Entry euk: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   10-MAY-2017, entry version 51.
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   Cyprinidae; 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.,
RA   Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L.,
RA   McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C.,
RA   Koch R., Rauch G.J., White S., Chow W., Kilian B., Quintais L.T.,
RA   Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T.,
RA   Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F.,
RA   Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H.,
RA   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., Eliott D., Threadgold G.,
RA   Harden G., Ware D., Mortimer B., Kerry G., Heath P., Phillimore B.,
RA   Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S.,
RA   Griffiths G., Smith M., Glithero R., Howden P., Barker N., Stevens C.,
RA   Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H.,
RA   Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C.,
RA   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.,
RA   Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S.,
RA   Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R.,
RA   Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R.,
RA   Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R.,
RA   Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A.,
RA   Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M.,
RA   Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M.,
RA   Rudolph-Geiger S., Teucke M., Osoegawa K., Zhu B., Rapp A., Widaa S.,
RA   Langford C., Yang F., Carter N.P., Harrow J., Ning Z., Herrero J.,
RA   Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C.,
RA   Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H.,
RA   Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J.,
RA   Stemple D.L.;
RT   "The zebrafish reference genome sequence and its relationship to the
RT   human 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.,
RA   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
CC       DNA replication, DNA repair and heterochromatin organization as
CC       well as in ribosomal RNA synthesis. Plays a role in DNA double-
CC       strand break (DSB) repair at the DNA replication fork during DNA
CC       replication recovery from DNA damage. Plays a role in the
CC       regulation of sister chromatid cohesion and mitotic chromosome
CC       segregation. Stimulates 5'-single-stranded DNA flap endonuclease
CC       activity of FEN1 in an ATP- and helicase-independent manner. Plays
CC       also a role in heterochromatin organization (By similarity).
CC       Involved in rRNA transcription activation through binding to
CC       active hypomethylated rDNA gene loci by recruiting UBTF and the
CC       RNA polymerase Pol I transcriptional machinery (PubMed:26089203).
CC       Plays a role in embryonic development (PubMed:26089203).
CC       Associates with chromatin at DNA replication fork regions. Binds
CC       to single- and double-stranded DNAs (By similarity).
CC       {ECO:0000250|UniProtKB:Q6AXC6, ECO:0000250|UniProtKB:Q96FC9,
CC       ECO:0000269|PubMed:26089203}.
CC   -!- CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
CC       {ECO:0000250|UniProtKB:Q96FC9}.
CC   -!- COFACTOR:
CC       Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC         Evidence={ECO:0000250};
CC       Note=Binds 1 [4Fe-4S] cluster. {ECO:0000250};
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q96FC9}.
CC       Nucleus, nucleolus {ECO:0000250|UniProtKB:Q96FC9}. Cytoplasm,
CC       cytoskeleton, spindle pole {ECO:0000250|UniProtKB:Q96FC9}. Midbody
CC       {ECO:0000250|UniProtKB:Q96FC9}. Cytoplasm, cytoskeleton,
CC       microtubule organizing center, centrosome
CC       {ECO:0000250|UniProtKB:Q96FC9}.
CC   -!- DISRUPTION PHENOTYPE: Morpholino knockdown of the protein leads to
CC       abnormal craniofacial and vertebrate development with shortened
CC       and twisted torsos, smaller eyes and low mouth positions at 3 days
CC       post-fertilization (dpf). {ECO:0000269|PubMed:26089203}.
CC   -!- SIMILARITY: Belongs to the DEAD box helicase family. DEAH
CC       subfamily. DDX11/CHL1 sub-subfamily. {ECO:0000305}.
CC   -----------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution-NoDerivs License
CC   -----------------------------------------------------------------------
DR   EMBL; CU928088; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; BC085645; AAH85645.1; -; mRNA.
DR   RefSeq; NP_001007320.1; NM_001007319.1.
DR   UniGene; Dr.37620; -.
DR   ProteinModelPortal; 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   eggNOG; COG1199; LUCA.
DR   GeneTree; ENSGT00530000063199; -.
DR   HOGENOM; HOG000241266; -.
DR   HOVERGEN; HBG058884; -.
DR   InParanoid; F1R345; -.
DR   KO; K11273; -.
DR   OMA; GTLKYIL; -.
DR   OrthoDB; EOG091G034C; -.
DR   TreeFam; TF300435; -.
DR   PRO; PR:F1R345; -.
DR   Proteomes; UP000000437; Chromosome 18.
DR   Bgee; ENSDARG00000011072; -.
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: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:0004003; F:ATP-dependent DNA helicase activity; IEA:InterPro.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR   GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR   GO; GO:0007275; P:multicellular organism development; IEA:UniProtKB-KW.
DR   GO; GO:1990700; P:nucleolar chromatin organization; IMP:ZFIN.
DR   GO; GO:1901836; P:regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter; IMP:ZFIN.
DR   GO; GO:0009303; P:rRNA transcription; IMP:ZFIN.
DR   InterPro; IPR006555; ATP-dep_Helicase_C.
DR   InterPro; IPR010614; DEAD_2.
DR   InterPro; IPR013020; DNA_helicase_DNA-repair_Rad3.
DR   InterPro; IPR014013; Helic_SF1/SF2_ATP-bd_DinG/Rad3.
DR   InterPro; IPR006554; Helicase-like_DEXD_c2.
DR   InterPro; IPR027417; P-loop_NTPase.
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; 2.
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; Complete proteome; Cytoplasm;
KW   Cytoskeleton; Developmental protein; DNA damage; DNA repair;
KW   DNA replication; DNA-binding; Helicase; Hydrolase; Iron; Iron-sulfur;
KW   Metal-binding; Nucleotide-binding; Nucleus; Reference proteome;
KW   RNA-binding; Transcription; Transcription regulation.
FT   CHAIN         1    890       ATP-dependent DNA helicase DDX11.
FT                                /FTId=PRO_0000438279.
FT   DOMAIN        4    424       Helicase ATP-binding.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00541}.
FT   NP_BIND      39     46       ATP. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00541}.
FT   MOTIF       372    375       DEAH box. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00541}.
FT   METAL       246    246       Iron-sulfur (4Fe-4S). {ECO:0000250}.
FT   METAL       264    264       Iron-sulfur (4Fe-4S). {ECO:0000250}.
FT   METAL       294    294       Iron-sulfur (4Fe-4S). {ECO:0000250}.
FT   METAL       329    329       Iron-sulfur (4Fe-4S). {ECO:0000250}.
FT   CONFLICT      5      5       S -> N (in Ref. 2; AAH85645).
FT                                {ECO:0000305}.
FT   CONFLICT    160    160       A -> S (in Ref. 2; AAH85645).
FT                                {ECO:0000305}.
FT   CONFLICT    516    516       G -> W (in Ref. 2; AAH85645).
FT                                {ECO:0000305}.
FT   CONFLICT    565    565       V -> I (in Ref. 2; AAH85645).
FT                                {ECO:0000305}.
CC   --------------------------------------------------------------------------
CC   The following FT lines are automated annotations from the MyHits database.
CC   --------------------------------------------------------------------------
FT   MYHIT       675    862       ipfam:Helicase_C_2 [T]
FT   MYHIT         4    424       iprf:HELICASE_ATP_BIND_2 [T]
FT   MYHIT       210    393       ipfam:DEAD_2 [T]
FT   MYHIT       693    849       ismart:HELICc2 [T]
FT   MYHIT         6    416       ismart:DEXDc2 [T]
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
//