ID   HDA18_ARATH             Reviewed;         682 AA.
AC   Q8LRK8; Q9FNQ7;
DT   06-MAR-2007, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2002, sequence version 1.
DT   27-MAR-2024, entry version 118.
DE   RecName: Full=Histone deacetylase 18 {ECO:0000303|PubMed:12466527};
DE            EC=3.5.1.98 {ECO:0000269|PubMed:23362208};
GN   Name=HDA18 {ECO:0000303|PubMed:12466527};
GN   OrderedLocusNames=At5g61070 {ECO:0000312|Araport:AT5G61070};
GN   ORFNames=MAF19.8 {ECO:0000312|EMBL:BAB10370.1};
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 [MRNA], 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   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=9405937; DOI=10.1093/dnares/4.4.291;
RA   Kotani H., Nakamura Y., Sato S., Kaneko T., Asamizu E., Miyajima N.,
RA   Tabata S.;
RT   "Structural analysis of Arabidopsis thaliana chromosome 5. II. Sequence
RT   features of the regions of 1,044,062 bp covered by thirteen physically
RT   assigned P1 clones.";
RL   DNA Res. 4:291-300(1997).
RN   [3]
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   [4]
RP   FUNCTION.
RX   PubMed=16176989; DOI=10.1073/pnas.0503143102;
RA   Xu C.-R., Liu C., Wang Y.-L., Li L.-C., Chen W.-Q., Xu Z.-H., Bai S.-N.;
RT   "Histone acetylation affects expression of cellular patterning genes in the
RT   Arabidopsis root epidermis.";
RL   Proc. Natl. Acad. Sci. U.S.A. 102:14469-14474(2005).
RN   [5]
RP   FUNCTION, CATALYTIC ACTIVITY, AND SUBCELLULAR LOCATION.
RX   PubMed=23362208; DOI=10.1105/tpc.112.107045;
RA   Liu C., Li L.C., Chen W.Q., Chen X., Xu Z.H., Bai S.N.;
RT   "HDA18 affects cell fate in Arabidopsis root epidermis via histone
RT   acetylation at four kinase genes.";
RL   Plant Cell 25:257-269(2013).
RN   [6]
RP   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).
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:23362208). Histone deacetylation gives a tag for epigenetic
CC       repression and plays an important role in transcriptional regulation,
CC       cell cycle progression and developmental events (Probable). Histone
CC       deacetylases act via the formation of large multiprotein complexes
CC       (Probable). Required for appropriate cellular patterning in the root
CC       epidermis (PubMed:16176989, PubMed:23362208). Involved in the
CC       differentiation of hair and non-hair cells in the root epidermis
CC       (PubMed:23362208). Is not directly involved in the regulation of the
CC       expression of pattern genes (PubMed:23362208). Regulates the
CC       transcription of certain kinase genes, which are components of a
CC       positional information relay system, by changing their histone
CC       acetylation status (PubMed:23362208). {ECO:0000269|PubMed:16176989,
CC       ECO:0000269|PubMed:23362208, ECO:0000305|PubMed:23362208}.
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:23362208};
CC       PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:58197;
CC         Evidence={ECO:0000269|PubMed:23362208};
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   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:23362208}. Cytoplasm
CC       {ECO:0000269|PubMed:23362208}.
CC   -!- TISSUE SPECIFICITY: Expressed in roots, stems, young rosette leaves,
CC       flowers and siliques. {ECO:0000269|PubMed:22363501}.
CC   -!- MISCELLANEOUS: HDA5, a tandem duplication of HDA18, is not required for
CC       the cellular patterning in the root epidermis.
CC       {ECO:0000269|PubMed:16176989}.
CC   -!- SIMILARITY: Belongs to the histone deacetylase family. HD type 2
CC       subfamily. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAB10370.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AF510670; AAM34783.1; -; mRNA.
DR   EMBL; AB006696; BAB10370.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; CP002688; AED97419.1; -; Genomic_DNA.
DR   RefSeq; NP_200915.2; NM_125500.3.
DR   AlphaFoldDB; Q8LRK8; -.
DR   SMR; Q8LRK8; -.
DR   BioGRID; 21472; 1.
DR   STRING; 3702.Q8LRK8; -.
DR   PaxDb; 3702-AT5G61070-1; -.
DR   ProteomicsDB; 230287; -.
DR   EnsemblPlants; AT5G61070.1; AT5G61070.1; AT5G61070.
DR   GeneID; 836228; -.
