DHX9_XENLA
ID DHX9_XENLA Reviewed; 1262 AA.
AC Q68FK8;
DT 19-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2004, sequence version 1.
DT 03-AUG-2022, entry version 94.
DE RecName: Full=ATP-dependent RNA helicase A protein {ECO:0000250|UniProtKB:Q08211};
DE EC=3.6.4.13 {ECO:0000250|UniProtKB:Q08211};
DE AltName: Full=DEAH box protein 9 {ECO:0000250|UniProtKB:O70133};
DE AltName: Full=Nuclear DNA helicase II {ECO:0000250|UniProtKB:Q08211};
DE Short=NDH II {ECO:0000250|UniProtKB:Q08211};
GN Name=dhx9 {ECO:0000250|UniProtKB:Q08211};
OS Xenopus laevis (African clawed frog).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia;
OC Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Xenopus.
OX NCBI_TaxID=8355;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Embryo;
RG NIH - Xenopus Gene Collection (XGC) project;
RL Submitted (AUG-2004) to the EMBL/GenBank/DDBJ databases.
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. Plays a role as a transcriptional coactivator acting
CC as a bridging factor between polymerase II holoenzyme and transcription
CC factors or cofactors. Plays several roles in post-transcriptional
CC regulation of gene expression. Promotes pre-mRNA alternative splicing
CC activities of a subset of genes. As component of a large PER complex,
CC is involved in the negative regulation of 3' transcriptional
CC termination of circadian target genes. Component of the coding region
CC determinant (CRD)-mediated complex that promotes cytoplasmic MYC mRNA
CC stability. Plays a role in mRNA translation. Also plays a role in the
CC RNA-induced silencing complex (RISC) loading complex (RLC) assembly,
CC and hence functions in the RISC-mediated gene silencing process.
CC Mediates the attachment of heterogeneous nuclear ribonucleoproteins
CC (hnRNPs) to actin filaments in the nucleus.
CC {ECO:0000250|UniProtKB:Q08211}.
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 -!- 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; BC079701; AAH79701.1; -; mRNA.
DR RefSeq; NP_001087383.1; NM_001093914.1.
DR AlphaFoldDB; Q68FK8; -.
DR SMR; Q68FK8; -.
DR BioGRID; 104067; 1.
DR DNASU; 447207; -.
DR GeneID; 447207; -.
DR KEGG; xla:447207; -.
DR CTD; 447207; -.
DR Xenbase; XB-GENE-967780; dhx9.L.
DR OrthoDB; 278674at2759; -.
DR Proteomes; UP000186698; Chromosome 4L.
DR Bgee; 447207; Expressed in neurula embryo and 19 other tissues.
DR GO; GO:0015629; C:actin cytoskeleton; ISS:UniProtKB.
DR GO; GO:0070937; C:CRD-mediated mRNA stability complex; ISS:UniProtKB.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0036464; C:cytoplasmic ribonucleoprotein granule; ISS:UniProtKB.
DR GO; GO:0005815; C:microtubule organizing center; IEA:UniProtKB-SubCell.
DR GO; GO:0016604; C:nuclear body; ISS:UniProtKB.
DR GO; GO:0097165; C:nuclear stress granule; ISS:UniProtKB.
DR GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
DR GO; GO:0005654; C:nucleoplasm; ISS:UniProtKB.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0005726; C:perichromatin fibrils; ISS:UniProtKB.
DR GO; GO:0042788; C:polysomal ribosome; ISS:UniProtKB.
DR GO; GO:0005844; C:polysome; ISS:UniProtKB.
DR GO; GO:1990904; C:ribonucleoprotein complex; ISS:UniProtKB.
DR GO; GO:0016442; C:RISC complex; ISS:UniProtKB.
DR GO; GO:0070578; C:RISC-loading complex; ISS:UniProtKB.
DR GO; GO:0043138; F:3'-5' DNA helicase activity; ISS:UniProtKB.
DR GO; GO:0033679; F:3'-5' DNA/RNA helicase activity; ISS:UniProtKB.
DR GO; GO:0034458; F:3'-5' RNA helicase activity; ISS:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; ISS:UniProtKB.
DR GO; GO:0031490; F:chromatin DNA binding; ISS:UniProtKB.
DR GO; GO:0003677; F:DNA binding; ISS:UniProtKB.
DR GO; GO:0003678; F:DNA helicase activity; ISS:UniProtKB.
DR GO; GO:0003688; F:DNA replication origin binding; 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:0061676; F:importin-alpha family protein binding; ISS:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003729; F:mRNA binding; ISS:UniProtKB.
DR GO; GO:0017111; F:nucleoside-triphosphatase activity; ISS:UniProtKB.
