GenomeNet

Database: UniProt/SWISS-PROT
Entry: HDA10_DANRE
LinkDB: HDA10_DANRE
Original site: HDA10_DANRE 
ID   HDA10_DANRE             Reviewed;         675 AA.
AC   F1QCV2; Q803K0;
DT   16-JAN-2019, integrated into UniProtKB/Swiss-Prot.
DT   14-MAY-2014, sequence version 2.
DT   10-APR-2019, entry version 67.
DE   RecName: Full=Polyamine deacetylase HDAC10;
DE            EC=3.5.1.48 {ECO:0000269|PubMed:28516954};
DE            EC=3.5.1.62 {ECO:0000269|PubMed:28516954};
DE   AltName: Full=Histone deacetylase 10;
GN   Name=hdac10;
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   STRAIN=AB;
RG   NIH - Zebrafish Gene Collection (ZGC) project;
RL   Submitted (JAN-2003) to the EMBL/GenBank/DDBJ databases.
RN   [3] {ECO:0000244|PDB:5TD7}
RP   X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS) OF 2-676, FUNCTION, CATALYTIC
RP   ACTIVITY, MUTAGENESIS OF ASN-93; ASP-94 AND GLU-274,
RP   BIOPHYSICOCHEMICAL PROPERTIES, AND ACTIVE SITE.
RX   PubMed=28516954; DOI=10.1038/ncomms15368;
RA   Hai Y., Shinsky S.A., Porter N.J., Christianson D.W.;
RT   "Histone deacetylase 10 structure and molecular function as a
RT   polyamine deacetylase.";
RL   Nat. Commun. 8:15368-15368(2017).
CC   -!- FUNCTION: Polyamine deacetylase (PDAC), which acts preferentially
CC       on N(8)-acetylspermidine, and also on acetylcadaverine and
CC       acetylputrescine (PubMed:28516954). Exhibits attenuated catalytic
CC       activity toward N(1),N(8)-diacetylspermidine and very low
CC       activity, if any, toward N(1)-acetylspermidine (PubMed:28516954).
CC       Has a very weak lysine deacetylase, if any (PubMed:28516954).
CC       {ECO:0000269|PubMed:28516954}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=H2O + N(8)-acetylspermidine = acetate + spermidine;
CC         Xref=Rhea:RHEA:23928, ChEBI:CHEBI:15377, ChEBI:CHEBI:30089,
CC         ChEBI:CHEBI:57834, ChEBI:CHEBI:58535; EC=3.5.1.48;
CC         Evidence={ECO:0000269|PubMed:28516954};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=H2O + N-acetylputrescine = acetate + putrescine;
CC         Xref=Rhea:RHEA:23412, ChEBI:CHEBI:15377, ChEBI:CHEBI:30089,
CC         ChEBI:CHEBI:58263, ChEBI:CHEBI:326268; EC=3.5.1.62;
CC         Evidence={ECO:0000269|PubMed:28516954};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=H2O + N-acetylcadaverine = acetate + cadaverine;
CC         Xref=Rhea:RHEA:51892, ChEBI:CHEBI:15377, ChEBI:CHEBI:30089,
CC         ChEBI:CHEBI:58384, ChEBI:CHEBI:134408;
CC         Evidence={ECO:0000269|PubMed:28516954};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=90 uM for acetylcadaverine {ECO:0000269|PubMed:28516954};
CC         KM=160 uM for acetylputrescine {ECO:0000269|PubMed:28516954};
CC         KM=130 uM for N(8)-acetylspermidine
CC         {ECO:0000269|PubMed:28516954};
CC         KM=180 uM for N(1),N(8)-diacetylspermidine
CC         {ECO:0000269|PubMed:28516954};
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q969S8}.
CC       Nucleus {ECO:0000250|UniProtKB:Q969S8}. Note=Excluded from the
CC       nucleoli. {ECO:0000250|UniProtKB:Q969S8}.
CC   -!- SIMILARITY: Belongs to the histone deacetylase family. HD type 2
CC       subfamily. {ECO:0000305}.
CC   -!- CAUTION: Originally thought to be a histone deacetylase and shown
CC       in vitro to have this activity (By similarity). Has also been
CC       shown to be involved in MSH2 deacetylation (By similarity).
