HDA10_ORYSJ
ID HDA10_ORYSJ Reviewed; 443 AA.
AC Q2QWU2; Q0IPM4;
DT 29-SEP-2021, integrated into UniProtKB/Swiss-Prot.
DT 24-JAN-2006, sequence version 1.
DT 03-AUG-2022, entry version 134.
DE RecName: Full=Histone deacetylase 10, chloroplastic {ECO:0000303|PubMed:19505461};
DE Short=OsHDAC10 {ECO:0000303|PubMed:19505461};
DE EC=3.5.1.- {ECO:0000269|PubMed:29247559, ECO:0000269|Ref.10};
DE AltName: Full=N-acetylserotonin deacetylase {ECO:0000303|PubMed:29247559};
DE Flags: Precursor;
GN Name=HDAC10 {ECO:0000303|PubMed:19505461};
GN Synonyms=ASDAC {ECO:0000303|PubMed:29247559},
GN HDA714 {ECO:0000303|PubMed:17399684};
GN OrderedLocusNames=Os12g0182700 {ECO:0000312|EMBL:BAT16163.1},
GN LOC_Os12g08220 {ECO:0000312|EMBL:ABA95964.1};
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16188032; DOI=10.1186/1741-7007-3-20;
RG The rice chromosomes 11 and 12 sequencing consortia;
RT "The sequence of rice chromosomes 11 and 12, rich in disease resistance
RT genes and recent gene duplications.";
RL BMC Biol. 3:20-20(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [7]
RP TISSUE SPECIFICITY.
RX PubMed=17399684; DOI=10.1016/j.bbrc.2007.03.010;
RA Fu W., Wu K., Duan J.;
RT "Sequence and expression analysis of histone deacetylases in rice.";
RL Biochem. Biophys. Res. Commun. 356:843-850(2007).
RN [8]
RP SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RX PubMed=19505461; DOI=10.1016/j.febslet.2009.06.003;
RA Chung P.J., Kim Y.S., Park S.H., Nahm B.H., Kim J.K.;
RT "Subcellular localization of rice histone deacetylases in organelles.";
RL FEBS Lett. 583:2249-2254(2009).
RN [9]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY
RP REGULATION, SUBCELLULAR LOCATION, AND INDUCTION.
RX PubMed=29247559; DOI=10.1111/jpi.12460;
RA Lee K., Lee H.Y., Back K.;
RT "Rice histone deacetylase 10 and Arabidopsis histone deacetylase 14 genes
RT encode N-acetylserotonin deacetylase, which catalyzes conversion of N-
RT acetylserotonin into serotonin, a reverse reaction for melatonin
RT biosynthesis in plants.";
RL J. Pineal Res. 64:0-0(2018).
RN [10]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX DOI=10.32794/mr11250046;
RA Lee K., Hwang O.J., Back K.;
RT "Rice N-acetylserotonin deacetylase regulates melatonin levels in
RT transgenic rice.";
RL Melatonin Res. 3:32-42(2020).
CC -!- FUNCTION: Involved in the regulation of melatonin biosynthesis by
CC catalyzing the deacetylation of N-acetylserotonin to produce serotonin
CC (PubMed:29247559, Ref.10). N-acetylserotonin is methylated by
CC acetylserotonin O-methyltransferase (ASMT) to produce melatonin (N-
CC acetyl-5-methoxytryptamine) (Probable). Deacetylates melatonin to
CC produce 5-methoxytryptamine (PubMed:29247559, Ref.10). In vitro,
CC deacetylates N-acetyltyramine and N-acetyltryptamine to produce
CC tyramine and tryptamine, respectively (PubMed:29247559).
