DDX1_RAT
ID DDX1_RAT Reviewed; 740 AA.
AC Q641Y8;
DT 27-SEP-2005, integrated into UniProtKB/Swiss-Prot.
DT 25-OCT-2004, sequence version 1.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=ATP-dependent RNA helicase DDX1;
DE EC=3.6.4.13;
DE AltName: Full=DEAD box protein 1;
GN Name=Ddx1;
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Testis;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [2]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-481, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22673903; DOI=10.1038/ncomms1871;
RA Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C.,
RA Olsen J.V.;
RT "Quantitative maps of protein phosphorylation sites across 14 different rat
RT organs and tissues.";
RL Nat. Commun. 3:876-876(2012).
CC -!- FUNCTION: Acts as an ATP-dependent RNA helicase, able to unwind both
CC RNA-RNA and RNA-DNA duplexes. Possesses 5' single-stranded RNA overhang
CC nuclease activity. Possesses ATPase activity on various RNA, but not
CC DNA polynucleotides. May play a role in RNA clearance at DNA double-
CC strand breaks (DSBs), thereby facilitating the template-guided repair
CC of transcriptionally active regions of the genome. Together with RELA,
CC acts as a coactivator to enhance NF-kappa-B-mediated transcriptional
CC activation. Acts as a positive transcriptional regulator of cyclin
CC CCND2 expression. Binds to the cyclin CCND2 promoter region. Associates
CC with chromatin at the NF-kappa-B promoter region via association with
CC RELA. Binds to poly(A) RNA. May be involved in 3'-end cleavage and
CC polyadenylation of pre-mRNAs. Component of the tRNA-splicing ligase
CC complex required to facilitate the enzymatic turnover of catalytic
CC subunit RTCB: together with archease (ZBTB8OS), acts by facilitating
CC the guanylylation of RTCB, a key intermediate step in tRNA ligation.
CC Component of a multi-helicase-TICAM1 complex that acts as a cytoplasmic
CC sensor of viral double-stranded RNA (dsRNA) and plays a role in the
CC activation of a cascade of antiviral responses including the induction
CC of pro-inflammatory cytokines via the adapter molecule TICAM1.
CC Specifically binds (via helicase ATP-binding domain) on both short and
CC long poly(I:C) dsRNA (By similarity). {ECO:0000250|UniProtKB:Q91VR5,
CC ECO:0000250|UniProtKB:Q92499}.
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 -!- SUBUNIT: Found in a multi-helicase-TICAM1 complex at least composed of
CC DHX36, DDX1, DDX21 and TICAM1; this complex exists in resting cells
CC with or without poly(I:C) RNA ligand stimulation (By similarity).
CC Interacts with DHX36 (By similarity). Interacts (via B30.2/SPRY domain)
CC with DDX21 (via N-terminus); this interaction serves as bridges to
CC TICAM1 (By similarity). Interacts with FAM98A (via N- and C-terminus)
CC (By similarity). Interacts with PHF5A (via C-terminus) (By similarity).
CC Interacts with MBNL1 (By similarity). Interacts with CSTF2 (By
CC similarity). Interacts with HNRNPK (By similarity). Interacts with ATM
CC (By similarity). Interacts with RELA (via C-terminus) (By similarity).
CC Component of the tRNA-splicing ligase complex (By similarity).
CC Interacts with PQBP1 (By similarity). Interacts with ERCC6 (By
CC similarity). {ECO:0000250|UniProtKB:Q91VR5,
CC ECO:0000250|UniProtKB:Q92499}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q92499}. Cytoplasm
CC {ECO:0000250|UniProtKB:Q92499}. Cytoplasmic granule
CC {ECO:0000250|UniProtKB:Q92499}. Cytoplasm, cytosol
CC {ECO:0000250|UniProtKB:Q91VR5}. Mitochondrion
CC {ECO:0000250|UniProtKB:Q91VR5}. Note=Localized with MBNL1, TIAL1 and
CC YBX1 in stress granules upon stress. Localized with CSTF2 in cleavage
CC bodies. Forms large aggregates called DDX1 bodies. Relocalized into
CC multiple foci (IR-induced foci or IRIF) after IR treatment, a process
CC that depends on the presence of chromosomal DNA and/or RNA-DNA
CC duplexes. Relocalized at sites of DNA double-strand breaks (DSBs) in an
CC ATM-dependent manner after IR treatment. Colocalized with RELA in the
CC nucleus upon TNF-alpha induction. Enters into the nucleus in case of
CC active transcription while it accumulates in cytosol when transcription
CC level is low. Colocalizes in the cytosol with DDX21, DHX36 and TICAM1.
