GenomeNet

Database: UniProt
Entry: D3ZD32
LinkDB: D3ZD32
Original site: D3ZD32 
ID   CHD5_RAT                Reviewed;        1948 AA.
AC   D3ZD32;
DT   11-JUN-2014, integrated into UniProtKB/Swiss-Prot.
DT   20-APR-2010, sequence version 1.
DT   13-NOV-2019, entry version 73.
DE   RecName: Full=Chromodomain-helicase-DNA-binding protein 5;
DE            Short=CHD-5;
DE            EC=3.6.4.12;
DE   AltName: Full=ATP-dependent helicase CHD5;
GN   Name=Chd5;
OS   Rattus norvegicus (Rat).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
OC   Muroidea; Muridae; Murinae; Rattus.
OX   NCBI_TaxID=10116;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Brown Norway;
RX   PubMed=15057822; DOI=10.1038/nature02426;
RA   Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J.,
RA   Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G.,
RA   Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G.,
RA   Morgan M., Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G.,
RA   Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S.,
RA   Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T.,
RA   Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T.,
RA   Smith D., Lee H.-M., Gustafson E., Cahill P., Kana A.,
RA   Doucette-Stamm L., Weinstock K., Fechtel K., Weiss R.B., Dunn D.M.,
RA   Green E.D., Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K.,
RA   Zhu B., Marra M., Schein J., Bosdet I., Fjell C., Jones S.,
RA   Krzywinski M., Mathewson C., Siddiqui A., Wye N., McPherson J.,
RA   Zhao S., Fraser C.M., Shetty J., Shatsman S., Geer K., Chen Y.,
RA   Abramzon S., Nierman W.C., Havlak P.H., Chen R., Durbin K.J., Egan A.,
RA   Ren Y., Song X.-Z., Li B., Liu Y., Qin X., Cawley S., Cooney A.J.,
RA   D'Souza L.M., Martin K., Wu J.Q., Gonzalez-Garay M.L., Jackson A.R.,
RA   Kalafus K.J., McLeod M.P., Milosavljevic A., Virk D., Volkov A.,
RA   Wheeler D.A., Zhang Z., Bailey J.A., Eichler E.E., Tuzun E.,
RA   Birney E., Mongin E., Ureta-Vidal A., Woodwark C., Zdobnov E.,
RA   Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J.,
RA   Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D.,
RA   Schmidt J., Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M.,
RA   Abril J.F., Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O.,
RA   Poliakov A., Huebner N., Ganten D., Goesele C., Hummel O.,
RA   Kreitler T., Lee Y.-A., Monti J., Schulz H., Zimdahl H.,
RA   Himmelbauer H., Lehrach H., Jacob H.J., Bromberg S.,
RA   Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E., Lazar J.,
RA   Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M.,
RA   Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E.,
RA   Webber C., Brandt P., Nyakatura G., Adetobi M., Chiaromonte F.,
RA   Elnitski L., Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K.,
RA   Miller W., Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S.,
RA   Zhang Y., Lindpaintner K., Andrews T.D., Caccamo M., Clamp M.,
RA   Clarke L., Curwen V., Durbin R.M., Eyras E., Searle S.M., Cooper G.M.,
RA   Batzoglou S., Brudno M., Sidow A., Stone E.A., Payseur B.A.,
RA   Bourque G., Lopez-Otin C., Puente X.S., Chakrabarti K., Chatterji S.,
RA   Dewey C., Pachter L., Bray N., Yap V.B., Caspi A., Tesler G.,
RA   Pevzner P.A., Haussler D., Roskin K.M., Baertsch R., Clawson H.,
RA   Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J., Rosenbloom K.R.,
RA   Trumbower H., Weirauch M., Cooper D.N., Stenson P.D., Ma B., Brent M.,
RA   Arumugam M., Shteynberg D., Copley R.R., Taylor M.S., Riethman H.,
RA   Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S., Mockrin S.,
RA   Collins F.S.;
RT   "Genome sequence of the Brown Norway rat yields insights into
RT   mammalian evolution.";
RL   Nature 428:493-521(2004).
RN   [2]
RP   FUNCTION IN TRANSCRIPTION, SUBCELLULAR LOCATION, AND TISSUE
RP   SPECIFICITY.
