQGNHGNSYGRREDDRSH -> D (in isoform c).
FT                                {ECO:0000305}.
FT                                /FTId=VSP_057996.
FT   VAR_SEQ      73     78       Missing (in isoform b). {ECO:0000305}.
FT                                /FTId=VSP_057997.
FT   MUTAGEN     430    430       K->A: RNAi gene targeting defect.
FT                                {ECO:0000269|PubMed:24684931}.
FT   MUTAGEN     540    540       E->Q: Results in accumulation in
FT                                cytoplasm. {ECO:0000269|PubMed:24684930}.
FT   MUTAGEN     578    580       SAT->AAA: Results in accumulation in
FT                                cytoplasm. {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
//
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