DDX11_DANRE
ID DDX11_DANRE Reviewed; 890 AA.
AC F1R345; Q5U399;
DT 02-NOV-2016, integrated into UniProtKB/Swiss-Prot.
DT 03-MAY-2011, sequence version 1.
DT 03-AUG-2022, entry version 74.
DE RecName: Full=ATP-dependent DNA helicase DDX11 {ECO:0000305};
DE EC=3.6.4.12 {ECO:0000250|UniProtKB:Q96FC9};
DE AltName: Full=DEAD/H-box protein 11 {ECO:0000250|UniProtKB:Q96FC9};
GN Name=ddx11 {ECO:0000250|UniProtKB:Q96FC9}; Synonyms=zgc:92172;
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen;
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Embryo;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=26089203; DOI=10.1093/hmg/ddv213;
RA Sun X., Chen H., Deng Z., Hu B., Luo H., Zeng X., Han L., Cai G., Ma L.;
RT "The Warsaw breakage syndrome-related protein DDX11 is required for
RT ribosomal RNA synthesis and embryonic development.";
RL Hum. Mol. Genet. 24:4901-4915(2015).
CC -!- FUNCTION: DNA-dependent ATPase and ATP-dependent DNA helicase that
CC participates in various functions in genomic stability, including DNA
CC replication, DNA repair and heterochromatin organization as well as in
CC ribosomal RNA synthesis. Plays a role in DNA double-strand break (DSB)
CC repair at the DNA replication fork during DNA replication recovery from
CC DNA damage. Plays a role in the regulation of sister chromatid cohesion
CC and mitotic chromosome segregation. Stimulates 5'-single-stranded DNA
CC flap endonuclease activity of FEN1 in an ATP- and helicase-independent
CC manner. Also plays a role in heterochromatin organization (By
CC similarity). Involved in rRNA transcription activation through binding
CC to active hypomethylated rDNA gene loci by recruiting UBTF and the RNA
CC polymerase Pol I transcriptional machinery (PubMed:26089203). Plays a
CC role in embryonic development (PubMed:26089203). Associates with
CC chromatin at DNA replication fork regions. Binds to single- and double-
CC stranded DNAs (By similarity). {ECO:0000250|UniProtKB:Q6AXC6,
CC ECO:0000250|UniProtKB:Q96FC9, ECO:0000269|PubMed:26089203}.
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=3.6.4.12;
CC Evidence={ECO:0000250|UniProtKB:Q96FC9};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; Evidence={ECO:0000250};
CC Note=Binds 1 [4Fe-4S] cluster. {ECO:0000250};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q96FC9}. Nucleus,
CC nucleolus {ECO:0000250|UniProtKB:Q96FC9}. Cytoplasm, cytoskeleton,
CC spindle pole {ECO:0000250|UniProtKB:Q96FC9}. Midbody
CC {ECO:0000250|UniProtKB:Q96FC9}. Cytoplasm, cytoskeleton, microtubule
CC organizing center, centrosome {ECO:0000250|UniProtKB:Q96FC9}.
CC -!- DISRUPTION PHENOTYPE: Morpholino knockdown of the protein leads to
CC abnormal craniofacial and vertebrate development with shortened and
CC twisted torsos, smaller eyes and low mouth positions at 3 days post-
CC fertilization (dpf). {ECO:0000269|PubMed:26089203}.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DEAH subfamily.
CC DDX11/CHL1 sub-subfamily. {ECO:0000305}.
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DR EMBL; CU928088; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC085645; AAH85645.1; -; mRNA.
DR RefSeq; NP_001007320.1; NM_001007319.1.
DR AlphaFoldDB; F1R345; -.
DR SMR; F1R345; -.
DR STRING; 7955.ENSDARP00000025514; -.
DR PaxDb; F1R345; -.
DR Ensembl; ENSDART00000009217; ENSDARP00000025514; ENSDARG00000011072.
DR GeneID; 492353; -.
DR KEGG; dre:492353; -.
DR CTD; 1663; -.
DR ZFIN; ZDB-GENE-041114-191; ddx11.
DR eggNOG; KOG1133; Eukaryota.
DR GeneTree; ENSGT00950000182970; -.
DR HOGENOM; CLU_006515_2_1_1; -.
DR InParanoid; F1R345; -.
DR OMA; QTHQFRD; -.
DR OrthoDB; 186062at2759; -.
DR PhylomeDB; F1R345; -.
DR TreeFam; TF300435; -.
DR PRO; PR:F1R345; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 18.
DR Bgee; ENSDARG00000011072; Expressed in mature ovarian follicle and 27 other tissues.
DR ExpressionAtlas; F1R345; baseline.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-KW.
DR GO; GO:0005815; C:microtubule organizing center; IEA:UniProtKB-SubCell.
DR GO; GO:0030496; C:midbody; IEA:UniProtKB-SubCell.
DR GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0000922; C:spindle pole; IEA:UniProtKB-SubCell.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003678; F:DNA helicase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0032508; P:DNA duplex unwinding; IBA:GO_Central.