RX   PubMed=21931736; DOI=10.1371/journal.pone.0024515;
RA   Potts R.C., Zhang P., Wurster A.L., Precht P., Mughal M.R., Wood W.H.,
RA   Zhang Y., Becker K.G., Mattson M.P., Pazin M.J.;
RT   "CHD5, a brain-specific paralog of Mi2 chromatin remodeling enzymes,
RT   regulates expression of neuronal genes.";
RL   PLoS ONE 6:E24515-E24515(2011).
CC   -!- FUNCTION: Chromatin-remodeling protein that binds DNA through
CC       histones and regulates gene transcription. May specifically
CC       recognize and bind trimethylated 'Lys-27' (H3K27me3) and non-
CC       methylated 'Lys-4' of histone H3. Plays a role in the development
CC       of the nervous system by activating the expression of genes
CC       promoting neuron terminal differentiation. In parallel, it may
CC       also positively regulate the trimethylation of histone H3 at 'Lys-
CC       27' thereby specifically repressing genes that promote the
CC       differentiation into non-neuronal cell lineages. Tumor suppressor,
CC       it regulates the expression of genes involved in cell
CC       proliferation and differentiation. Downstream activated genes may
CC       include CDKN2A that positively regulates the p53/TP53 pathway,
CC       which in turn, prevents cell proliferation. In spermatogenesis, it
CC       probably regulates histone hyperacetylation and the replacement of
CC       histones by transition proteins in chromatin, a crucial step in
CC       the condensation of spermatid chromatin and the production of
CC       functional spermatozoa. {ECO:0000269|PubMed:21931736}.
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   -!- SUBUNIT: May be part of a nucleosome remodeling and histone
CC       deacetylation, NuRD-like, complex composed at least of GATAD2B,
CC       HDAC1, HDAC2 and MTA3. {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:21931736}.
CC       Note=Associates with heterochromatin.
CC   -!- TISSUE SPECIFICITY: Expressed in brain regions enriched in neurons
CC       and not in regions rich in glial cells (at protein level).
CC       {ECO:0000269|PubMed:21931736}.
CC   -!- DOMAIN: The PHD domains mediate specific binding to histone H3
CC       unmethylated at 'Lys-4' and may preferentially recruit the protein
CC       to transcriptionally inactive genes. {ECO:0000250}.
CC   -!- DOMAIN: The chromo domains mediate specific binding to histone H3
CC       trimethylated at 'Lys-27' (H3K27me3) and may be required in neuron
CC       differentiation for proper gene regulation. {ECO:0000250}.
CC   -!- PTM: Methylated at Gln-1388 by N6AMT1.
CC       {ECO:0000250|UniProtKB:Q8TDI0}.
CC   -!- SIMILARITY: Belongs to the SNF2/RAD54 helicase family.
CC       {ECO:0000305}.
DR   EMBL; AABR06041085; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   SMR; D3ZD32; -.
DR   IntAct; D3ZD32; 1.
DR   STRING; 10116.ENSRNOP00000024732; -.
DR   jPOST; D3ZD32; -.
DR   PaxDb; D3ZD32; -.
DR   PeptideAtlas; D3ZD32; -.
DR   PRIDE; D3ZD32; -.
DR   RGD; 1582725; Chd5.
DR   eggNOG; KOG0383; Eukaryota.
DR   eggNOG; COG0553; LUCA.
DR   InParanoid; D3ZD32; -.
DR   TreeFam; TF106448; -.
DR   PRO; PR:D3ZD32; -.
DR   Proteomes; UP000002494; Unplaced.
DR   GO; GO:0000792; C:heterochromatin; ISS:UniProtKB.
DR   GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR   GO; GO:0016581; C:NuRD complex; ISS:UniProtKB.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0003682; F:chromatin binding; IDA:RGD.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0003678; F:DNA helicase activity; IEA:UniProtKB-EC.
DR   GO; GO:0061628; F:H3K27me3 modified histone binding; ISS:UniProtKB.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0021895; P:cerebral cortex neuron differentiation; ISS:UniProtKB.
DR   GO; GO:0098532; P:histone H3-K27 trimethylation; ISS:UniProtKB.
DR   GO; GO:0043967; P:histone H4 acetylation; ISS:UniProtKB.
DR   GO; GO:1901798; P:positive regulation of signal transduction by p53 class mediator; ISS:UniProtKB.
