HDA15_ARATH
ID HDA15_ARATH Reviewed; 552 AA.
AC Q8GXJ1; F4J8S2; Q3EB46; Q8LD93; Q9LS38;
DT 06-MAR-2007, integrated into UniProtKB/Swiss-Prot.
DT 16-NOV-2011, sequence version 2.
DT 03-AUG-2022, entry version 117.
DE RecName: Full=Histone deacetylase 15 {ECO:0000303|PubMed:12466527};
DE EC=3.5.1.98 {ECO:0000269|PubMed:23548744};
GN Name=HDA15 {ECO:0000303|PubMed:12466527};
GN OrderedLocusNames=At3g18520 {ECO:0000312|EMBL:AEE76110.1};
GN ORFNames=MYF24_23 {ECO:0000312|EMBL:BAB01118.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10819329; DOI=10.1093/dnares/7.2.131;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:131-135(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=12466527; DOI=10.1093/nar/gkf660;
RA Pandey R., Mueller A., Napoli C.A., Selinger D.A., Pikaard C.S.,
RA Richards E.J., Bender J., Mount D.W., Jorgensen R.A.;
RT "Analysis of histone acetyltransferase and histone deacetylase families of
RT Arabidopsis thaliana suggests functional diversification of chromatin
RT modification among multicellular eukaryotes.";
RL Nucleic Acids Res. 30:5036-5055(2002).
RN [6]
RP SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RX PubMed=22363501; DOI=10.1371/journal.pone.0030846;
RA Alinsug M.V., Chen F.F., Luo M., Tai R., Jiang L., Wu K.;
RT "Subcellular localization of class II HDAs in Arabidopsis thaliana:
RT nucleocytoplasmic shuttling of HDA15 is driven by light.";
RL PLoS ONE 7:e30846-e30846(2012).
RN [7]
RP FUNCTION, ACTIVITY REGULATION, INTERACTION WITH PIF3, AND SUBCELLULAR
RP LOCATION.
RX PubMed=23548744; DOI=10.1105/tpc.113.109710;
RA Liu X., Chen C.Y., Wang K.C., Luo M., Tai R., Yuan L., Zhao M., Yang S.,
RA Tian G., Cui Y., Hsieh H.L., Wu K.;
RT "PHYTOCHROME INTERACTING FACTOR3 associates with the histone deacetylase
RT HDA15 in repression of chlorophyll biosynthesis and photosynthesis in
RT etiolated Arabidopsis seedlings.";
RL Plant Cell 25:1258-1273(2013).
RN [8]
RP FUNCTION, AND INTERACTION WITH MYB96.
RX PubMed=30979883; DOI=10.1038/s41467-019-09417-1;
RA Lee H.G., Seo P.J.;
RT "MYB96 recruits the HDA15 protein to suppress negative regulators of ABA
RT signaling in Arabidopsis.";
RL Nat. Commun. 10:1713-1713(2019).
RN [9]
RP FUNCTION.
RX PubMed=31400169; DOI=10.1111/tpj.14492;
RA Shen Y., Lei T., Cui X., Liu X., Zhou S., Zheng Y., Guerard F.,
RA Issakidis-Bourguet E., Zhou D.X.;
RT "Arabidopsis histone deacetylase HDA15 directly represses plant response to
RT elevated ambient temperature.";
RL Plant J. 100:991-1006(2019).
RN [10]
RP FUNCTION, ACTIVE SITE, INTERACTION WITH HY5, SUBCELLULAR LOCATION, AND
RP MUTAGENESIS OF HIS-276; HIS-277; HIS-282; ASP-313; HIS-315 AND HIS-316.
RX PubMed=31061103; DOI=10.1104/pp.19.00055;
RA Zhao L., Peng T., Chen C.Y., Ji R., Gu D., Li T., Zhang D., Tu Y.T., Wu K.,
RA Liu X.;
RT "HY5 interacts with the histone deacetylase HDA15 to repress hypocotyl cell
RT elongation in photomorphogenesis.";
RL Plant Physiol. 180:1450-1466(2019).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (2.36 ANGSTROMS) OF 146-509 IN COMPLEX WITH ZINC
RP IONS, COFACTOR, AND HOMOTETRAMERIZATION.