DR GO; GO:0047429; F:nucleoside-triphosphate diphosphatase activity; ISS:UniProtKB.
DR GO; GO:1905538; F:polysome binding; ISS:UniProtKB.
DR GO; GO:1990841; F:promoter-specific chromatin binding; ISS:UniProtKB.
DR GO; GO:1905172; F:RISC complex binding; ISS:UniProtKB.
DR GO; GO:0003723; F:RNA binding; ISS:UniProtKB.
DR GO; GO:0003724; F:RNA helicase activity; ISS:UniProtKB.
DR GO; GO:0070063; F:RNA polymerase binding; ISS:UniProtKB.
DR GO; GO:0000978; F:RNA polymerase II cis-regulatory region sequence-specific DNA binding; ISS:UniProtKB.
DR GO; GO:0035613; F:RNA stem-loop binding; ISS:UniProtKB.
DR GO; GO:1990825; F:sequence-specific mRNA binding; ISS:UniProtKB.
DR GO; GO:1990518; F:single-stranded 3'-5' DNA helicase activity; ISS:UniProtKB.
DR GO; GO:0003697; F:single-stranded DNA binding; ISS:UniProtKB.
DR GO; GO:0003727; F:single-stranded RNA binding; ISS:UniProtKB.
DR GO; GO:0003713; F:transcription coactivator activity; ISS:UniProtKB.
DR GO; GO:0045142; F:triplex DNA binding; ISS:UniProtKB.
DR GO; GO:0000380; P:alternative mRNA splicing, via spliceosome; ISS:UniProtKB.
DR GO; GO:0071356; P:cellular response to tumor necrosis factor; ISS:UniProtKB.
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:0044806; P:G-quadruplex DNA unwinding; ISS:UniProtKB.
DR GO; GO:0098795; P:global gene silencing by mRNA cleavage; ISS:UniProtKB.
DR GO; GO:0051028; P:mRNA transport; IEA:UniProtKB-KW.
DR GO; GO:2000767; P:positive regulation of cytoplasmic translation; ISS:UniProtKB.
DR GO; GO:0045739; P:positive regulation of DNA repair; ISS:UniProtKB.
DR GO; GO:0045740; P:positive regulation of DNA replication; ISS:UniProtKB.
DR GO; GO:2000373; P:positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity; ISS:UniProtKB.
DR GO; GO:0048146; P:positive regulation of fibroblast proliferation; ISS:UniProtKB.
DR GO; GO:2000637; P:positive regulation of miRNA-mediated gene silencing; ISS:UniProtKB.
DR GO; GO:0051092; P:positive regulation of NF-kappaB transcription factor activity; ISS:UniProtKB.
DR GO; GO:1905698; P:positive regulation of polysome binding; ISS:UniProtKB.
DR GO; GO:0046833; P:positive regulation of RNA export from nucleus; ISS:UniProtKB.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; ISS:UniProtKB.
DR GO; GO:2000765; P:regulation of cytoplasmic translation; ISS:UniProtKB.
DR GO; GO:0050684; P:regulation of mRNA processing; ISS:UniProtKB.
DR GO; GO:0070922; P:RISC complex assembly; ISS:UniProtKB.
DR GO; GO:0010501; P:RNA secondary structure unwinding; ISS:UniProtKB.
DR CDD; cd17972; DEXHc_DHX9; 1.
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; IPR044447; DHX9_DEXHc.
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; Cytoplasm; Cytoskeleton; DNA replication;
KW DNA-binding; Helicase; Hydrolase; Manganese; Metal-binding;
KW mRNA processing; mRNA splicing; mRNA transport; Nucleotide-binding;
KW Nucleus; Reference proteome; Repeat; RNA-binding;
KW RNA-mediated gene silencing; Transcription; Transcription regulation;
KW Transcription termination; Translation regulation; Transport.