DR   GO; GO:0060850; P:regulation of transcription involved in cell fate commitment; ISS:UniProtKB.
DR   GO; GO:0035093; P:spermatogenesis, exchange of chromosomal proteins; ISS:UniProtKB.
DR   GO; GO:0006366; P:transcription by RNA polymerase II; IMP:UniProtKB.
DR   Gene3D; 3.30.40.10; -; 2.
DR   Gene3D; 3.40.50.10810; -; 1.
DR   InterPro; IPR028727; CHD5.
DR   InterPro; IPR012957; CHD_C2.
DR   InterPro; IPR012958; CHD_N.
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; IPR009462; DUF1086.
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; IPR011011; Znf_FYVE_PHD.
DR   InterPro; IPR001965; Znf_PHD.
DR   InterPro; IPR019787; Znf_PHD-finger.
DR   InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR   PANTHER; PTHR45623:SF6; PTHR45623:SF6; 1.
DR   Pfam; PF08074; CHDCT2; 1.
DR   Pfam; PF08073; CHDNT; 1.
DR   Pfam; PF00385; Chromo; 1.
DR   Pfam; PF06461; DUF1086; 1.
DR   Pfam; PF06465; DUF1087; 1.
DR   Pfam; PF00271; Helicase_C; 1.
DR   Pfam; PF00628; PHD; 2.
DR   Pfam; PF00176; SNF2_N; 1.
DR   SMART; SM00298; CHROMO; 2.
DR   SMART; SM00487; DEXDc; 1.
DR   SMART; SM01146; DUF1086; 1.
DR   SMART; SM01147; DUF1087; 1.
DR   SMART; SM00490; HELICc; 1.
DR   SMART; SM00249; PHD; 2.
DR   SUPFAM; SSF52540; SSF52540; 2.
DR   SUPFAM; SSF54160; SSF54160; 2.
DR   SUPFAM; SSF57903; SSF57903; 1.
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; 2.
DR   PROSITE; PS50016; ZF_PHD_2; 2.
PE   1: Evidence at protein level;
KW   ATP-binding; Chromatin regulator; Complete proteome; Differentiation;
KW   DNA-binding; Helicase; Hydrolase; Metal-binding; Methylation;
KW   Neurogenesis; Nucleotide-binding; Nucleus; Phosphoprotein;
KW   Reference proteome; Repeat; Spermatogenesis; Transcription;
KW   Transcription regulation; Tumor suppressor; Zinc; Zinc-finger.
FT   CHAIN         1   1948       Chromodomain-helicase-DNA-binding protein
FT                                5.
FT                                /FTId=PRO_0000429327.
FT   DOMAIN      495    552       Chromo 1. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00053}.
FT   DOMAIN      590    651       Chromo 2. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00053}.
FT   DOMAIN      710    894       Helicase ATP-binding.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00541}.
FT   DOMAIN     1026   1191       Helicase C-terminal.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00542}.
FT   ZN_FING     341    388       PHD-type 1. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00146}.
FT   ZN_FING     414    461       PHD-type 2. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00146}.
FT   NP_BIND     723    730       ATP. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00541}.
FT   REGION      341    651       Histone-binding. {ECO:0000250}.
FT   MOTIF       845    848       DEAH box.
FT   COMPBIAS     49    114       Lys-rich.
FT   MOD_RES    1388   1388       N5-methylglutamine.
FT                                {ECO:0000250|UniProtKB:Q8TDI0}.
FT   MOD_RES    1552   1552       Phosphoserine.
FT                                {ECO:0000250|UniProtKB:A2A8L1}.