CC Colocalizes in the mitochondria with TICAM1 and poly(I:C) RNA ligand.
CC The multi-helicase-TICAM1 complex may translocate to the mitochondria
CC upon poly(I:C) stimulation (By similarity).
CC {ECO:0000250|UniProtKB:Q91VR5, ECO:0000250|UniProtKB:Q92499}.
CC -!- DOMAIN: The helicase domain is involved in the stimulation of RELA
CC transcriptional activity. {ECO:0000250|UniProtKB:Q92499}.
CC -!- PTM: Phosphorylated by ATM kinase; phosphorylation is increased in
CC response to ionizing radiation (IR). {ECO:0000250|UniProtKB:Q92499}.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DDX1 subfamily.
CC {ECO:0000305}.
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DR EMBL; BC082049; AAH82049.1; -; mRNA.
DR RefSeq; NP_445866.1; NM_053414.1.
DR AlphaFoldDB; Q641Y8; -.
DR SMR; Q641Y8; -.
DR BioGRID; 249974; 3.
DR IntAct; Q641Y8; 3.
DR STRING; 10116.ENSRNOP00000009100; -.
DR iPTMnet; Q641Y8; -.
DR PhosphoSitePlus; Q641Y8; -.
DR jPOST; Q641Y8; -.
DR PaxDb; Q641Y8; -.
DR PRIDE; Q641Y8; -.
DR Ensembl; ENSRNOT00000009100; ENSRNOP00000009100; ENSRNOG00000006652.
DR GeneID; 84474; -.
DR KEGG; rno:84474; -.
DR CTD; 1653; -.
DR RGD; 619903; Ddx1.
DR eggNOG; KOG0349; Eukaryota.
DR GeneTree; ENSGT00940000155678; -.
DR HOGENOM; CLU_016321_0_0_1; -.
DR InParanoid; Q641Y8; -.
DR OMA; EYCIRAI; -.
DR OrthoDB; 973872at2759; -.
DR PhylomeDB; Q641Y8; -.
DR TreeFam; TF106114; -.
DR PRO; PR:Q641Y8; -.
DR Proteomes; UP000002494; Chromosome 6.
DR Bgee; ENSRNOG00000006652; Expressed in skeletal muscle tissue and 20 other tissues.
DR Genevisible; Q641Y8; RN.
DR GO; GO:0071920; C:cleavage body; ISS:UniProtKB.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0010494; C:cytoplasmic stress granule; ISS:UniProtKB.
DR GO; GO:0005829; C:cytosol; ISS:UniProtKB.
DR GO; GO:0005739; C:mitochondrion; ISS:UniProtKB.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:1990904; C:ribonucleoprotein complex; ISO:RGD.
DR GO; GO:0072669; C:tRNA-splicing ligase complex; ISS:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0003682; F:chromatin binding; ISS:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0033677; F:DNA/RNA helicase activity; ISS:UniProtKB.
DR GO; GO:0003725; F:double-stranded RNA binding; ISO:RGD.
DR GO; GO:0004527; F:exonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0004518; F:nuclease activity; ISS:UniProtKB.
DR GO; GO:0008143; F:poly(A) binding; ISS:UniProtKB.
DR GO; GO:0003724; F:RNA helicase activity; ISS:UniProtKB.
DR GO; GO:0003712; F:transcription coregulator activity; ISS:UniProtKB.
DR GO; GO:0051607; P:defense response to virus; IEA:UniProtKB-KW.
DR GO; GO:0032508; P:DNA duplex unwinding; ISS:UniProtKB.
DR GO; GO:0006302; P:double-strand break repair; ISS:UniProtKB.
DR GO; GO:0045087; P:innate immune response; IEA:UniProtKB-KW.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0090305; P:nucleic acid phosphodiester bond hydrolysis; ISO:RGD.
DR GO; GO:0043123; P:positive regulation of I-kappaB kinase/NF-kappaB signaling; ISS:UniProtKB.
DR GO; GO:0002735; P:positive regulation of myeloid dendritic cell cytokine production; ISO:RGD.
DR GO; GO:1903608; P:protein localization to cytoplasmic stress granule; ISO:RGD.
DR GO; GO:0043330; P:response to exogenous dsRNA; ISO:RGD.
DR GO; GO:0009615; P:response to virus; ISO:RGD.