CC {ECO:0000269|PubMed:29247559, ECO:0000269|Ref.10,
CC ECO:0000305|PubMed:29247559, ECO:0000305|Ref.10}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N-acetylserotonin = acetate + serotonin;
CC Xref=Rhea:RHEA:67196, ChEBI:CHEBI:15377, ChEBI:CHEBI:17697,
CC ChEBI:CHEBI:30089, ChEBI:CHEBI:350546;
CC Evidence={ECO:0000269|PubMed:29247559, ECO:0000269|Ref.10};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:67197;
CC Evidence={ECO:0000269|PubMed:29247559, ECO:0000269|Ref.10};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N-acetyltyramine = acetate + tyramine;
CC Xref=Rhea:RHEA:67200, ChEBI:CHEBI:15377, ChEBI:CHEBI:30089,
CC ChEBI:CHEBI:125610, ChEBI:CHEBI:327995;
CC Evidence={ECO:0000269|PubMed:29247559};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:67201;
CC Evidence={ECO:0000269|PubMed:29247559};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N-acetyltryptamine = acetate + tryptamine;
CC Xref=Rhea:RHEA:67204, ChEBI:CHEBI:15377, ChEBI:CHEBI:30089,
CC ChEBI:CHEBI:55515, ChEBI:CHEBI:57887;
CC Evidence={ECO:0000269|PubMed:29247559};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:67205;
CC Evidence={ECO:0000269|PubMed:29247559};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + melatonin = 5-methoxytryptamine + acetate;
CC Xref=Rhea:RHEA:67208, ChEBI:CHEBI:15377, ChEBI:CHEBI:16796,
CC ChEBI:CHEBI:30089, ChEBI:CHEBI:166874;
CC Evidence={ECO:0000269|PubMed:29247559, ECO:0000269|Ref.10};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:67209;
CC Evidence={ECO:0000269|PubMed:29247559, ECO:0000269|Ref.10};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000250|UniProtKB:Q8GXJ1};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000250|UniProtKB:Q8GXJ1};
CC -!- ACTIVITY REGULATION: The activity of this enzyme is not inhibited by
CC butyrate, a well-known histone deacetylase inhibitor.
CC {ECO:0000269|PubMed:29247559}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=409 uM for N-acetylserotonin {ECO:0000269|PubMed:29247559};
CC Vmax=1 pmol/sec/mg enzyme with N-acetylserotonin as substrate
CC {ECO:0000269|PubMed:29247559};
CC pH dependence:
CC Optimum pH is 6.8-8.8. {ECO:0000269|PubMed:29247559};
CC Temperature dependence:
CC Optimum temperature is 30 degrees Celsius.
CC {ECO:0000269|PubMed:29247559};
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:19505461, ECO:0000269|PubMed:29247559}.
CC Mitochondrion {ECO:0000269|PubMed:19505461}.
CC -!- TISSUE SPECIFICITY: Expressed in leaves (PubMed:17399684). Expressed in
CC coleoptiles, leaves, flag leaves and flowers (PubMed:19505461).
CC Expressed at low levels in roots (PubMed:19505461).
CC {ECO:0000269|PubMed:17399684, ECO:0000269|PubMed:19505461}.
CC -!- INDUCTION: Down-regulated by treatment with cadmium.
CC {ECO:0000269|PubMed:29247559}.
CC -!- SIMILARITY: Belongs to the histone deacetylase family. {ECO:0000305}.
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DR EMBL; DP000011; ABA95964.1; -; Genomic_DNA.
DR EMBL; AP008218; BAF29341.1; -; Genomic_DNA.
DR EMBL; AP014968; BAT16163.1; -; Genomic_DNA.
DR EMBL; CM000149; EEE52876.1; -; Genomic_DNA.
DR EMBL; AK072557; BAG93031.1; -; mRNA.
DR RefSeq; XP_015618357.1; XM_015762871.1.
DR AlphaFoldDB; Q2QWU2; -.
DR SMR; Q2QWU2; -.
DR STRING; 4530.OS12T0182700-01; -.
DR PaxDb; Q2QWU2; -.
DR PRIDE; Q2QWU2; -.
DR EnsemblPlants; Os12t0182700-01; Os12t0182700-01; Os12g0182700.
DR GeneID; 4351682; -.
DR Gramene; Os12t0182700-01; Os12t0182700-01; Os12g0182700.
