DHX9_CAEEL
ID DHX9_CAEEL Reviewed; 1301 AA.
AC Q22307;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 15-DEC-1998, sequence version 3.
DT 03-AUG-2022, entry version 166.
DE RecName: Full=ATP-dependent RNA helicase A {ECO:0000305};
DE EC=3.6.4.13 {ECO:0000250|UniProtKB:Q08211};
DE AltName: Full=Nuclear DNA helicase II {ECO:0000250|UniProtKB:Q08211};
DE Short=NDH II {ECO:0000250|UniProtKB:Q08211};
GN Name=rha-1; ORFNames=T07D4.3;
OS Caenorhabditis elegans.
OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
OC Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae;
OC Caenorhabditis.
OX NCBI_TaxID=6239;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Bristol N2;
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]
RP FUNCTION, AND TISSUE SPECIFICITY.
RX PubMed=15817227; DOI=10.1016/j.mod.2004.12.002;
RA Walstrom K.M., Schmidt D., Bean C.J., Kelly W.G.;
RT "RNA helicase A is important for germline transcriptional control,
RT proliferation, and meiosis in C. elegans.";
RL Mech. Dev. 122:707-720(2005).
CC -!- FUNCTION: Multifunctional ATP-dependent nucleic acid helicase that
CC unwinds DNA and RNA in a 3' to 5' direction and that plays important
CC roles in many processes, such as DNA replication, transcriptional
CC activation, post-transcriptional RNA regulation, mRNA translation and
CC RNA-mediated gene silencing. Requires a 3'-single-stranded tail as
CC entry site for acid nuclei unwinding activities as well as the binding
CC and hydrolyzing of any of the four ribo- or deoxyribo-nucleotide
CC triphosphates (NTPs). Binds to DNA, RNA and small interfering siRNA.
CC Plays a role in DNA replication at origins of replication and cell
CC cycle progression (By similarity). Plays a role as a transcriptional
CC coactivator acting as a bridging factor between polymerase II
CC holoenzyme and transcription factors or cofactors (PubMed:15817227).
CC Plays several roles in post-transcriptional regulation of gene
CC expression. Promotes pre-mRNA alternative splicing activities of a
CC subset of genes. As component of a large PER complex, is involved in
CC the negative regulation of 3' transcriptional termination of circadian
CC target genes. Component of the coding region determinant (CRD)-mediated
CC complex that promotes cytoplasmic MYC mRNA stability. Plays a role in
CC mRNA translation. Also plays a role in the RNA-induced silencing
CC complex (RISC) loading complex (RLC) assembly, and hence functions in
CC the RISC-mediated gene silencing process. Mediates the attachment of
CC heterogeneous nuclear ribonucleoproteins (hnRNPs) to actin filaments in
CC the nucleus (By similarity). {ECO:0000250|UniProtKB:Q08211,
CC ECO:0000269|PubMed:15817227}.
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:Q08211};
CC -!- SUBUNIT: Component of the coding region determinant (CRD)-mediated
CC complex. Identified in mRNP granule complexes containing untranslated
CC mRNAs. Associates with the RISC complex. Associates with the SMN
CC complex. Associates with polysomes. {ECO:0000250|UniProtKB:Q08211}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q08211}. Nucleus,
CC nucleoplasm {ECO:0000250|UniProtKB:Q08211}. Nucleus, nucleolus
CC {ECO:0000250|UniProtKB:Q08211}. Cytoplasm
CC {ECO:0000250|UniProtKB:Q08211}. Cytoplasm, cytoskeleton, microtubule
CC organizing center, centrosome {ECO:0000250|UniProtKB:Q08211}.
CC Note=Nucleoplasmic shuttling protein. Its nuclear import involves the
CC nucleocytoplasmic transport receptor Importin alpha/Importin beta
CC receptor pathway in a Ran-dependent manner. In interphase, localizes in
CC nuclear stress granules and at perichromatin fibrils and in cytoplasmic
CC ribonucleoprotein granules. Excluded from the mitotic nucleus as early
CC as prophase and re-entered the nucleus at telophase. Localized in
CC cytoplasmic mRNP granules containing untranslated mRNAs.
CC {ECO:0000250|UniProtKB:Q08211}.
CC -!- TISSUE SPECIFICITY: Expressed in the pachytene region of the gonad and
CC in the oocytes. {ECO:0000269|PubMed:15817227}.
CC -!- DOMAIN: DRBM domains cooperate for the binding to nucleic acid but not
CC for unwinding helicase activity. The helicase-associated domain-2 (HA2)
CC region is essential for the duplex RNA unwinding helicase activity. The
CC minimal transactivation region (MTAD) mediates interaction with the RNA
CC polymerase II holoenzyme and stimulates transcriptional activation. The
CC oligonucleotide- or oligosaccharide-binding (OB-fold) and the repeated
CC arginine and glycine-glycine (RGG) regions are dispensable for both
CC RNA-binding and unwinding helicase activities. The RGG region contains
CC both nuclear localization signal (NLS) and nuclear export signal (NES)
CC and is necessary and sufficient for nucleocytoplasmic shuttling in a
CC RNA-independent manner. {ECO:0000250|UniProtKB:Q08211}.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DEAH subfamily.