RX PubMed=32878973; DOI=10.1104/pp.20.00604;
RA Chen C.Y., Tu Y.T., Hsu J.C., Hung H.C., Liu T.C., Lee Y.H., Chou C.C.,
RA Cheng Y.S., Wu K.;
RT "Structure of Arabidopsis HISTONE DEACETYLASE15.";
RL Plant Physiol. 184:1585-1600(2020).
CC -!- FUNCTION: Responsible for the deacetylation of lysine residues on the
CC N-terminal part of the core histones (H2A, H2B, H3 and H4)
CC (PubMed:23548744). Histone deacetylation gives a tag for epigenetic
CC repression and plays an important role in transcriptional regulation,
CC cell cycle progression and developmental events (PubMed:23548744).
CC Histone deacetylases act via the formation of large multiprotein
CC complexes (Probable). Represses chlorophyll biosynthesis and
CC photosynthesis in the dark (PubMed:23548744). Is recruited by PIF3 to
CC the promoters of chlorophyll biosynthetic and photosynthetic genes, and
CC represses their transcription by histone deacetylation
CC (PubMed:23548744). Involved in the repression of hypocotyl cell
CC elongation to promote photomorphogenesis (PubMed:31061103). Is
CC recruited by HY5 to the promoters of a subset of cell wall organization
CC and auxin signaling-related genes, and represses gene expression by
CC decreasing the levels of histone H4 acetylation in a light-dependent
CC manner (PubMed:31061103). Promotes abscisic acid (ABA) signaling
CC (PubMed:30979883). Is recruited by MYB96 to the promoters of a subset
CC of Rho GTPase (ROP) genes, which repress ABA signaling at the early
CC stages of signal transduction (PubMed:30979883). Represses ROP
CC expression by removing acetyl groups of histone H3 and H4 from the
CC cognate regions, particularly in the presence of ABA (PubMed:30979883).
CC Represses the plant response to elevated ambient temperature by
CC directly repressing warm temperature-responsive genes
CC (PubMed:31400169). {ECO:0000269|PubMed:23548744,
CC ECO:0000269|PubMed:30979883, ECO:0000269|PubMed:31061103,
CC ECO:0000269|PubMed:31400169, ECO:0000305|PubMed:23548744}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N(6)-acetyl-L-lysyl-[histone] = acetate + L-lysyl-
CC [histone]; Xref=Rhea:RHEA:58196, Rhea:RHEA-COMP:9845, Rhea:RHEA-
CC COMP:11338, ChEBI:CHEBI:15377, ChEBI:CHEBI:29969, ChEBI:CHEBI:30089,
CC ChEBI:CHEBI:61930; EC=3.5.1.98;
CC Evidence={ECO:0000269|PubMed:23548744};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:58197;
CC Evidence={ECO:0000269|PubMed:23548744};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:32878973};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000269|PubMed:32878973};
CC -!- ACTIVITY REGULATION: Inhibited by trichostatin A (TSA), a well-known
CC histone deacetylase inhibitor. {ECO:0000269|PubMed:23548744}.
CC -!- SUBUNIT: Interacts with PIF3 in the dark (PubMed:23548744). Interacts
CC with HY5 (PubMed:31061103). Interacts with MYB96 (PubMed:30979883).
CC Forms homotetramers (PubMed:32878973). {ECO:0000269|PubMed:23548744,
CC ECO:0000269|PubMed:30979883, ECO:0000269|PubMed:31061103,
CC ECO:0000269|PubMed:32878973}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:22363501,
CC ECO:0000269|PubMed:23548744, ECO:0000269|PubMed:31061103}. Cytoplasm
CC {ECO:0000269|PubMed:22363501}. Note=Shuttles in and out of the nucleus
CC upon light exposure. In the absence of light, is exported out of the
CC nucleus, and upon further exposition to light is imported to the
CC nucleus. {ECO:0000269|PubMed:22363501}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q8GXJ1-1; Sequence=Displayed;
CC -!- TISSUE SPECIFICITY: Expressed in stems, leaves, flowers, siliques and
CC mature seeds. {ECO:0000269|PubMed:22363501}.
CC -!- SIMILARITY: Belongs to the histone deacetylase family. HD type 2
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB01118.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AB026658; BAB01118.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE76110.1; -; Genomic_DNA.
DR EMBL; AK118211; BAC42833.1; -; mRNA.
DR EMBL; AY086135; AAM63340.1; -; mRNA.