CC       However, protein deacetylase activity is a matter of debate, as 3D
CC       structure analysis shows that a glutamate gatekeeper and a
CC       sterically constricted active site confer specificity for N(8)-
CC       acetylspermidine hydrolysis and disfavour acetyllysine hydrolysis.
CC       Supporting this observation, has been shown to exhibit only very
CC       low activity, if any, towards acetyl-lysine peptide substrates (By
CC       similarity). {ECO:0000250|UniProtKB:Q969S8}.
DR   EMBL; FP102808; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; BC044446; AAH44446.1; -; mRNA.
DR   RefSeq; NP_956069.1; NM_199775.1.
DR   UniGene; Dr.1758; -.
DR   PDB; 5TD7; X-ray; 2.85 A; A=2-675.
DR   PDBsum; 5TD7; -.
DR   STRING; 7955.ENSDARP00000109870; -.
DR   Ensembl; ENSDART00000127600; ENSDARP00000109870; ENSDARG00000086458.
DR   GeneID; 327253; -.
DR   KEGG; dre:327253; -.
DR   CTD; 83933; -.
DR   ZFIN; ZDB-GENE-030131-5464; hdac10.
DR   eggNOG; KOG1343; Eukaryota.
DR   eggNOG; COG0123; LUCA.
DR   GeneTree; ENSGT00940000160061; -.
DR   HOGENOM; HOG000225183; -.
DR   HOVERGEN; HBG051892; -.
DR   InParanoid; F1QCV2; -.
DR   KO; K18671; -.
DR   OrthoDB; 1484694at2759; -.
DR   TreeFam; TF106173; -.
DR   Reactome; R-DRE-3214815; HDACs deacetylate histones.
DR   Proteomes; UP000000437; Chromosome 25.
DR   Bgee; ENSDARG00000086458; Expressed in 28 organ(s), highest expression level in mature ovarian follicle.
DR   GO; GO:0005737; C:cytoplasm; ISS:ZFIN.
DR   GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR   GO; GO:0047609; F:acetylputrescine deacetylase activity; IEA:UniProtKB-EC.
DR   GO; GO:0047611; F:acetylspermidine deacetylase activity; IDA:ZFIN.
DR   GO; GO:0008270; F:zinc ion binding; IDA:ZFIN.
DR   GO; GO:0035825; P:homologous recombination; ISS:UniProtKB.
DR   GO; GO:0016236; P:macroautophagy; ISS:UniProtKB.
DR   GO; GO:0106047; P:polyamine deacetylation; IDA:ZFIN.
DR   GO; GO:0006476; P:protein deacetylation; IEA:GOC.
DR   GO; GO:0106048; P:spermidine deacetylation; IDA:ZFIN.
DR   Gene3D; 3.40.800.20; -; 2.
DR   InterPro; IPR000286; His_deacetylse.
DR   InterPro; IPR023801; His_deacetylse_dom.
DR   InterPro; IPR037138; His_deacetylse_dom_sf.
DR   InterPro; IPR023696; Ureohydrolase_dom_sf.
DR   PANTHER; PTHR10625; PTHR10625; 2.
DR   Pfam; PF00850; Hist_deacetyl; 1.
DR   PRINTS; PR01270; HDASUPER.
DR   SUPFAM; SSF52768; SSF52768; 2.
PE   1: Evidence at protein level;
KW   3D-structure; Complete proteome; Cytoplasm; Hydrolase; Metal-binding;
KW   Nucleus; Reference proteome; Zinc.
FT   CHAIN         1    675       Polyamine deacetylase HDAC10.
FT                                /FTId=PRO_0000446065.
FT   MOTIF        23     26       Substrate specificity.
FT                                {ECO:0000269|PubMed:28516954}.
FT   ACT_SITE    137    137       Proton donor/acceptor.
FT                                {ECO:0000244|PDB:5TD7,
FT                                ECO:0000269|PubMed:28516954}.
FT   METAL       174    174       Zinc. {ECO:0000244|PDB:5TD7,
FT                                ECO:0000269|PubMed:28516954}.
FT   METAL       176    176       Zinc; via pros nitrogen.
FT                                {ECO:0000244|PDB:5TD7,
FT                                ECO:0000269|PubMed:28516954}.
FT   METAL       267    267       Zinc. {ECO:0000244|PDB:5TD7,
FT                                ECO:0000269|PubMed:28516954}.
