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Database: UniProt
Entry: D0PV95
LinkDB: D0PV95
Original site: D0PV95 
ID   DDX3_CAEEL              Reviewed;         708 AA.
AC   D0PV95; Q4W5R4;
DT   30-NOV-2016, integrated into UniProtKB/Swiss-Prot.
DT   15-DEC-2009, sequence version 1.
DT   13-NOV-2019, entry version 85.
DE   RecName: Full=ATP-dependent RNA helicase laf-1 {ECO:0000305};
DE            EC=3.6.4.13 {ECO:0000269|PubMed:27546789};
DE   AltName: Full=DEAD-box RNA helicase laf-1 {ECO:0000303|PubMed:19361491};
GN   Name=laf-1 {ECO:0000303|PubMed:19361491,
GN   ECO:0000312|WormBase:Y71H2AM.19b};
GN   ORFNames=Y71H2AM.19 {ECO:0000312|WormBase:Y71H2AM.19b};
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:0000305}
RP   NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM B), FUNCTION, SUBCELLULAR
RP   LOCATION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, DISRUPTION
RP   PHENOTYPE, AND MUTAGENESIS OF ARG-426; MET-430 AND THR-434.
RX   PubMed=19361491; DOI=10.1016/j.ydbio.2009.04.003;
RA   Hubert A., Anderson P.;
RT   "The C. elegans sex determination gene laf-1 encodes a putative DEAD-
RT   box RNA helicase.";
RL   Dev. Biol. 330:358-367(2009).
RN   [2] {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   [3] {ECO:0000305}
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RX   PubMed=9043090;
RA   Goodwin E.B., Hofstra K., Hurney C.A., Mango S., Kimble J.;
RT   "A genetic pathway for regulation of tra-2 translation.";
RL   Development 124:749-758(1997).
RN   [4] {ECO:0000305}
RP   FUNCTION.
RX   PubMed=9321409; DOI=10.1093/emboj/16.20.6301;
RA   Jan E., Yoon J.W., Walterhouse D., Iannaccone P., Goodwin E.B.;
RT   "Conservation of the C.elegans tra-2 3'UTR translational control.";
RL   EMBO J. 16:6301-6313(1997).
RN   [5] {ECO:0000305}
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RX   PubMed=24844228; DOI=10.1371/journal.pone.0097924;
RA   Paz-Gomez D., Villanueva-Chimal E., Navarro R.E.;
RT   "The DEAD Box RNA helicase VBH-1 is a new player in the stress
RT   response in C. elegans.";
RL   PLoS ONE 9:E97924-E97924(2014).
RN   [6] {ECO:0000305}
RP   FUNCTION, SUBCELLULAR LOCATION, DOMAIN, AND DISRUPTION PHENOTYPE.
RX   PubMed=26015579; DOI=10.1073/pnas.1504822112;
RA   Elbaum-Garfinkle S., Kim Y., Szczepaniak K., Chen C.C., Eckmann C.R.,
RA   Myong S., Brangwynne C.P.;
RT   "The disordered P granule protein LAF-1 drives phase separation into
RT   droplets with tunable viscosity and dynamics.";
RL   Proc. Natl. Acad. Sci. U.S.A. 112:7189-7194(2015).
RN   [7] {ECO:0000305}
RP   FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT,
RP   AND DOMAIN.
RX   PubMed=27546789; DOI=10.1016/j.molcel.2016.07.010;
RA   Kim Y., Myong S.;
RT   "RNA remodeling activity of DEAD box proteins tuned by protein
RT   concentration, RNA length, and ATP.";
RL   Mol. Cell 63:865-876(2016).
CC   -!- FUNCTION: ATP-dependent RNA helicase (PubMed:27546789). Plays a
CC       role in RNA remodeling, but is not required for RNA unwinding
CC       (PubMed:27546789). Binds to RNA in a concentration-dependent
CC       manner to stimulate annealing between two complementary strands of
CC       RNA (PubMed:26015579, PubMed:27546789). This process is also
CC       dependent upon ATP; ATP reduces binding to RNA and subsequently
CC       diminishes RNA annealing (PubMed:27546789). Promotes liquid-liquid
CC       phase separation of P granules, which is a process important for
CC       intracellular organization and stress granule assembly
CC       (PubMed:26015579). Required for embryonic development
CC       (PubMed:19361491, PubMed:26015579). Plays a role in sexual cell
CC       fate determination by negatively regulating the translation of the
CC       sex determining protein tra-2 (PubMed:9043090, PubMed:9321409,
CC       PubMed:26015579). May play a protective role in the response to
CC       heat and oxidative stress (PubMed:24844228).