DR GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR GO; GO:0034085; P:establishment of sister chromatid cohesion; IBA:GO_Central.
DR GO; GO:1990700; P:nucleolar chromatin organization; IMP:ZFIN.
DR GO; GO:1901836; P:regulation of transcription of nucleolar large rRNA by RNA polymerase I; IMP:ZFIN.
DR GO; GO:0009303; P:rRNA transcription; IMP:ZFIN.
DR Gene3D; 3.40.50.300; -; 3.
DR InterPro; IPR006555; ATP-dep_Helicase_C.
DR InterPro; IPR028331; CHL1/DDX11.
DR InterPro; IPR010614; DEAD_2.
DR InterPro; IPR045028; DinG/Rad3-like.
DR InterPro; IPR014013; Helic_SF1/SF2_ATP-bd_DinG/Rad3.
DR InterPro; IPR006554; Helicase-like_DEXD_c2.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR013020; Rad3/Chl1-like.
DR PANTHER; PTHR11472; PTHR11472; 1.
DR PANTHER; PTHR11472:SF41; PTHR11472:SF41; 1.
DR Pfam; PF06733; DEAD_2; 1.
DR Pfam; PF13307; Helicase_C_2; 1.
DR SMART; SM00488; DEXDc2; 1.
DR SMART; SM00491; HELICc2; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR00604; rad3; 1.
DR PROSITE; PS51193; HELICASE_ATP_BIND_2; 1.
PE 2: Evidence at transcript level;
KW 4Fe-4S; Activator; ATP-binding; Cytoplasm; Cytoskeleton;
KW Developmental protein; DNA damage; DNA repair; DNA replication;
KW DNA-binding; Helicase; Hydrolase; Iron; Iron-sulfur; Metal-binding;
KW Nucleotide-binding; Nucleus; Reference proteome; RNA-binding;
KW Transcription; Transcription regulation.
FT CHAIN 1..890
FT /note="ATP-dependent DNA helicase DDX11"
FT /id="PRO_0000438279"
FT DOMAIN 4..424
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT REGION 71..95
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 176..199
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 372..375
FT /note="DEAH box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT BINDING 39..46
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT BINDING 246
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 264
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 294
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 329
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT CONFLICT 5
FT /note="S -> N (in Ref. 2; AAH85645)"
FT /evidence="ECO:0000305"
FT CONFLICT 160
FT /note="A -> S (in Ref. 2; AAH85645)"
FT /evidence="ECO:0000305"
FT CONFLICT 516
FT /note="G -> W (in Ref. 2; AAH85645)"
FT /evidence="ECO:0000305"
FT CONFLICT 565
FT /note="V -> I (in Ref. 2; AAH85645)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 890 AA; 100475 MW; CC029C3566C23BA9 CRC64;
MESKSGRFPF PFQPYPIQES FMEALYTALD QRKVGIFESP TGTGKSLSLI CGALTWLRDY
EEQRKQEAAR LLEGQKDSDV VKEKNSNSGP PEPDWVSEFV QKKAERDMVN KLKDEELKRK
KREERLEMIR HNAQLRYAMK RKADEDDEAV KLLQLSREGA EPETHSPEEE GLIVAEYESD
DEATPKSRLC DDDNDDDDDL EEEHVTKIYY CSRTHSQLAQ FVHEVQKSPY GDAVRLVNLG
SRQNLCINPE VVRLGNVQMM NERCLEMQKN KHEKRQKASD SESKRSRGLA KATCVFSRFE
NLMAMKDEVL VKVRDVEQLI QHGRETHTCP YYSTRMSIPA AQVVVLPYQS LLHASTRKAS
GIKLKDQIVI IDEAHNLMDT ISAIHSAEIS GGQLCRAHSQ LSQYCERYRS RLKAKNLMYI
KQILFVLEGL VRTLGGKVGQ NPNTQSCQTG SELLTINDFL FKAQVDNINL FKVQKYFEKS
MISRKLCGFA EKYEGSGINT HSSSKNKENR RTEGLGRFLQ TLQSKPTDVS EQQMAVEDKP
IMASPMMLAE SFLFALTNAN KDGRVVIQRQ ACVAQSSLKF LLLNAAVHFA QILQECRAVI
IAGGTMQPVA DFKEQLLFSA GVTEERILEF SCGHVIPPEN ILPIVLCAGP SGQQLEFTFQ
TRDSPQMMEE TGRVLSNLCN IVPGGVVCFF PSYEYEKRIL GHWESTGILQ RLQSKKKIFQ
EPKKASQVEQ VLSEYSKCIQ RCSNIGGGQT GALLFSVVGG KMSEGINFSD DLGRCIVMVG
MPYPNIKSPE LQEKMAYLDK HMPHVAGKSP GKALVESLCM KAVNQSIGRA IRHRGDYACI
VLCDHRYART GTLQKLPEWI RSSTHTHATF GPAFASARRF FLEKRQKATL