SQ   SEQUENCE   1948 AA;  222263 MW;  FB8312CE53C5B1CE CRC64;
     MRGPLGTEEE LPRLFAEEME NEEEMSEEED GGLEGFEDFF PAEPVSLPKK KPKKLKESKS
     KGKRKKKEGS NDELSENEED LEEKSESEGS DYSPTKKKKK KLKEKKEKKA KRKKRDEDEE
     DNEDGGLKEP KSSGQLMAEW GLDDVDYLFS EDDYHTLTNY KAFSQFLRPL IAKKNPKIPM
     SKMMTVLGAK WREFSANNPF KGSSAAAAAA AVAAAVETVT IAPPLAISPQ QVPQPLPVRK
     AKTKEGKGPG VRKKNKGAKD SKKKGRGKRV AGLKFRFGGI SKRKKGSSSE EDEPEDSDLD
     NASIHSSSVR SECSAALGKK NKRRRKKKRI DDGDGYETDH QDYCEVCQQG GEIILCDTCP
     RAYHLVCLDP ELEKAPEGKW SCPHCEKEGI QWEPKDDDEE EEEGGCEEEE DDHMEFCRVC
     KDGGELLCCD ACPSSYHLHC LNPPLPEIPN GEWLCPRCTC PPLKGKVQRI LHWRWTEPPA
     PFMVGLPGPE VEPGMPPPRP LEGIPEREFF VKWAGLSYWH CSWVKELQLE LYHTVMYRNY
     QRKNDMDEPP PFDYGSGDED GKSEKRKNKD PLYAKMEERF YRYGIKPEWM MVHRILNHSF
     DKKGDVHYLI KWKDLPYDQC TWEIDEIDIP YYDNLKQTYW GHRELMLGED ARLPKRLVKK
     GKKLKDDKQE KPPDTPIVDP TVKFDKQPWY IDSTGGTLHP YQLEGLNWLR FSWAQGTDTI
     LADEMGLGKT VQTIVFLYSL YKEGHSKGPY LVSAPLSTII NWEREFEMWA PDFYVVTYTG
     DKESRSVIRE NEFSFEDNAI RGGKKVFRMK KEVQIKFHVL LTSYELITID QAILGSIEWA
     CLVVDEAHRL KNNQSKFFRV LNSYKIDYKL LLTGTPLQNN LEELFHLLNF LTPERFNNLE
     GFLEEFADIS KEDQIKKLHD LLGPHMLRRL KADVFKNMPA KTELIVRVEL SQMQKKYYKF
     ILTRNFEALN SKGGGNQVSL LNIMMDLKKC CNHPYLFPVA AVEAPMLPNG SYDGSSLVKS
     SGKLMLLQKM LKKLRDEGHR VLIFSQMTKM LDLLEDFLEY EGYKYERIDG GITGGLRQEA
     IDRFNAPGAQ QFCFLLSTRA GGLGINLATA DTVIIYDSDW NPHNDIQAFS RAHRIGQNKK
     VMIYRFVTRA SVEERITQVA KRKMMLTHLV VRPGLGSKSG SMTKQELDDI LKFGTEELFK
     DDVEGMMSQG QRPTTPIPDV QSTKGGSLAA GAKKKHGGTP PGDNKDVEDS SVIHYDDAAI
     SKLLDRNQDA TDDTELQNMN EYLSSFKVAQ YVVREEDGVE EVEREVIKQE ENVDPDYWEK
     LLRHHYEQQQ EDLARNLGKG KRIRKQVNYN DASQEDQEWQ DELSDNQSEY SIGSEDEDED
     FEERPEGQSG RRQSRRQLKS DRDKPLPPLL ARVGGNIEVL GFNARQRKAF LNAIMRWGMP
     PQDAFNSHWL VRDLRGKSEK EFRAYVSLFM RHLCEPGADG AETFADGVPR EGLSRQHVLT
     RIGVMSLVRK KVQEFEHVNG KYSTPDLVPE GPEGKKPGEV ISSDPNTPVP ASPAQLPPAP
     LGLPDKMEAQ LGYTDEKESG TQKPKKSLEI QALPTALDRV EAEDKHQSSD SKDRAREERM
     EEVEKAQGSP EQPLKEETLP DKEPVPDKLE LSLSHSNDFR PDDPKAEEKE PTETQQNGDR
     EEDEEGKKED KNGKFKFMFN IADGGFTELH TLWQNEERAA VSSGKIYEIW HRRHDYWLLA
     GIVTHGYARW QDIQNDPRYM ILNEPFKSEV HKGNYLEMKN KFLARRFKLL EQALVIEEQL
     RRAAYLNMTQ DPNHPAMALN ARLAEVECLA ESHQHLSKES LAGNKPANAV LHKVLNQLEE
     LLSDMKADVT RLPSMLSRIP PVAARLQMSE RSILSRLTNR AGDPTIQQGA FGSSQMYNNS
     FGPNFRGPGP GGIVNYNQMP LGPYVTGR
//
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