CHD3_DROME
ID CHD3_DROME Reviewed; 892 AA.
AC O16102; Q8SYJ8; Q9VVZ3;
DT 15-NOV-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 3.
DT 03-AUG-2022, entry version 185.
DE RecName: Full=Chromodomain-helicase-DNA-binding protein 3 {ECO:0000303|PubMed:18250149};
DE EC=3.6.4.12 {ECO:0000269|PubMed:18250149};
DE AltName: Full=ATP-dependent helicase Chd3 {ECO:0000305|PubMed:18250149};
GN Name=Chd3 {ECO:0000303|PubMed:18250149, ECO:0000312|FlyBase:FBgn0023395};
GN ORFNames=CG9594 {ECO:0000312|FlyBase:FBgn0023395};
OS Drosophila melanogaster (Fruit fly).
OC Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea;
OC Drosophilidae; Drosophila; Sophophora.
OX NCBI_TaxID=7227 {ECO:0000312|EMBL:AAF49162.2};
RN [1] {ECO:0000305}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Berkeley;
RX PubMed=10731132; DOI=10.1126/science.287.5461.2185;
RA Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
RA Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
RA George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
RA Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X., Brandon R.C.,
RA Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C.,
RA Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A.,
RA An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A.,
RA Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V.,
RA Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J.,
RA Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E.,
RA Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B.,
RA Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I.,
RA Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C.,
RA Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S.,
RA Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M.,
RA Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M.,
RA Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D.,
RA Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F.,
RA Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D.,
RA Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A.,
RA Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C.,
RA McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C.,
RA Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L.,
RA Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R.,
RA Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V.,
RA Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F.,
RA Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J.,
RA Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R.,
RA Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y.,
RA Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T.,
RA Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S.,
RA Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W.,
RA Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M.,
RA Venter J.C.;
RT "The genome sequence of Drosophila melanogaster.";
RL Science 287:2185-2195(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=Berkeley;
RX PubMed=12537572; DOI=10.1186/gb-2002-3-12-research0083;
RA Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S.,
RA Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E.,
RA Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P.,
RA Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A.,
RA Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q., Stapleton M.,
RA Yamada C., Ashburner M., Gelbart W.M., Rubin G.M., Lewis S.E.;
RT "Annotation of the Drosophila melanogaster euchromatic genome: a systematic
RT review.";
RL Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=Berkeley; TISSUE=Embryo;
RX PubMed=12537569; DOI=10.1186/gb-2002-3-12-research0080;
RA Stapleton M., Carlson J.W., Brokstein P., Yu C., Champe M., George R.A.,
RA Guarin H., Kronmiller B., Pacleb J.M., Park S., Wan K.H., Rubin G.M.,
RA Celniker S.E.;
RT "A Drosophila full-length cDNA resource.";
RL Genome Biol. 3:RESEARCH0080.1-RESEARCH0080.8(2002).
RN [4] {ECO:0000305}
RP NUCLEOTIDE SEQUENCE [MRNA] OF 1-812.
RX PubMed=9326634; DOI=10.1073/pnas.94.21.11472;
RA Woodage T., Basrai M.A., Baxevanis A.D., Hieter P., Collins F.S.;
RT "Characterization of the CHD family of proteins.";
RL Proc. Natl. Acad. Sci. U.S.A. 94:11472-11477(1997).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, SUBUNIT, SUBCELLULAR
RP LOCATION, DEVELOPMENTAL STAGE, AND MUTAGENESIS OF 1-MET--ILE-80;
RP 1-MET--ARG-240 AND 801-SER--MET-892.
RX PubMed=18250149; DOI=10.1128/mcb.01839-07;
RA Murawska M., Kunert N., van Vugt J., Laengst G., Kremmer E., Logie C.,
RA Brehm A.;
RT "dCHD3, a novel ATP-dependent chromatin remodeler associated with sites of
RT active transcription.";
RL Mol. Cell. Biol. 28:2745-2757(2008).
CC -!- FUNCTION: Helicase which acts in nucleosome-remodeling by catalyzing
CC ATP-dependent nucleosome mobilization (PubMed:18250149). Likely to be
CC involved in the regulation of transcription (PubMed:18250149).
CC {ECO:0000269|PubMed:18250149}.
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:0000269|PubMed:18250149};
CC -!- ACTIVITY REGULATION: ATPase activity is stimulated by binding to DNA or
CC nucleosomes, but is strongly activated by nucleosomes.
CC {ECO:0000269|PubMed:18250149}.