CC {ECO:0000305}.
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DR EMBL; Z50071; CAA90409.2; -; Genomic_DNA.
DR PIR; T24664; T24664.
DR RefSeq; NP_495890.2; NM_063489.5.
DR AlphaFoldDB; Q22307; -.
DR SMR; Q22307; -.
DR BioGRID; 39744; 5.
DR STRING; 6239.T07D4.3; -.
DR EPD; Q22307; -.
DR PaxDb; Q22307; -.
DR PeptideAtlas; Q22307; -.
DR EnsemblMetazoa; T07D4.3a.1; T07D4.3a.1; WBGene00004355.
DR GeneID; 174417; -.
DR UCSC; T07D4.3; c. elegans.
DR CTD; 174417; -.
DR WormBase; T07D4.3a; CE39177; WBGene00004355; rha-1.
DR eggNOG; KOG0921; Eukaryota.
DR GeneTree; ENSGT00940000155924; -.
DR HOGENOM; CLU_001832_1_2_1; -.
DR InParanoid; Q22307; -.
DR OMA; YGPETRM; -.
DR OrthoDB; 278674at2759; -.
DR PhylomeDB; Q22307; -.
DR Reactome; R-CEL-3134963; DEx/H-box helicases activate type I IFN and inflammatory cytokines production.
DR Reactome; R-CEL-72163; mRNA Splicing - Major Pathway.
DR PRO; PR:Q22307; -.
DR Proteomes; UP000001940; Chromosome II.
DR Bgee; WBGene00004355; Expressed in adult organism and 4 other tissues.
DR ExpressionAtlas; Q22307; baseline and differential.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005815; C:microtubule organizing center; IEA:UniProtKB-SubCell.
DR GO; GO:0005730; C:nucleolus; IBA:GO_Central.
DR GO; GO:0005654; C:nucleoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:1990904; C:ribonucleoprotein complex; ISS:UniProtKB.
DR GO; GO:0043138; F:3'-5' DNA helicase activity; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0003678; F:DNA helicase activity; ISS:UniProtKB.
DR GO; GO:0003690; F:double-stranded DNA binding; ISS:UniProtKB.
DR GO; GO:0003725; F:double-stranded RNA binding; ISS:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0003724; F:RNA helicase activity; IEA:UniProtKB-EC.
DR GO; GO:0007049; P:cell cycle; IEA:UniProtKB-KW.
DR GO; GO:0051301; P:cell division; IEA:UniProtKB-KW.
DR GO; GO:0032508; P:DNA duplex unwinding; ISS:UniProtKB.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR GO; GO:0006353; P:DNA-templated transcription, termination; IEA:UniProtKB-KW.
DR GO; GO:0031047; P:gene silencing by RNA; IEA:UniProtKB-KW.
DR GO; GO:0007281; P:germ cell development; IMP:WormBase.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0051028; P:mRNA transport; IEA:UniProtKB-KW.
DR GO; GO:0045814; P:negative regulation of gene expression, epigenetic; IMP:WormBase.
DR GO; GO:2000373; P:positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity; ISS:UniProtKB.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0050684; P:regulation of mRNA processing; IBA:GO_Central.
DR GO; GO:0006417; P:regulation of translation; IEA:UniProtKB-KW.
DR GO; GO:0008380; P:RNA splicing; IEA:UniProtKB-KW.
DR CDD; cd19854; DSRM_DHX9_rpt1; 1.
DR CDD; cd19855; DSRM_DHX9_rpt2; 1.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR011709; DEAD-box_helicase_OB_fold.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR044445; DHX9_DSRM_1.
DR InterPro; IPR044446; DHX9_DSRM_2.
DR InterPro; IPR002464; DNA/RNA_helicase_DEAH_CS.
DR InterPro; IPR014720; dsRBD_dom.
DR InterPro; IPR007502; Helicase-assoc_dom.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF00035; dsrm; 2.
DR Pfam; PF04408; HA2; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF07717; OB_NTP_bind; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00358; DSRM; 2.
DR SMART; SM00847; HA2; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR PROSITE; PS00690; DEAH_ATP_HELICASE; 1.
DR PROSITE; PS50137; DS_RBD; 2.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
PE 2: Evidence at transcript level;
KW Activator; ATP-binding; Cell cycle; Cell division; Cytoplasm; Cytoskeleton;
KW Developmental protein; DNA replication; DNA-binding; Helicase; Hydrolase;
KW Manganese; Metal-binding; Mitosis; mRNA processing; mRNA splicing;
KW mRNA transport; Nucleotide-binding; Nucleus; Reference proteome; Repeat;
KW RNA-binding; RNA-mediated gene silencing; Transcription;
KW Transcription regulation; Transcription termination;
KW Translation regulation; Transport.