CC       {ECO:0000269|PubMed:19361491, ECO:0000269|PubMed:24844228,
CC       ECO:0000269|PubMed:26015579, ECO:0000269|PubMed:27546789,
CC       ECO:0000269|PubMed:9043090, ECO:0000269|PubMed:9321409}.
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:0000269|PubMed:27546789};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=1.3156 mM for ATP {ECO:0000269|PubMed:27546789};
CC   -!- SUBUNIT: Binds RNA as a monomer at low laf-1 concentrations and as
CC       a dimer at high laf-1 concentrations.
CC       {ECO:0000269|PubMed:27546789}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:19361491,
CC       ECO:0000269|PubMed:26015579}. Cytoplasmic granule
CC       {ECO:0000269|PubMed:19361491, ECO:0000269|PubMed:26015579}.
CC       Note=Localizes to P granules in germline precursor cells.
CC       {ECO:0000269|PubMed:19361491}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=b {ECO:0000312|WormBase:Y71H2AM.19b};
CC         IsoId=D0PV95-1; Sequence=Displayed;
CC       Name=a {ECO:0000312|WormBase:Y71H2AM.19a};
CC         IsoId=D0PV95-2; Sequence=VSP_058672;
CC   -!- TISSUE SPECIFICITY: Expressed in the germline and soma of young
CC       adult hermaphrodites. {ECO:0000269|PubMed:19361491}.
CC   -!- DEVELOPMENTAL STAGE: Expressed at all developmental stages. Highly
CC       expressed in embryos with levels decreasing during larval
CC       development and increasing as animals reach adulthood.
CC       {ECO:0000269|PubMed:19361491}.
CC   -!- DOMAIN: The N-terminal domain is required for the multimeric
CC       binding of laf-1 to RNA. {ECO:0000269|PubMed:26015579,
CC       ECO:0000269|PubMed:27546789}.
CC   -!- DISRUPTION PHENOTYPE: Embryonic lethal or lethal at the first
CC       larval stage of development (PubMed:9043090). Embryos exhibit
CC       severe morphological defects (PubMed:9043090). RNAi-mediated
CC       knockdown results in embryonic lethality in 88% of animals
CC       (PubMed:19361491, PubMed:26015579). Knockdown also results in
CC       disrupted P granule organization and assembly in the early embryo
CC       (PubMed:26015579). Reduced survival in response to heat and
CC       oxidative stress (PubMed:24844228). Double RNAi knockdown with
CC       vbh-1 results in a high number of female offspring
CC       (PubMed:19361491). {ECO:0000269|PubMed:19361491,
CC       ECO:0000269|PubMed:24844228, ECO:0000269|PubMed:26015579,
CC       ECO:0000269|PubMed:9043090}.
CC   -!- SIMILARITY: Belongs to the DEAD box helicase family. DDX3/DED1
CC       subfamily. {ECO:0000305}.
DR   EMBL; FJ348231; ACO56244.1; -; mRNA.
DR   EMBL; BX284603; CCD73871.1; -; Genomic_DNA.
DR   EMBL; BX284603; CCG28150.1; -; Genomic_DNA.
DR   RefSeq; NP_001254858.1; NM_001267929.1. [D0PV95-2]
DR   RefSeq; NP_001254859.1; NM_001267930.1. [D0PV95-1]
DR   SMR; D0PV95; -.
DR   STRING; 6239.Y71H2AM.19b; -.
DR   EPD; D0PV95; -.
DR   PeptideAtlas; D0PV95; -.
DR   EnsemblMetazoa; Y71H2AM.19a.1; Y71H2AM.19a.1; WBGene00002244. [D0PV95-2]
DR   EnsemblMetazoa; Y71H2AM.19b.1; Y71H2AM.19b.1; WBGene00002244. [D0PV95-1]
DR   GeneID; 190611; -.
DR   KEGG; cel:CELE_Y71H2AM.19; -.
DR   CTD; 190611; -.
DR   WormBase; Y71H2AM.19a; CE38657; WBGene00002244; laf-1. [D0PV95-2]
DR   WormBase; Y71H2AM.19b; CE47305; WBGene00002244; laf-1. [D0PV95-1]
DR   eggNOG; KOG0335; Eukaryota.
DR   eggNOG; ENOG410XNTI; LUCA.
DR   GeneTree; ENSGT00940000168275; -.
DR   HOGENOM; HOG000268804; -.
DR   InParanoid; D0PV95; -.
DR   KO; K11594; -.
DR   OMA; CYRSWVR; -.