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:18250149}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:18250149}. Chromosome
CC {ECO:0000269|PubMed:18250149}. Note=During embryogenesis, detected in
CC nuclei before and after their migration to the membrane of the
CC preblastoderm embryo (PubMed:18250149). Remains associated with
CC condensed chromosomes in mitotic nuclei. Not detected in nuclei
CC postgastrulation (PubMed:18250149). In polytene chromosomes of third
CC instar larvae, weakly expressed at the chromocenter and fourth
CC chromosome localizing mainly to the interbands (PubMed:18250149).
CC {ECO:0000269|PubMed:18250149}.
CC -!- DEVELOPMENTAL STAGE: Strongly expressed in early embryos 0 to 3 hours
CC after egg deposition (at protein level) (PubMed:18250149). Expression
CC then decreases and is undetectable in larvae and pupae (at protein
CC level) (PubMed:18250149). Strongly expressed in adult females but
CC expression is absent in adult males (at protein level)
CC (PubMed:18250149). {ECO:0000269|PubMed:18250149}.
CC -!- SIMILARITY: Belongs to the SNF2/RAD54 helicase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB87384.1; Type=Miscellaneous discrepancy; Note=Cloning artifacts.; Evidence={ECO:0000305};
CC Sequence=AAL49125.1; Type=Erroneous termination; Note=Truncated C-terminus.; Evidence={ECO:0000305};
CC Sequence=AAL49125.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AE014296; AAF49162.2; -; Genomic_DNA.
DR EMBL; AY071503; AAL49125.1; ALT_FRAME; mRNA.
DR EMBL; AF007780; AAB87384.1; ALT_SEQ; mRNA.
DR RefSeq; NP_649111.1; NM_140854.3.
DR AlphaFoldDB; O16102; -.
DR SMR; O16102; -.
DR BioGRID; 65382; 2.
DR DIP; DIP-21327N; -.
DR IntAct; O16102; 1.
DR STRING; 7227.FBpp0074766; -.
DR PaxDb; O16102; -.
DR PRIDE; O16102; -.
DR EnsemblMetazoa; FBtr0074998; FBpp0074766; FBgn0023395.
DR GeneID; 40111; -.
DR KEGG; dme:Dmel_CG9594; -.
DR UCSC; CG9594-RA; d. melanogaster.
DR CTD; 1107; -.
DR FlyBase; FBgn0023395; Chd3.
DR VEuPathDB; VectorBase:FBgn0023395; -.
DR eggNOG; KOG0383; Eukaryota.
DR GeneTree; ENSGT00940000169383; -.
DR HOGENOM; CLU_000315_8_4_1; -.
DR InParanoid; O16102; -.
DR OMA; SVYHRTC; -.
DR OrthoDB; 54215at2759; -.
DR PhylomeDB; O16102; -.
DR Reactome; R-DME-3214815; HDACs deacetylate histones.
DR Reactome; R-DME-6804758; Regulation of TP53 Activity through Acetylation.
DR Reactome; R-DME-8943724; Regulation of PTEN gene transcription.
DR BioGRID-ORCS; 40111; 0 hits in 3 CRISPR screens.
DR GenomeRNAi; 40111; -.
DR PRO; PR:O16102; -.
DR Proteomes; UP000000803; Chromosome 3L.
DR Bgee; FBgn0023395; Expressed in cleaving embryo and 11 other tissues.
DR ExpressionAtlas; O16102; baseline and differential.
DR Genevisible; O16102; DM.
DR GO; GO:0000785; C:chromatin; IBA:GO_Central.
DR GO; GO:0000791; C:euchromatin; IDA:FlyBase.
DR GO; GO:0005634; C:nucleus; IDA:FlyBase.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IDA:FlyBase.
DR GO; GO:0140658; F:ATP-dependent chromatin remodeler activity; IDA:FlyBase.
DR GO; GO:0003682; F:chromatin binding; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IBA:GO_Central.
DR GO; GO:0003678; F:DNA helicase activity; IEA:UniProtKB-EC.
DR GO; GO:0042393; F:histone binding; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006325; P:chromatin organization; NAS:UniProtKB.
DR GO; GO:0006338; P:chromatin remodeling; IBA:GO_Central.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0034728; P:nucleosome organization; IDA:FlyBase.
DR Gene3D; 3.30.40.10; -; 1.
DR Gene3D; 3.40.50.10810; -; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR016197; Chromo-like_dom_sf.
DR InterPro; IPR000953; Chromo/chromo_shadow_dom.
DR InterPro; IPR023780; Chromo_domain.
DR InterPro; IPR002464; DNA/RNA_helicase_DEAH_CS.
DR InterPro; IPR009463; DUF1087.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR038718; SNF2-like_sf.
DR InterPro; IPR000330; SNF2_N.
