ID V7AUN9_PHAVU Unreviewed; 498 AA.
AC V7AUN9;
DT 19-FEB-2014, integrated into UniProtKB/TrEMBL.
DT 19-FEB-2014, sequence version 1.
DT 24-JAN-2024, entry version 51.
DE RecName: Full=Histone deacetylase {ECO:0000256|ARBA:ARBA00012111, ECO:0000256|PIRNR:PIRNR037913};
DE EC=3.5.1.98 {ECO:0000256|ARBA:ARBA00012111, ECO:0000256|PIRNR:PIRNR037913};
GN ORFNames=PHAVU_009G115300g {ECO:0000313|EMBL:ESW09289.1};
OS Phaseolus vulgaris (Kidney bean) (French bean).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade;
OC NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Phaseolus.
OX NCBI_TaxID=3885 {ECO:0000313|EMBL:ESW09289.1, ECO:0000313|Proteomes:UP000000226};
RN [1] {ECO:0000313|Proteomes:UP000000226}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. G19833 {ECO:0000313|Proteomes:UP000000226};
RX PubMed=24908249; DOI=10.1038/ng.3008;
RA Schmutz J., McClean P.E., Mamidi S., Wu G.A., Cannon S.B., Grimwood J.,
RA Jenkins J., Shu S., Song Q., Chavarro C., Torres-Torres M., Geffroy V.,
RA Moghaddam S.M., Gao D., Abernathy B., Barry K., Blair M., Brick M.A.,
RA Chovatia M., Gepts P., Goodstein D.M., Gonzales M., Hellsten U.,
RA Hyten D.L., Jia G., Kelly J.D., Kudrna D., Lee R., Richard M.M.,
RA Miklas P.N., Osorno J.M., Rodrigues J., Thareau V., Urrea C.A., Wang M.,
RA Yu Y., Zhang M., Wing R.A., Cregan P.B., Rokhsar D.S., Jackson S.A.;
RT "A reference genome for common bean and genome-wide analysis of dual
RT domestications.";
RL Nat. Genet. 46:707-713(2014).
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:0000256|ARBA:ARBA00001028,
CC ECO:0000256|PIRNR:PIRNR037913};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000256|ARBA:ARBA00001947};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000256|PIRNR:PIRNR037913}.
CC -!- SIMILARITY: Belongs to the histone deacetylase family. HD Type 1
CC subfamily. {ECO:0000256|PIRNR:PIRNR037913}.
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DR EMBL; CM002296; ESW09289.1; -; Genomic_DNA.
DR RefSeq; XP_007137295.1; XM_007137233.1.
DR AlphaFoldDB; V7AUN9; -.
DR STRING; 3885.V7AUN9; -.
DR EnsemblPlants; ESW09289; ESW09289; PHAVU_009G115300g.
DR GeneID; 18619848; -.
DR Gramene; ESW09289; ESW09289; PHAVU_009G115300g.
DR KEGG; pvu:PHAVU_009G115300g; -.
DR eggNOG; KOG1342; Eukaryota.
DR OMA; FHSEEYM; -.
DR OrthoDB; 1327607at2759; -.
DR Proteomes; UP000000226; Chromosome 9.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0004407; F:histone deacetylase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR Gene3D; 3.40.800.20; Histone deacetylase domain; 1.
DR InterPro; IPR000286; His_deacetylse.
DR InterPro; IPR003084; His_deacetylse_1.
DR InterPro; IPR023801; His_deacetylse_dom.
DR InterPro; IPR037138; His_deacetylse_dom_sf.
DR InterPro; IPR023696; Ureohydrolase_dom_sf.
DR PANTHER; PTHR48252:SF19; HISTONE DEACETYLASE 19; 1.
DR PANTHER; PTHR48252; HISTONE DEACETYLASE 2-RELATED; 1.
DR Pfam; PF00850; Hist_deacetyl; 1.
DR PIRSF; PIRSF037913; His_deacetylse_1; 1.
DR PRINTS; PR01270; HDASUPER.
DR PRINTS; PR01271; HISDACETLASE.
DR SUPFAM; SSF52768; Arginase/deacetylase; 1.
PE 3: Inferred from homology;
KW Chromatin regulator {ECO:0000256|ARBA:ARBA00022853,
KW ECO:0000256|PIRNR:PIRNR037913}; Hydrolase {ECO:0000256|PIRNR:PIRNR037913};
KW Metal-binding {ECO:0000256|PIRSR:PIRSR037913-3};
KW Nucleus {ECO:0000256|PIRNR:PIRNR037913};
KW Reference proteome {ECO:0000313|Proteomes:UP000000226};
KW Repressor {ECO:0000256|ARBA:ARBA00022491};
KW Transcription {ECO:0000256|ARBA:ARBA00023163,
KW ECO:0000256|PIRNR:PIRNR037913};
KW Transcription regulation {ECO:0000256|ARBA:ARBA00023015,
KW ECO:0000256|PIRNR:PIRNR037913}.
FT DOMAIN 36..324
FT /note="Histone deacetylase"
FT /evidence="ECO:0000259|Pfam:PF00850"
FT REGION 384..458
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 400..417
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 418..458
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 149
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|PIRSR:PIRSR037913-1"
FT BINDING 107
FT /ligand="substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR037913-2"
FT BINDING 157
FT /ligand="substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR037913-2"
FT BINDING 184
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|PIRSR:PIRSR037913-3"
FT BINDING 186
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|PIRSR:PIRSR037913-3"
FT BINDING 272
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000256|PIRSR:PIRSR037913-3"
FT BINDING 311
FT /ligand="substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR037913-2"
SQ SEQUENCE 498 AA; 56133 MW; EA42DA3779C1BB6E CRC64;
MDSGGNSLPS APDAVKRKVC YFYDPEVGNY YYGQGHPMKP HRIRMTHALL AHYGLLQHMQ
VHKPFPARDR DLCRFHADDY VAFLRSITPE TQQDHLRQLK RFNVGEDCPV FDGLYSFCQT
YAGGSVGGAV KLNHDQCDIA VNWAGGLHHA KKCEASGFCY VNDIVLAILE LLKQHERVLY
VDIDIHHGDG VEEAFYTTDR VMTVSFHKFG DYFPGTGDVR DIGYGKGKYY SLNVPLDDGI
DDESYHFLFK PLIGKVMEVF RPGAVVLQCG ADSLSGDRLG CFNLSIRGHA ECVKYMRSFN
VPLLLLGGGG YTIRNVARCW CYETGVALGI EVDDKMPEHE YYEYFGPDYT LHVAPSNMEN
KNSRYLLEEI QSKLLENLSK LQHAPSVQFQ ERPPDSDLGE ADEDHDNGDE TWDPDSDMDV
DVERGLVPSR VKKEIVEPQL NDPDDQRRSG EHLRDSDTAV AETCMKALDI SSQKADEDNV
KVEHNTVNDL TKETGLKC
//