FT   BINDING      22     22       Substrate. {ECO:0000244|PDB:5TD7,
FT                                ECO:0000269|PubMed:28516954}.
FT   BINDING      94     94       Substrate. {ECO:0000244|PDB:5TD7,
FT                                ECO:0000269|PubMed:28516954}.
FT   BINDING     307    307       Substrate. {ECO:0000244|PDB:5TD7,
FT                                ECO:0000269|PubMed:28516954}.
FT   SITE        274    274       Substrate specificity.
FT                                {ECO:0000269|PubMed:28516954}.
FT   MUTAGEN      93     93       N->A: No effect on steady-state kinetic
FT                                parameters.
FT                                {ECO:0000269|PubMed:28516954}.
FT   MUTAGEN      94     94       D->A: No effect on steady-state kinetic
FT                                parameters.
FT                                {ECO:0000269|PubMed:28516954}.
FT   MUTAGEN     274    274       E->L: Affects substrate specificity,
FT                                diminishing N(8)-acetyl-spermidine
FT                                deacetylase activity by 20-fold and
FT                                enhancing acetyl-lysine deacetylase
FT                                activity by about 100-fold.
FT                                {ECO:0000269|PubMed:28516954}.
FT   CONFLICT    154    154       I -> F (in Ref. 2; AAH44446).
FT                                {ECO:0000305}.
FT   CONFLICT    548    548       S -> T (in Ref. 2; AAH44446).
FT                                {ECO:0000305}.
FT   CONFLICT    586    586       G -> E (in Ref. 2; AAH44446).
FT                                {ECO:0000305}.
FT   CONFLICT    593    596       GLMT -> RLMR (in Ref. 2; AAH44446).
FT                                {ECO:0000305}.
FT   CONFLICT    613    613       T -> M (in Ref. 2; AAH44446).
FT                                {ECO:0000305}.
FT   CONFLICT    646    646       L -> P (in Ref. 2; AAH44446).
FT                                {ECO:0000305}.
FT   CONFLICT    675    675       S -> SW (in Ref. 2; AAH44446).
FT                                {ECO:0000305}.
FT   STRAND        5      8       {ECO:0000244|PDB:5TD7}.
FT   HELIX        11     14       {ECO:0000244|PDB:5TD7}.
FT   TURN         23     27       {ECO:0000244|PDB:5TD7}.
FT   HELIX        31     42       {ECO:0000244|PDB:5TD7}.
FT   HELIX        46     48       {ECO:0000244|PDB:5TD7}.
FT   STRAND       49     52       {ECO:0000244|PDB:5TD7}.
FT   HELIX        59     62       {ECO:0000244|PDB:5TD7}.
FT   TURN         63     65       {ECO:0000244|PDB:5TD7}.
FT   HELIX        68     75       {ECO:0000244|PDB:5TD7}.
FT   HELIX        77     79       {ECO:0000244|PDB:5TD7}.
FT   HELIX        82     89       {ECO:0000244|PDB:5TD7}.
FT   STRAND       92     94       {ECO:0000244|PDB:5TD7}.
FT   HELIX       101    120       {ECO:0000244|PDB:5TD7}.
FT   STRAND      125    129       {ECO:0000244|PDB:5TD7}.
FT   STRAND      147    149       {ECO:0000244|PDB:5TD7}.
FT   HELIX       151    163       {ECO:0000244|PDB:5TD7}.
FT   STRAND      168    172       {ECO:0000244|PDB:5TD7}.
FT   STRAND      174    176       {ECO:0000244|PDB:5TD7}.
FT   HELIX       179    184       {ECO:0000244|PDB:5TD7}.
FT   TURN        185    187       {ECO:0000244|PDB:5TD7}.
FT   STRAND      191    198       {ECO:0000244|PDB:5TD7}.
FT   TURN        200    203       {ECO:0000244|PDB:5TD7}.
FT   HELIX       209    211       {ECO:0000244|PDB:5TD7}.
FT   HELIX       219    221       {ECO:0000244|PDB:5TD7}.
FT   STRAND      224    230       {ECO:0000244|PDB:5TD7}.
FT   HELIX       237    246       {ECO:0000244|PDB:5TD7}.
FT   HELIX       248    255       {ECO:0000244|PDB:5TD7}.
