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Protein

Histone deacetylase HDA1

Gene

HDA1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes.

Miscellaneous

Present with 3050 molecules/cell in log phase SD medium.1 Publication

Catalytic activityi

Hydrolysis of an N6-acetyl-lysine residue of a histone to yield a deacetylated histone.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei206By similarity1

GO - Molecular functioni

  • chromatin binding Source: SGD
  • identical protein binding Source: IntAct
  • NAD-dependent histone deacetylase activity (H3-K14 specific) Source: UniProtKB-EC

GO - Biological processi

  • gene silencing by RNA Source: SGD
  • gene silencing involved in chronological cell aging Source: SGD
  • histone deacetylation Source: SGD
  • negative regulation of chromatin silencing involved in replicative cell aging Source: SGD
  • negative regulation of transcription by RNA polymerase II Source: SGD
  • negative regulation of transcription by transcription factor localization Source: SGD
  • positive regulation of transcription by RNA polymerase II Source: SGD
  • regulation of chromatin silencing at telomere Source: SGD
  • transcription, DNA-templated Source: UniProtKB-KW

Keywordsi

Molecular functionChromatin regulator, Hydrolase, Repressor
Biological processTranscription, Transcription regulation

Enzyme and pathway databases

BioCyciYEAST:G3O-33059-MONOMER
ReactomeiR-SCE-3214815 HDACs deacetylate histones
R-SCE-3371511 HSF1 activation
R-SCE-5617833 Cilium Assembly

Names & Taxonomyi

Protein namesi
Recommended name:
Histone deacetylase HDA1 (EC:3.5.1.98)
Gene namesi
Name:HDA1
Ordered Locus Names:YNL021W
ORF Names:N2819
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIV

Organism-specific databases

EuPathDBiFungiDB:YNL021W
SGDiS000004966 HDA1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001147381 – 706Histone deacetylase HDA1Add BLAST706

Proteomic databases

MaxQBiP53973
PaxDbiP53973
PRIDEiP53973

PTM databases

iPTMnetiP53973

Interactioni

Binary interactionsi

Show more details

GO - Molecular functioni

  • identical protein binding Source: IntAct

Protein-protein interaction databases

BioGridi35805, 714 interactors
DIPiDIP-1360N
IntActiP53973, 24 interactors
MINTiP53973
STRINGi4932.YNL021W

Structurei

Secondary structure

1706
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi457 – 473Combined sources17
Beta strandi483 – 485Combined sources3
Helixi487 – 489Combined sources3
Beta strandi490 – 492Combined sources3
Helixi496 – 498Combined sources3
Beta strandi500 – 508Combined sources9
Beta strandi511 – 513Combined sources3
Turni518 – 520Combined sources3
Helixi525 – 527Combined sources3
Beta strandi529 – 531Combined sources3
Helixi535 – 542Combined sources8
Turni543 – 545Combined sources3
Beta strandi547 – 553Combined sources7
Beta strandi558 – 561Combined sources4
Helixi563 – 579Combined sources17
Turni580 – 583Combined sources4
Beta strandi590 – 595Combined sources6
Helixi596 – 598Combined sources3
Helixi599 – 608Combined sources10
Turni612 – 614Combined sources3
Beta strandi615 – 623Combined sources9
Helixi637 – 644Combined sources8
Beta strandi646 – 650Combined sources5
Helixi667 – 669Combined sources3
Beta strandi672 – 674Combined sources3
Helixi680 – 696Combined sources17

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5J8JX-ray2.72A457-698[»]
ProteinModelPortaliP53973
SMRiP53973
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni67 – 396Histone deacetylaseAdd BLAST330

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00530000062809
HOGENOMiHOG000161343
InParanoidiP53973
KOiK11407
OMAiCYDDRMK
OrthoDBiEOG092C3GJU

Family and domain databases

Gene3Di3.40.800.20, 1 hit
InterProiView protein in InterPro
IPR019154 Arb2_domain
IPR000286 His_deacetylse
IPR023801 His_deacetylse_dom
IPR037138 His_deacetylse_dom_sf
IPR017321 Hist_deAcase_II_yeast
IPR023696 Ureohydrolase_dom_sf
PANTHERiPTHR10625 PTHR10625, 1 hit
PfamiView protein in Pfam
PF09757 Arb2, 1 hit
PF00850 Hist_deacetyl, 1 hit
PIRSFiPIRSF037919 HDAC_II_yeast, 1 hit
PRINTSiPR01270 HDASUPER
SUPFAMiSSF52768 SSF52768, 1 hit

Sequencei

Sequence statusi: Complete.

P53973-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDSVMVKKEV LENPDHDLKR KLEENKEEEN SLSTTSKSKR QVIVPVCMPK
60 70 80 90 100
IHYSPLKTGL CYDVRMRYHA KIFTSYFEYI DPHPEDPRRI YRIYKILAEN
110 120 130 140 150
GLINDPTLSG VDDLGDLMLK IPVRAATSEE ILEVHTKEHL EFIESTEKMS
160 170 180 190 200
REELLKETEK GDSVYFNNDS YASARLPCGG AIEACKAVVE GRVKNSLAVV
210 220 230 240 250
RPPGHHAEPQ AAGGFCLFSN VAVAAKNILK NYPESVRRIM ILDWDIHHGN
260 270 280 290 300
GTQKSFYQDD QVLYVSLHRF EMGKYYPGTI QGQYDQTGEG KGEGFNCNIT
310 320 330 340 350
WPVGGVGDAE YMWAFEQVVM PMGREFKPDL VIISSGFDAA DGDTIGQCHV
360 370 380 390 400
TPSCYGHMTH MLKSLARGNL CVVLEGGYNL DAIARSALSV AKVLIGEPPD
410 420 430 440 450
ELPDPLSDPK PEVIEMIDKV IRLQSKYWNC FRRRHANSGC NFNEPINDSI
460 470 480 490 500
ISKNFPLQKA IRQQQQHYLS DEFNFVTLPL VSMDLPDNTV LCTPNISESN
510 520 530 540 550
TIIIVVHDTS DIWAKRNVIS GTIDLSSSVI IDNSLDFIKW GLDRKYGIID
560 570 580 590 600
VNIPLTLFEP DNYSGMITSQ EVLIYLWDNY IKYFPSVAKI AFIGIGDSYS
610 620 630 640 650
GIVHLLGHRD TRAVTKTVIN FLGDKQLKPL VPLVDETLSE WYFKNSLIFS
660 670 680 690 700
NNSHQCWKEN ESRKPRKKFG RVLRCDTDGL NNIIEERFEE ATDFILDSFE

EWSDEE
Length:706
Mass (Da):80,070
Last modified:October 1, 1996 - v1
Checksum:i4E7069E66D03264D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z71297 Genomic DNA Translation: CAA95883.1
BK006947 Genomic DNA Translation: DAA10524.1
PIRiS62933
RefSeqiNP_014377.1, NM_001182860.1

Genome annotation databases

EnsemblFungiiYNL021W; YNL021W; YNL021W
GeneIDi855710
KEGGisce:YNL021W

Similar proteinsi

Entry informationi

Entry nameiHDA1_YEAST
AccessioniPrimary (citable) accession number: P53973
Secondary accession number(s): D6W1F8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: March 28, 2018
This is version 151 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health