DR KEGG; osa:4351682; -.
DR eggNOG; KOG1343; Eukaryota.
DR HOGENOM; CLU_007727_8_2_1; -.
DR InParanoid; Q2QWU2; -.
DR OMA; CTSPAMG; -.
DR OrthoDB; 1484694at2759; -.
DR BRENDA; 3.5.1.98; 8948.
DR Proteomes; UP000000763; Chromosome 12.
DR Proteomes; UP000007752; Chromosome 12.
DR Proteomes; UP000059680; Chromosome 12.
DR GO; GO:0009507; C:chloroplast; IDA:UniProtKB.
DR GO; GO:0009570; C:chloroplast stroma; IEA:EnsemblPlants.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IEA:EnsemblPlants.
DR GO; GO:0000118; C:histone deacetylase complex; IBA:GO_Central.
DR GO; GO:0005739; C:mitochondrion; IDA:UniProtKB.
DR GO; GO:0043014; F:alpha-tubulin binding; IEA:EnsemblPlants.
DR GO; GO:0048487; F:beta-tubulin binding; IEA:EnsemblPlants.
DR GO; GO:0019213; F:deacetylase activity; IDA:UniProtKB.
DR GO; GO:0004407; F:histone deacetylase activity; IBA:GO_Central.
DR GO; GO:0051721; F:protein phosphatase 2A binding; IEA:EnsemblPlants.
DR GO; GO:0043621; F:protein self-association; IEA:EnsemblPlants.
DR GO; GO:0042903; F:tubulin deacetylase activity; IEA:EnsemblPlants.
DR GO; GO:0008270; F:zinc ion binding; ISS:UniProtKB.
DR GO; GO:0016575; P:histone deacetylation; IBA:GO_Central.
DR GO; GO:0030186; P:melatonin metabolic process; IDA:UniProtKB.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0042548; P:regulation of photosynthesis, light reaction; IEA:EnsemblPlants.
DR GO; GO:0090042; P:tubulin deacetylation; IEA:EnsemblPlants.
DR Gene3D; 3.40.800.20; -; 1.
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 Pfam; PF00850; Hist_deacetyl; 1.
DR PRINTS; PR01270; HDASUPER.
DR SUPFAM; SSF52768; SSF52768; 1.
PE 1: Evidence at protein level;
KW Chloroplast; Hydrolase; Metal-binding; Mitochondrion; Plastid;
KW Reference proteome; Transit peptide; Zinc.
FT TRANSIT 1..65
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 66..443
FT /note="Histone deacetylase 10, chloroplastic"
FT /id="PRO_0000453207"
FT REGION 82..412
FT /note="Histone deacetylase"
FT ACT_SITE 222
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT BINDING 259
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT BINDING 261
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT BINDING 346
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT SITE 390
FT /note="Polarizes the scissile carbonyl of the substrate"
FT /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
SQ SEQUENCE 443 AA; 48100 MW; E5FAF7F81672B6CC CRC64;
MEQLWVPSLP ILGGRILPML RHYCGFGSHH PLTWRSLQIT GRKQKHNGCW IAYCLPSHNG
TSISDTNGVR KDLALPDNLL RDAHILYCTS PAMGHNKEAH PETNKRVPAI VDALEKLELT
SKHRGSQVLE IQDFQPASLD DIALVHSRSY ITGLEKAMSR ASDEGLIFIE GTGPTYATQT
TFQECLLSAG AGITLVDSVV AASKLGPKPP LGFALVRPPG HHAVPEGPMG FCVFGNIAVA
ARYAQNQHGL KRVMIIDFDV HHGNGTCDAF YEDPDIFFLS THQLGSYPGT GKIHQVGQGN
GEGTTLNLPL PGGSGDYAMR CAFDEVIAPA AQRFKPDIIL VSAGYDAHAL DPLAGLQFTT
GTFYMLAARI REVAAELCGG RCVFFLEGGY NLESLSSSVA DTFRAFLGEP SLAARFDDPA
MLYEEPTRKI REAIDKAKHL HSL