FT CHAIN 1..1262
FT /note="ATP-dependent RNA helicase A protein"
FT /id="PRO_0000055160"
FT DOMAIN 3..71
FT /note="DRBM 1"
FT /evidence="ECO:0000250|UniProtKB:Q08211,
FT ECO:0000255|PROSITE-ProRule:PRU00266"
FT DOMAIN 183..255
FT /note="DRBM 2"
FT /evidence="ECO:0000250|UniProtKB:Q08211,
FT ECO:0000255|PROSITE-ProRule:PRU00266"
FT DOMAIN 400..566
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000250|UniProtKB:Q08211,
FT ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 638..811
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 5..9
FT /note="siRNA-binding"
FT /evidence="ECO:0000250|UniProtKB:Q08211"
FT REGION 53..55
FT /note="siRNA-binding"
FT /evidence="ECO:0000250|UniProtKB:Q08211"
FT REGION 94..141
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 185..189
FT /note="siRNA-binding"
FT /evidence="ECO:0000250|UniProtKB:Q08211"
FT REGION 237..239
FT /note="siRNA-binding"
FT /evidence="ECO:0000250|UniProtKB:Q08211"
FT REGION 334..382
FT /note="MTAD"
FT /evidence="ECO:0000250|UniProtKB:Q08211"
FT REGION 400..811
FT /note="Core helicase"
FT /evidence="ECO:0000250|UniProtKB:Q08211"
FT REGION 588..614
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 833..921
FT /note="HA2"
FT /evidence="ECO:0000250|UniProtKB:Q08211"
FT REGION 960..1076
FT /note="OB-fold"
FT /evidence="ECO:0000250|UniProtKB:Q08211"
FT REGION 1152..1262
FT /note="RGG"
FT /evidence="ECO:0000250|UniProtKB:Q08211"
FT REGION 1197..1262
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 513..516
FT /note="DEIH box"
FT MOTIF 588..597
FT /note="Nuclear localization signal (NLS1)"
FT /evidence="ECO:0000255"
FT MOTIF 1158..1170
FT /note="Nuclear localization signal (NLS2)"
FT /evidence="ECO:0000250|UniProtKB:Q08211"
FT COMPBIAS 1230..1248
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 413..421
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q08211,
FT ECO:0000255|PROSITE-ProRule:PRU00541"
FT BINDING 420
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000250|UniProtKB:Q08211"
FT BINDING 514
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000250|UniProtKB:Q08211"
SQ SEQUENCE 1262 AA; 140529 MW; EDBAD68B70946D5F CRC64;
MADIKNFLYA WCGKKKLTPN YEIRAAGNKN RQKFMCEVRI DGFNYIGMGN STNKKDAQTN
SARDFVNYLV RVGEMRSDEV PSLGAELGDS IDGASLKSEG FSGPTGGPLP PHLSLQAESS
GAAPMRSNTG FNPPAYGGGA QWERGANLKD YYAKREEQEA QATLESEEVD LNAGLHGNWT
LENAKARLNQ FFQKEKTQGE YKYSQVGPDH NRSFIAEMTL YVKQLGRKII AREHGSNKKL
AAQSCALSIV RQLYHLSVIE PYSGLTKKKE GESVEPYQVN LNPDIVKQLQ STIQELGIEL
PYPPEDPSQP VSLNLGKLVH FEPSQKQSHS GVVPWSPPQE NWNPWTSSNI DEGPLAFATQ
EQISLELKNE HMYHIQDPNI KQVLIDRESL PVKKFEEEIM HAVHNSPVVI IRGATGCGKT
TQVPQYILDE YIRNDRAAQC NIVVTQPRRI SAVSVAERVA FERGEEIGKS CGYSVRFESV
LPRPHASMLF CTVGVLLRKL ESGIRGISHV IVDEIHERDI NTDFLLVVLR DVIQAFPEIR
VILMSATIDT SMFCEYFFNC PIIEVFGRTF PVQEYYLEDC IQMTQFIPPP RDKKKKDKDE
EGGDDEETNC NLVCGDDYGP ETRRSMSQLS EKETPLELIE ALLKYIETLN VPGAVLVFLP
GWNLIYAMQK HLEMNPHFGS HSYCILPLHS QIPRDEQRKV FDPVPDGIIK VILSTNIAET
SITINDVVYV IDSCKQKVKL FTSHNNMTNY ATVWASKTNL EQRKGRAGRV RPGFCFHLCS
KARFDKLETH LTPEIFRTPL HEVALSIKLL RLGGIGHFLS KAIEPPPLDA VIEAEHTLRE
LDALDSNDEL TPLGRILAKL PIEPRLGKMM IIGCIFYVGD ALCTISAATC FPEPFISEGR
RLGYVHRNFA GNRFSDHVAL LSVFQAWDDA RMGGEDAETR FCEHKRLNMA TLRMTWEAKV
QLKDILVNAG FPEECLMNQV FNNTGPDNNL DVVISLLAFG VYPNVCYHKE KRKILTTEGR
NALIHKSSVN CPFSNQDLKY PSPFFVFSEK IRTRAISAKG MTMVSPLQLL LFASKKVMSD
GEFIHLDDWI KLSMAHEESA CITALRAALE ALVVEVTKEP EILSQLDPVN EKMLNMIRVI
SKPSTAGISL VMGNSRFGDG PRPPKMARFD SGFQGNRGRG YHGGYNSGGG FRGAGNRGFR
GSRGGSGPRG GYQGGGFRGN YRGGNQGGGF RGGYQSQGGY QSQGGGGYGG NFQGRGGFRG
GF