DR InterPro; IPR019786; Zinc_finger_PHD-type_CS.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR019787; Znf_PHD-finger.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR Pfam; PF00385; Chromo; 2.
DR Pfam; PF06465; DUF1087; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF00628; PHD; 1.
DR Pfam; PF00176; SNF2-rel_dom; 1.
DR SMART; SM00298; CHROMO; 2.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SMART; SM00249; PHD; 1.
DR SUPFAM; SSF52540; SSF52540; 2.
DR SUPFAM; SSF54160; SSF54160; 2.
DR PROSITE; PS50013; CHROMO_2; 2.
DR PROSITE; PS00690; DEAH_ATP_HELICASE; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS01359; ZF_PHD_1; 1.
DR PROSITE; PS50016; ZF_PHD_2; 1.
PE 1: Evidence at protein level;
KW Activator; ATP-binding; Chromosome; DNA-binding; Helicase; Hydrolase;
KW Metal-binding; Nucleotide-binding; Nucleus; Reference proteome; Repeat;
KW Transcription; Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..892
FT /note="Chromodomain-helicase-DNA-binding protein 3"
FT /id="PRO_0000080235"
FT DOMAIN 84..156
FT /note="Chromo 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00053"
FT DOMAIN 179..240
FT /note="Chromo 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00053"
FT DOMAIN 279..458
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 590..739
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT ZN_FING 35..82
FT /note="PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 1..29
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 839..892
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 409..412
FT /note="DEAH box"
FT COMPBIAS 875..892
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 292..299
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541,
FT ECO:0000305"
FT MUTAGEN 1..240
FT /note="Missing: Abolishes nucleosome mobilization. Retains
FT ATPase activity but is unable to bind DNA or
FT mononucleosomes."
FT /evidence="ECO:0000269|PubMed:18250149"
FT MUTAGEN 1..80
FT /note="Missing: No effect on ATPase activity or nucleosome
FT mobilization, and is able to bind DNA and mononucleosomes."
FT /evidence="ECO:0000269|PubMed:18250149"
FT MUTAGEN 801..892
FT /note="Missing: No effect on ATPase activity or nucleosome
FT mobilization, and is able to bind DNA and mononucleosomes."
FT /evidence="ECO:0000269|PubMed:18250149"
FT CONFLICT 617
FT /note="V -> I (in Ref. 4; AAB87384)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 892 AA; 103022 MW; E11DF7F65A1F6D6D CRC64;
MSSKRGADPD WKTPGKASKD KRPKTNAKKQ KFRDEEYCKV CSDGGDLLCC DSCPSVYHRT
CLSPPLKSIP KGDWICPRCI PLPGKAEKIL SWRWALDRSV ELRTSKGEKR REYFIKWHGM
SYWHCEWIPE GQMLLHHASM VASFQRRSDM EEPSLEELDD QDGNLHERFY RYGIKPEWLL
VQRVINHSEE PNGGTMYLVK WRELSYNDSS WERESDSIPG LNQAIALYKK LRSSNKGRQR
DRPAPTIDLN KKYEDQPVFL KEAGLKLHPF QIEGVSWLRY SWGQGIPTIL ADEMGLGKTI
QTVVFLYSLF KEGHCRGPFL ISVPLSTLTN WERELELWAP ELYCVTYVGG KTARAVIRKH
EISFEEVTTK TMRENQTQYK FNVMLTSYEF ISVDAAFLGC IDWAALVVDE AHRLRSNQSK
FFRILSKYRI GYKLLLTGTP LQNNLEELFH LLNFLSSGKF NDLQTFQAEF TDVSKEEQVK
RLHEILEPHM LRRLKADVLK SMPPKSEFIV RVELSSMQKK FYKHILTKNF KALNQKGGGR
VCSLLNIMMD LRKCCNHPYL FPSAAEEATI SPSGLYEMSS LTKASGKLDL LSKMLKQLKA
DNHRVLLFSQ MTKMLNVLEH FLEGEGYQYD RIDGSIKGDL RQKAIDRFND PVSEHFVFLL
STRAGGLGIN LATADTVIIF DSDWNPHNDV QAFSRAHRMG QKKKVMIYRF VTHNSVEERI
MQVAKHKMML THLVVRPGMG GMTTNFSKDE LEDILRFGTE DLFKDGKSEA IHYDDKAVAD
LLDRTNRGIE EKESWANEYL SSFKVASYAT KEDHEEHDDY NNDAENTDPF YWENLMGKSQ
PKLPKKQKKQ SQQSQVDVES IMGKGKRIRK EIDYSNQYPS PNRATPSSIV LM
