HDA18_ARATH
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 03-AUG-2022, entry version 111.
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.AT5G61070.1; -.
DR PaxDb; Q8LRK8; -.
DR PRIDE; Q8LRK8; -.
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; locus:2159461; AT5G61070.
DR eggNOG; KOG1343; Eukaryota.
DR HOGENOM; CLU_019490_0_0_1; -.
DR InParanoid; Q8LRK8; -.
DR OMA; ERLCTYW; -.
DR OrthoDB; 1484694at2759; -.
DR PhylomeDB; Q8LRK8; -.
DR PRO; PR:Q8LRK8; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q8LRK8; baseline and differential.
DR Genevisible; Q8LRK8; AT.
DR GO; GO:0005737; C:cytoplasm; IDA:TAIR.
DR GO; GO:0000118; C:histone deacetylase complex; IBA:GO_Central.
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:0016575; P:histone deacetylation; IBA:GO_Central.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IBA:GO_Central.
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; -; 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 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
