CHD5_RAT
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 03-AUG-2022, entry version 83.
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; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC 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., Smith D.,
RA Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L.,
RA Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D.,
RA Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M.,
RA Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C.,
RA Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J.,
RA Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H.,
RA Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X.,
RA Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q.,
RA Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P.,
RA Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A.,
RA Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C.,
RA Zdobnov E., 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., Schmidt J.,
RA Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F.,
RA Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A.,
RA Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A.,
RA Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J.,
RA Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E.,
RA Lazar J., 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., Webber C.,
RA Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L.,
RA Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W.,
RA Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y.,
RA Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V.,
RA Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M.,
RA Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S.,
RA Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B.,
RA Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R.,
RA Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J.,
RA Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D.,
RA Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S.,
RA Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S.,
RA Mockrin S., Collins F.S.;
RT "Genome sequence of the Brown Norway rat yields insights into mammalian
RT evolution.";
RL Nature 428:493-521(2004).
RN [2]
RP FUNCTION IN TRANSCRIPTION, SUBCELLULAR LOCATION, AND TISSUE 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 histones
CC and regulates gene transcription. May specifically recognize and bind
CC trimethylated 'Lys-27' (H3K27me3) and non-methylated 'Lys-4' of histone
CC H3. Plays a role in the development of the nervous system by activating
CC the expression of genes promoting neuron terminal differentiation. In
CC parallel, it may also positively regulate the trimethylation of histone
CC H3 at 'Lys-27' thereby specifically repressing genes that promote the
CC differentiation into non-neuronal cell lineages. Tumor suppressor, it
CC regulates the expression of genes involved in cell proliferation and
CC differentiation. Downstream activated genes may include CDKN2A that
CC positively regulates the p53/TP53 pathway, which in turn, prevents cell
CC proliferation. In spermatogenesis, it probably regulates histone
CC hyperacetylation and the replacement of histones by transition proteins
CC in chromatin, a crucial step in the condensation of spermatid chromatin
CC and the production of functional spermatozoa.
CC {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, HDAC1,
CC 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 and
CC 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 to
CC 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. {ECO:0000250|UniProtKB:Q8TDI0}.
CC -!- SIMILARITY: Belongs to the SNF2/RAD54 helicase family. {ECO:0000305}.
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DR EMBL; AABR06041085; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR AlphaFoldDB; D3ZD32; -.
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 HOGENOM; CLU_000315_22_1_1; -.
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:0016887; F:ATP hydrolysis activity; IBA:GO_Central.
DR GO; GO:0140658; F:ATP-dependent chromatin remodeler activity; IBA:GO_Central.
DR GO; GO:0003682; F:chromatin binding; IDA:RGD.
DR GO; GO:0003677; F:DNA binding; IBA:GO_Central.
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:0042393; F:histone binding; ISO:RGD.
DR GO; GO:0042826; F:histone deacetylase binding; ISO:RGD.
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:0006338; P:chromatin remodeling; IBA:GO_Central.
DR GO; GO:0098532; P:histone H3-K27 trimethylation; ISS:UniProtKB.
DR GO; GO:0043967; P:histone H4 acetylation; ISS:UniProtKB.
DR GO; GO:0008285; P:negative regulation of cell population proliferation; ISO:RGD.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; ISS:UniProtKB.
DR GO; GO:1901798; P:positive regulation of signal transduction by p53 class mediator; ISS:UniProtKB.
DR GO; GO:0045595; P:regulation of cell differentiation; ISO:RGD.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; ISO:RGD.
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 Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR028727; CHD5.
DR InterPro; IPR012957; CHD_C2.
DR InterPro; IPR009462; CHD_II_SANT-like.
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; 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-rel_dom; 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; Differentiation; DNA-binding; Helicase;
KW Hydrolase; Metal-binding; Methylation; Neurogenesis; Nucleotide-binding;
KW Nucleus; Phosphoprotein; Reference proteome; Repeat; Spermatogenesis;
KW Transcription; Transcription regulation; Tumor suppressor; Zinc;
KW Zinc-finger.
FT CHAIN 1..1948
FT /note="Chromodomain-helicase-DNA-binding protein 5"
FT /id="PRO_0000429327"
FT DOMAIN 495..552
FT /note="Chromo 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00053"
FT DOMAIN 590..651
FT /note="Chromo 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00053"
FT DOMAIN 710..894
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 1026..1191
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT ZN_FING 341..388
FT /note="PHD-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT ZN_FING 414..461
FT /note="PHD-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 1..136
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 228..268
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 281..336
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 341..651
FT /note="Histone-binding"
FT /evidence="ECO:0000250"
FT REGION 547..569
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1206..1250
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1349..1409
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1521..1566
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1595..1692
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 845..848
FT /note="DEAH box"
FT COMPBIAS 15..36
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 111..128
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 240..255
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1208..1222
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1384..1406
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1598..1692
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 723..730
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MOD_RES 1388
FT /note="N5-methylglutamine"
FT /evidence="ECO:0000250|UniProtKB:Q8TDI0"
FT MOD_RES 1552
FT /note="Phosphoserine"
FT /evidence="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