DR   OrthoDB; 595675at2759; -.
DR   Reactome; R-CEL-6798695; Neutrophil degranulation.
DR   PRO; PR:D0PV95; -.
DR   Proteomes; UP000001940; Chromosome III.
DR   Bgee; WBGene00002244; Expressed in 4 organ(s), highest expression level in material anatomical entity.
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:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0042803; F:protein homodimerization activity; IMP:UniProtKB.
DR   GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR   GO; GO:0003724; F:RNA helicase activity; IEA:UniProtKB-EC.
DR   GO; GO:0033592; F:RNA strand annealing activity; IMP:UniProtKB.
DR   GO; GO:0008186; F:RNA-dependent ATPase activity; IDA:UniProtKB.
DR   GO; GO:0030154; P:cell differentiation; IBA:GO_Central.
DR   GO; GO:0007276; P:gamete generation; IBA:GO_Central.
DR   GO; GO:0042006; P:masculinization of hermaphroditic germ-line; IMP:UniProtKB.
DR   GO; GO:0010629; P:negative regulation of gene expression; IMP:UniProtKB.
DR   GO; GO:0040019; P:positive regulation of embryonic development; IMP:UniProtKB.
DR   GO; GO:1905516; P:positive regulation of fertilization; IMP:UniProtKB.
DR   GO; GO:0006417; P:regulation of translation; IEA:UniProtKB-KW.
DR   DisProt; DP01113; -.
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   RNA-binding; Transcription; Transcription regulation;
KW   Translation regulation.
FT   CHAIN         1    708       ATP-dependent RNA helicase laf-1.
FT                                {ECO:0000305}.
FT                                /FTId=PRO_0000438522.
FT   DOMAIN      262    453       Helicase ATP-binding.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00541}.
FT   DOMAIN      465    626       Helicase C-terminal.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00542}.
FT   NP_BIND     275    282       ATP. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00541}.
FT   MOTIF       231    259       Q motif. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00552}.
FT   MOTIF       397    400       DEAD box. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00541}.
FT   COMPBIAS      9    168       Gly-rich. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00008}.
FT   COMPBIAS    624    691       Gly-rich. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00008}.
FT   VAR_SEQ      41    105       Missing (in isoform a). {ECO:0000305}.
FT                                /FTId=VSP_058672.
FT   MUTAGEN     426    426       R->C: In q80; embryonic lethal.
FT                                {ECO:0000269|PubMed:19361491}.
FT   MUTAGEN     430    430       M->I: In q217; embryonic lethal.
FT                                {ECO:0000269|PubMed:19361491}.
FT   MUTAGEN     434    434       T->I: In q267; embryonic lethal.
FT                                {ECO:0000269|PubMed:19361491}.
SQ   SEQUENCE   708 AA;  76343 MW;  13644AD830B03888 CRC64;
     MESNQSNNGG SGNAALNRGG RYVPPHLRGG DGGAAAAASA GGDDRRGGAG GGGYRRGGGN
     SGGGGGGGYD RGYNDNRDDR DNRGGSGGYG RDRNYEDRGY NGGGGGGGNR GYNNNRGGGG
     GGYNRQDRGD GGSSNFSRGG YNNRDEGSDN RGSGRSYNND RRDNGGDGQN TRWNNLDAPP
     SRGTSKWENR GARDERIEQE LFSGQLSGIN FDKYEEIPVE ATGDDVPQPI SLFSDLSLHE
     WIEENIKTAG YDRPTPVQKY SIPALQGGRD LMSCAQTGSG KTAAFLVPLV NAILQDGPDA
     VHRSVTSSGG RKKQYPSALV LSPTRELSLQ IFNESRKFAY RTPITSALLY GGRENYKDQI
     HKLRLGCHIL IATPGRLIDV MDQGLIGMEG CRYLVLDEAD RMLDMGFEPQ IRQIVECNRM
     PSKEERITAM FSATFPKEIQ LLAQDFLKEN YVFLAVGRVG STSENIMQKI VWVEEDEKRS
     YLMDLLDATG DSSLTLVFVE TKRGASDLAY YLNRQNYEVV TIHGDLKQFE REKHLDLFRT
     GTAPILVATA VAARGLDIPN VKHVINYDLP SDVDEYVHRI GRTGRVGNVG LATSFFNDKN
     RNIARELMDL IVEANQELPD WLEGMSGDMR SGGGYRGRGG RGNGQRFGGR DHRYQGGSGN
     GGGGNGGGGG FGGGGQRSGG GGGFQSGGGG GRQQQQQQRA QPQQDWWS
//
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