DR   Gramene; AT5G61070.1; AT5G61070.1; AT5G61070.
DR   KEGG; ath:AT5G61070; -.
DR   Araport; AT5G61070; -.
DR   TAIR; AT5G61070; HDA18.
DR   eggNOG; KOG1343; Eukaryota.
DR   HOGENOM; CLU_019490_0_0_1; -.
DR   InParanoid; Q8LRK8; -.
DR   OMA; ERLCTYW; -.
DR   OrthoDB; 691053at2759; -.
DR   PhylomeDB; Q8LRK8; -.
DR   PRO; PR:Q8LRK8; -.
DR   Proteomes; UP000006548; Chromosome 5.
DR   ExpressionAtlas; Q8LRK8; baseline and differential.
DR   GO; GO:0005737; C:cytoplasm; IDA:TAIR.
DR   GO; GO:0005634; C:nucleus; IDA:TAIR.
DR   GO; GO:0004407; F:histone deacetylase activity; IDA:TAIR.
DR   GO; GO:0008270; F:zinc ion binding; ISS:UniProtKB.
DR   GO; GO:0006338; P:chromatin remodeling; ISS:TAIR.
DR   GO; GO:0045604; P:regulation of epidermal cell differentiation; IMP:TAIR.
DR   GO; GO:0010053; P:root epidermal cell differentiation; IMP:TAIR.
DR   Gene3D; 3.40.800.20; Histone deacetylase domain; 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   PANTHER; PTHR10625:SF37; HISTONE DEACETYLASE 18-RELATED; 1.
DR   PANTHER; PTHR10625; HISTONE DEACETYLASE HDAC1-RELATED; 1.
DR   Pfam; PF00850; Hist_deacetyl; 1.
DR   PRINTS; PR01270; HDASUPER.
DR   SUPFAM; SSF52768; Arginase/deacetylase; 1.
DR   Genevisible; Q8LRK8; AT.
PE   1: Evidence at protein level;
KW   Chromatin regulator; Coiled coil; Cytoplasm; Hydrolase; Metal-binding;
KW   Nucleus; Reference proteome; Repressor; Transcription;
KW   Transcription regulation; Zinc.
FT   CHAIN           1..682
FT                   /note="Histone deacetylase 18"
FT                   /id="PRO_0000280093"
FT   REGION          59..382
FT                   /note="Histone deacetylase"
FT   COILED          430..608
FT                   /evidence="ECO:0000255"
FT   ACT_SITE        191
FT                   /note="Proton donor/acceptor"
FT                   /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT   BINDING         231
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT   BINDING         233
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT   BINDING         324
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
FT   SITE            364
FT                   /note="Polarizes the scissile carbonyl of the substrate"
FT                   /evidence="ECO:0000250|UniProtKB:Q8GXJ1"
SQ   SEQUENCE   682 AA;  76634 MW;  67D91533AB998840 CRC64;
     MLLKFEASSE LRLVDPSVSL TVLRKIRLSH LPDMTMTSES SGKKCGEGDG KVAGKSQRKV
     GLVYDETMCK HDTPNGKVDV ECPDRIRVIW EKLQLAGVTQ RCVVLGGSKA EDKHLKLVHT
     KKHVNLVKSI STKKKDSRRN KIASQLDSIY LNGGSSEAAY LAAGSVVKVA EKVAEGELDC
     GFAIVRPPGH HAESDEAMGF CLFNNVAVAA SFLLNERPDL DVKKILIVDW DIHHGNGTQK
     MFWKDSRVLI FSVHRHDHGS FYPFGDDGDF NMVGEGPGEG FNINVPWEQG GCGDADYLAV
     WNHILIPVTK EFKPDIILLS AGFDAAIGDP LGGCCVTPYG YSVMLKKLME FAHGKIVLAL
     EGGYNLESLG KSSLACVQVL LEDKQIHGSS ETYPLESTRR VIQAVRERLC TYWPSLDASM
     ASNENLKNPS AERNSADALL REVEELKSLM AARDGELEAR RKELKAKNKE LEANEKELEA
     GLMLIRARED VICGLHAKIE SLQQERDEAV AKAERIDKEL QEDRARSQEF KEDTEFCLST
     LRREKELAIM AKNKDLEAKE KELEARLMLV HAREDKIHAK IERLQQERDE AVAKAERIDK
     ELQEDRSRSR VGNGSFAFSQ EFYEDMDLDE LEPLSPEFNE DMDSEELEPF QVIKKNMERS
     HKKFIKDMEC IKFIASERAR VL
//