DR RefSeq; NP_566612.1; NM_112737.3. [Q8GXJ1-1]
DR PDB; 6J6T; X-ray; 2.36 A; A/B/C/D=146-509.
DR PDBsum; 6J6T; -.
DR AlphaFoldDB; Q8GXJ1; -.
DR SMR; Q8GXJ1; -.
DR BioGRID; 6715; 3.
DR STRING; 3702.AT3G18520.2; -.
DR PaxDb; Q8GXJ1; -.
DR PRIDE; Q8GXJ1; -.
DR ProteomicsDB; 230289; -. [Q8GXJ1-1]
DR EnsemblPlants; AT3G18520.1; AT3G18520.1; AT3G18520. [Q8GXJ1-1]
DR GeneID; 821382; -.
DR Gramene; AT3G18520.1; AT3G18520.1; AT3G18520. [Q8GXJ1-1]
DR KEGG; ath:AT3G18520; -.
DR Araport; AT3G18520; -.
DR eggNOG; KOG1343; Eukaryota.
DR HOGENOM; CLU_007727_8_6_1; -.
DR InParanoid; Q8GXJ1; -.
DR BRENDA; 3.5.1.98; 399.
DR PRO; PR:Q8GXJ1; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q8GXJ1; baseline and differential.
DR Genevisible; Q8GXJ1; AT.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0000118; C:histone deacetylase complex; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0004407; F:histone deacetylase activity; IDA:UniProtKB.
DR GO; GO:0008270; F:zinc ion binding; IDA:UniProtKB.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0016575; P:histone deacetylation; IDA:UniProtKB.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0009789; P:positive regulation of abscisic acid-activated signaling pathway; IDA:UniProtKB.
DR GO; GO:2000306; P:positive regulation of photomorphogenesis; IDA:UniProtKB.
DR GO; GO:0051289; P:protein homotetramerization; IDA:UniProtKB.
DR GO; GO:0040008; P:regulation of growth; IEA:UniProtKB-KW.
DR GO; GO:0042548; P:regulation of photosynthesis, light reaction; IDA:UniProtKB.
DR GO; GO:0009408; P:response to heat; IMP:UniProtKB.
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 InterPro; IPR001876; Znf_RanBP2.
DR Pfam; PF00850; Hist_deacetyl; 1.
DR PRINTS; PR01270; HDASUPER.
DR SUPFAM; SSF52768; SSF52768; 1.
DR PROSITE; PS01358; ZF_RANBP2_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Chromatin regulator; Cytoplasm;
KW Developmental protein; Growth regulation; Hydrolase; Metal-binding;
KW Nucleus; Reference proteome; Repressor; Transcription;
KW Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..552
FT /note="Histone deacetylase 15"
FT /id="PRO_0000280091"
FT ZN_FING 86..115
FT /note="RanBP2-type"
FT REGION 149..462
FT /note="Histone deacetylase"
FT ACT_SITE 277
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:31061103"
FT BINDING 313
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:32878973,
FT ECO:0007744|PDB:6J6T"
FT BINDING 315
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:32878973,
FT ECO:0007744|PDB:6J6T"
FT BINDING 404
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:32878973,
FT ECO:0007744|PDB:6J6T"
FT SITE 444
FT /note="Polarizes the scissile carbonyl of the substrate"
FT /evidence="ECO:0000269|PubMed:32878973,
FT ECO:0007744|PDB:6J6T"
FT MUTAGEN 276
FT /note="H->A: Loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:31061103"
FT MUTAGEN 277
FT /note="H->A: Loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:31061103"
FT MUTAGEN 282
FT /note="H->A: No effect on enzymatic activity."