FT CHAIN 1..1301
FT /note="ATP-dependent RNA helicase A"
FT /id="PRO_0000055161"
FT DOMAIN 4..73
FT /note="DRBM 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00266"
FT DOMAIN 171..244
FT /note="DRBM 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00266"
FT DOMAIN 391..563
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000250|UniProtKB:Q08211,
FT ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 645..818
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 6..10
FT /note="siRNA-binding"
FT /evidence="ECO:0000250|UniProtKB:Q08211"
FT REGION 55..57
FT /note="siRNA-binding"
FT /evidence="ECO:0000250|UniProtKB:Q08211"
FT REGION 226..228
FT /note="siRNA-binding"
FT /evidence="ECO:0000250|UniProtKB:Q08211"
FT REGION 326..373
FT /note="MTAD"
FT /evidence="ECO:0000250|UniProtKB:Q08211"
FT REGION 391..818
FT /note="Core helicase"
FT /evidence="ECO:0000250|UniProtKB:Q08211"
FT REGION 584..621
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 840..931
FT /note="HA2"
FT /evidence="ECO:0000250|UniProtKB:Q08211"
FT REGION 971..1089
FT /note="OB-fold"
FT /evidence="ECO:0000250|UniProtKB:Q08211"
FT REGION 1172..1301
FT /note="RGG"
FT /evidence="ECO:0000250|UniProtKB:Q08211"
FT REGION 1190..1239
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1275..1301
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 504..507
FT /note="DEAH box"
FT COMPBIAS 584..601
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1190..1205
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 404..412
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q08211,
FT ECO:0000255|PROSITE-ProRule:PRU00541"
FT BINDING 505
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000250|UniProtKB:Q08211"
SQ SEQUENCE 1301 AA; 144214 MW; 43801B81EAD2DF8F CRC64;
MSRDVKEFLY AWLGKNKYGN PTYDTKSETR SGRQRFKCEL RITGFGYTAF GNSTNKKDAA
TNAAQDFCQY LVREGKMQQS DIPTLTSSSL EASSTWQDSE TATMFCGGED GNSFQESQQP
IPQKRFPWSN NAYQRNEGTH EQYITQKAEE IAASETVDLK SEIHGGWTME NSKKALNEFL
QKMRLPQVNY GTKIRESNTV KTMETTAQIF VPQINKNLVG KGTGSNKKVS EAACAMNIVR
QMFHLNIMQS YSGPIKKSKV STLPEIAISI PEDLSTRVTE YVRSCGLELP EINETSATPE
APTSLLTDVK LAQFPVSEIC SASNISWAPP LQNWNPWRAS NIDEEPLAFM SMEQISQRIM
EKEDFKRGEA LDKITAQRGE LPVAQYRENI VQTVAENRVT LIKGETGCGK STQVAQFLLE
SFLENSNGAS FNAVVSQPRR ISAISLAERV ANERGEEVGE TCGYNVRFDS ATPRPYGSIM
FCTVGVLLRM MENGLRGISH VIIDEIHERD VDTDFVLIVL REMISTYRDL RVVLMSATID
TDLFTNFFSS IPDVGPTPVI TMHGRTFPVQ SFYLEDILHN LQHMPEEPDQ KKRKKGGPPP
PDDDEGDEEV DDKGRNMNIL TDPSINESLK TAMSRISEKD IPFGVIEAIL NDIASRGVDG
AVLVFLPGWA EIMTLCNRLL EHQEFGQANK YEILPLHSQL TSQEQRKVFN HYPGKRKIIV
STNIAETSIT IDDVVYVIDS CKAKERMYTS NNNMVHFATV WASKTNVIQR RGRAGRVRAG
YAFHLCSKMR FEALDDHGTA EMLRIPLHQI ALTIKLLRLG SVGEFLGKAL QPPPYDMVVE
SEAVLQAMGA LDRNLELTSL GKMLARMPIE PVIAKVLILG TALGAGSVMC DVASAMSFPT
PFVPREKHHS RLSGTQRKFA GNKFSDHVAI VSVIQGYREA VQMGASAAER EFCERYSLSN
PVLKMTDGAR RQLIDVLRNQ CSFPEDILFD ISVNVNGPDR ELNLMRSLLV MALYPNVAYY
VGKRKVLTIE QSSALINKYS MLVPMNNRQE MDFPSPLLVF TEKVRTRCIS CKQMSVISAI
QLLVFGSRKV ECVGEGLVRI DETITIRMNV STAAALIGLR PCIEALLVKS CENPESLAGL
NPSDAELRQL LRDISSEEFM SEAGPIKDSL LTDNALIQKG PAPNRLEYAD WGPSNNNSSF
QNQDFPPAAG GKVHPYRGNR RGNHPYAQNR PYAPPNSGMG YQNFNNSGYG ASGDWNAGRG
NYGNVGSGYR GAGGGGGYRG GRGGRGGGRG GGGRGWNASN W