FT   STRAND      258    264       {ECO:0000244|PDB:5TD7}.
FT   TURN        273    275       {ECO:0000244|PDB:5TD7}.
FT   HELIX       282    291       {ECO:0000244|PDB:5TD7}.
FT   HELIX       294    297       {ECO:0000244|PDB:5TD7}.
FT   STRAND      299    303       {ECO:0000244|PDB:5TD7}.
FT   HELIX       309    324       {ECO:0000244|PDB:5TD7}.
FT   HELIX       339    352       {ECO:0000244|PDB:5TD7}.
FT   TURN        353    355       {ECO:0000244|PDB:5TD7}.
FT   HELIX       357    359       {ECO:0000244|PDB:5TD7}.
FT   STRAND      415    418       {ECO:0000244|PDB:5TD7}.
FT   HELIX       439    452       {ECO:0000244|PDB:5TD7}.
FT   HELIX       459    475       {ECO:0000244|PDB:5TD7}.
FT   STRAND      482    489       {ECO:0000244|PDB:5TD7}.
FT   HELIX       491    502       {ECO:0000244|PDB:5TD7}.
FT   TURN        503    506       {ECO:0000244|PDB:5TD7}.
FT   STRAND      508    518       {ECO:0000244|PDB:5TD7}.
FT   STRAND      526    537       {ECO:0000244|PDB:5TD7}.
FT   STRAND      546    550       {ECO:0000244|PDB:5TD7}.
FT   HELIX       557    567       {ECO:0000244|PDB:5TD7}.
FT   HELIX       569    576       {ECO:0000244|PDB:5TD7}.
FT   STRAND      579    585       {ECO:0000244|PDB:5TD7}.
FT   STRAND      587    592       {ECO:0000244|PDB:5TD7}.
FT   HELIX       593    596       {ECO:0000244|PDB:5TD7}.
FT   HELIX       598    604       {ECO:0000244|PDB:5TD7}.
FT   HELIX       605    607       {ECO:0000244|PDB:5TD7}.
FT   HELIX       609    611       {ECO:0000244|PDB:5TD7}.
FT   STRAND      613    619       {ECO:0000244|PDB:5TD7}.
FT   HELIX       622    633       {ECO:0000244|PDB:5TD7}.
FT   HELIX       648    661       {ECO:0000244|PDB:5TD7}.
FT   TURN        662    664       {ECO:0000244|PDB:5TD7}.
FT   HELIX       666    668       {ECO:0000244|PDB:5TD7}.
SQ   SEQUENCE   675 AA;  74543 MW;  4DDABEA59E275F36 CRC64;
     MASGSALIFD EEMSRYKLLW TDPACEIEVP ERLTVSYEAL RTHGLAQRCK AVPVRQATEQ
     EILLAHSEEY LEAVKQTPGM NVEELMAFSK KYNDVYFHQN IYHCAKLAAG ATLQLVDSVM
     KREVRNGMAL VRPPGHHSQR SAANGFCVFN NVAIAALYAK KNYNLNRILI VDWDVHHGQG
     IQYCFEEDPS VLYFSWHRYE HQSFWPNLPE SDYSSVGKGK GSGFNINLPW NKVGMTNSDY
     LAAFFHVLLP VAYEFDPELV IVSAGFDSAI GDPEGEMCAL PEIFAHLTHL LMPLAAGKMC
     VVLEGGYNLT SLGQSVCQTV HSLLGDPTPR ISGLGTACDS ALESIQNVRN VQSSYWSSFK
     HLAQSETNPK RPRLDATNGG PKESSEPASE SNPKKTAQDI VWPEPLKRMP ASVRTVVVPP
     PGVELTLPKN CQHSGDISES TAKEVQRIRD KHFHDLTDQN ILRSLGNIIS VLDRMMRSDE
     VCNGCVVVSD LSVSVQCALQ HALTEPAERV LVVYVGDGEL PVKTNDGKVF LVQICTKETE
     DKCVNRLSLC LREGESLTAG FMQALLGLIL PVAYEFNPAL VLGIVGETAA KTGLMTVWGH
     MTCLIQGLAR GRTLTLLQGY DKDLLELTVS ALSGASISPL GPLRALKPED VEMMEKQRQR
     LQERWGLLRC TVSES
//
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