FT /evidence="ECO:0000269|PubMed:31061103"
FT MUTAGEN 313
FT /note="D->A: Loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:31061103"
FT MUTAGEN 315
FT /note="H->A: Loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:31061103"
FT MUTAGEN 316
FT /note="H->A: Loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:31061103"
FT CONFLICT 172
FT /note="P -> T (in Ref. 4; AAM63340)"
FT /evidence="ECO:0000250|UniProtKB:Q48935"
FT CONFLICT 253
FT /note="A -> T (in Ref. 3; BAC42833)"
FT /evidence="ECO:0000305"
FT CONFLICT 342
FT /note="N -> I (in Ref. 3; BAC42833)"
FT /evidence="ECO:0000305"
FT STRAND 150..153
FT /evidence="ECO:0000305"
FT HELIX 156..160
FT /evidence="ECO:0007829|PDB:6J6T"
FT HELIX 176..187
FT /evidence="ECO:0007829|PDB:6J6T"
FT HELIX 190..194
FT /evidence="ECO:0007829|PDB:6J6T"
FT STRAND 195..197
FT /evidence="ECO:0007829|PDB:6J6T"
FT HELIX 205..208
FT /evidence="ECO:0007829|PDB:6J6T"
FT TURN 209..211
FT /evidence="ECO:0007829|PDB:6J6T"
FT HELIX 214..222
FT /evidence="ECO:0007829|PDB:6J6T"
FT HELIX 223..225
FT /evidence="ECO:0007829|PDB:6J6T"
FT STRAND 226..232
FT /evidence="ECO:0007829|PDB:6J6T"
FT STRAND 235..238
FT /evidence="ECO:0007829|PDB:6J6T"
FT HELIX 241..260
FT /evidence="ECO:0007829|PDB:6J6T"
FT STRAND 263..269
FT /evidence="ECO:0007829|PDB:6J6T"
FT STRAND 287..289
FT /evidence="ECO:0007829|PDB:6J6T"
FT HELIX 291..301
FT /evidence="ECO:0007829|PDB:6J6T"
FT STRAND 305..311
FT /evidence="ECO:0007829|PDB:6J6T"
FT STRAND 313..315
FT /evidence="ECO:0007829|PDB:6J6T"
FT HELIX 318..324
FT /evidence="ECO:0007829|PDB:6J6T"
FT STRAND 328..337
FT /evidence="ECO:0007829|PDB:6J6T"
FT HELIX 339..341
FT /evidence="ECO:0007829|PDB:6J6T"
FT HELIX 356..358
FT /evidence="ECO:0007829|PDB:6J6T"
FT STRAND 361..370
FT /evidence="ECO:0007829|PDB:6J6T"
FT HELIX 374..383
FT /evidence="ECO:0007829|PDB:6J6T"
FT HELIX 385..392
FT /evidence="ECO:0007829|PDB:6J6T"
FT STRAND 395..401
FT /evidence="ECO:0007829|PDB:6J6T"
FT TURN 410..412
FT /evidence="ECO:0007829|PDB:6J6T"
FT HELIX 418..429
FT /evidence="ECO:0007829|PDB:6J6T"
FT TURN 430..434
FT /evidence="ECO:0007829|PDB:6J6T"
FT STRAND 437..440
FT /evidence="ECO:0007829|PDB:6J6T"
FT HELIX 446..460
FT /evidence="ECO:0007829|PDB:6J6T"
FT HELIX 477..490
FT /evidence="ECO:0007829|PDB:6J6T"
FT TURN 491..493
FT /evidence="ECO:0007829|PDB:6J6T"
FT HELIX 497..501
FT /evidence="ECO:0007829|PDB:6J6T"
SQ SEQUENCE 552 AA; 60020 MW; 08BC902FCC99B886 CRC64;
MVVETIERSC EGSKRRHVNG GDIAVPCSGE ECSNGDINVA PGVSAKRARV SREMTFEDIY
GADALLNDDD DEDDDCDWEP VQAPMEFVKW CCVNCTMSNP GDMVHCCICG EHKESGILRH
GYLASPFFKD TGLIEVEEKY GGSSSATSST AVGFDERMLL HSEFEVKAQP HPERPDRLRA
IAASLATAGV FPGRCLPINA REITKQELQM VHTSEHVDAV DTTSQLLYSY FTSDTYANEY
SARAARLAAG LCADLATDIF TGRVKNGFAL VRPPGHHAGV RHAMGFCLHN NAAVAALVAQ
AAGAKKVLIV DWDVHHGNGT QEIFEQNKSV LYISLHRHEG GNFYPGTGAA DEVGSNGGEG
YCVNVPWSCG GVGDKDYIFA FQHVVLPIAS AFSPDFVIIS AGFDAARGDP LGCCDVTPAG
YSRMTQMLGD LCGGKMLVIL EGGYNLRSIS ASATAVIKVL LGENPENELP IATTPSVAGL
QTVLDVLNIQ LEFWPSLAIS YSKLLSELEA RLIENKKNQM KRKVVRVPTW WKWGRKKLLY
NFLSARMISR SK