DR GO; GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation; ISS:UniProtKB.
DR Gene3D; 2.60.120.920; -; 1.
DR Gene3D; 3.40.50.300; -; 3.
DR InterPro; IPR001870; B30.2/SPRY.
DR InterPro; IPR043136; B30.2/SPRY_sf.
DR InterPro; IPR013320; ConA-like_dom_sf.
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; IPR014014; RNA_helicase_DEAD_Q_motif.
DR InterPro; IPR003877; SPRY_dom.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF00622; SPRY; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SMART; SM00449; SPRY; 1.
DR SUPFAM; SSF49899; SSF49899; 1.
DR SUPFAM; SSF52540; SSF52540; 2.
DR PROSITE; PS50188; B302_SPRY; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 2.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS51195; Q_MOTIF; 1.
PE 1: Evidence at protein level;
KW Acetylation; Activator; Antiviral defense; ATP-binding; Cytoplasm;
KW DNA-binding; Exonuclease; Helicase; Hydrolase; Immunity; Innate immunity;
KW Isopeptide bond; Mitochondrion; mRNA processing; Nuclease;
KW Nucleotide-binding; Nucleus; Phosphoprotein; Reference proteome;
KW RNA-binding; Transcription; Transcription regulation; tRNA processing;
KW Ubl conjugation.
FT CHAIN 1..740
FT /note="ATP-dependent RNA helicase DDX1"
FT /id="PRO_0000054988"
FT DOMAIN 2..428
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 70..247
FT /note="B30.2/SPRY"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00548"
FT DOMAIN 493..681
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 1..525
FT /note="Necessary for interaction with RELA"
FT /evidence="ECO:0000250|UniProtKB:Q92499"
FT REGION 1..448
FT /note="Interaction with dsRNA"
FT /evidence="ECO:0000250|UniProtKB:Q91VR5"
FT REGION 1..295
FT /note="Necessary for interaction with HNRNPK"
FT /evidence="ECO:0000250|UniProtKB:Q92499"
FT REGION 525..740
FT /note="Necessary for interaction with HNRNPK"
FT /evidence="ECO:0000250|UniProtKB:Q92499"
FT MOTIF 370..373
FT /note="DEAD box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT BINDING 46..53
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MOD_RES 239
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q92499"
FT MOD_RES 268
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q92499"
FT MOD_RES 281
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q92499"
FT MOD_RES 481
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT CROSSLNK 281
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2); alternate"
FT /evidence="ECO:0000250|UniProtKB:Q92499"
SQ SEQUENCE 740 AA; 82497 MW; D128A389944F0BF8 CRC64;
MAAFSEMGVM PEIAQAVEEM DWLLPTDIQA ESIPLILGGG DVLMAAETGS GKTGAFSIPV
IQIVYETLKD QQEGKKGKAT IKTGASVLNK WQMNPYDRGS AFAIGSDGLC CQSREVKEWH
GCRATRGLLR GKHYYEVSCH DQGLCRVGWS TMQASLDLGT DKFGFGFGGT GKKSHNKQFD
NYGEEFTMHD TIGCYLDIDK GHVKFSKNGK DLGLAFEIPA HIKNQALFPA CVLKNAELKF
NFGEEEFKFP PKDGFVALSK APDSYVVKSQ HTGNAQVSQT KFLPNAPKAL IVEPSRELAE
QTLNNVKQFK KYIDNPKLRE LLIIGGVAAR DQLSVLDNGV DIVVGTPGRL DDLVSTGKLN
LSQVRFLVLD EADGLLSQGY SDFINRMHNQ IPQITSDGKR LQVIVCSATL HSFDVKKLSE
KIMHFPTWVD LKGEDSVPDT VHHVVVPVNP KTDRLWERLG KNHIRTDDVH AKDNTRPGAN
SPEMWSEAIK ILKGEYAVRA IKEHKMDQAI IFCRTKIDCD NLEQYFMQQG GGPDKKGHQF
SCVCLHGDRK PHERKQNLER FKKGDVRFLI CTDVAARGID IHGVPYVINV TLPDEKQNYV
HRIGRVGRAE RMGLAISLVA TEKEKVWYHV CSNRGKGCYN TRLKEDGGCT IWYNEMQLLS
EIEEHLNCTI SQVEPDIKVP VDEFDGKVTY GQKRAAGGGN YKGHVDILAP TVQELAALEK
EAQTSFLHLG YLPNQLFRTF
