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Entry version 169 (07 Oct 2020)
Sequence version 1 (01 Oct 1996)
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Protein

Histone deacetylase HDA1

Gene

HDA1

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

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei206By similarity1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

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

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-SCE-3214815, HDACs deacetylate histones
R-SCE-3371511, HSF1 activation
R-SCE-4551638, SUMOylation of chromatin organization proteins
R-SCE-5617833, Cilium Assembly

Protein family/group databases

ESTHER database of the Alpha/Beta-hydrolase fold superfamily of proteins

More...
ESTHERi
yeast-hda1, Arb2_domain

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Histone deacetylase HDA1 (EC:3.5.1.98)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:HDA1
Ordered Locus Names:YNL021W
ORF Names:N2819
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri559292 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002311 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome XIV

Organism-specific databases

Eukaryotic Pathogen Database Resources

More...
EuPathDBi
FungiDB:YNL021W

Saccharomyces Genome Database

More...
SGDi
S000004966, HDA1

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>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 & Seán O’Donoghue; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001147381 – 706Histone deacetylase HDA1Add BLAST706

Proteomic databases

MaxQB - The MaxQuant DataBase

More...
MaxQBi
P53973

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P53973

PRoteomics IDEntifications database

More...
PRIDEi
P53973

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
P53973

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction%5Fsection">Interaction</a>' section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="https://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated at every <a href="http://www.uniprot.org/help/synchronization">UniProt release</a>.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

Hide details

GO - Molecular functioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...
BioGRIDi
35805, 737 interactors

ComplexPortal: manually curated resource of macromolecular complexes

More...
ComplexPortali
CPX-1884, HDA1 complex

Database of interacting proteins

More...
DIPi
DIP-1360N

Protein interaction database and analysis system

More...
IntActi
P53973, 17 interactors

Molecular INTeraction database

More...
MINTi
P53973

STRING: functional protein association networks

More...
STRINGi
4932.YNL021W

Miscellaneous databases

RNAct, Protein-RNA interaction predictions for model organisms.

More...
RNActi
P53973, protein

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1706
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
P53973

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni67 – 396Histone deacetylaseAdd BLAST330

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG1343, Eukaryota

Ensembl GeneTree

More...
GeneTreei
ENSGT00940000159563

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_007727_4_0_1

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P53973

KEGG Orthology (KO)

More...
KOi
K11407

Identification of Orthologs from Complete Genome Data

More...
OMAi
FQKIVMP

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.40.800.20, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View 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

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF09757, Arb2, 1 hit
PF00850, Hist_deacetyl, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF037919, HDAC_II_yeast, 1 hit

Protein Motif fingerprint database; a protein domain database

More...
PRINTSi
PR01270, HDASUPER

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF52768, SSF52768, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i4E7069E66D03264D
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
Z71297 Genomic DNA Translation: CAA95883.1
BK006947 Genomic DNA Translation: DAA10524.1

Protein sequence database of the Protein Information Resource

More...
PIRi
S62933

NCBI Reference Sequences

More...
RefSeqi
NP_014377.1, NM_001182860.1

Genome annotation databases

Ensembl fungal genome annotation project

More...
EnsemblFungii
YNL021W_mRNA; YNL021W; YNL021W

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
855710

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
sce:YNL021W

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

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

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5J8JX-ray2.72A457-698[»]
SMRiP53973
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi35805, 737 interactors
ComplexPortaliCPX-1884, HDA1 complex
DIPiDIP-1360N
IntActiP53973, 17 interactors
MINTiP53973
STRINGi4932.YNL021W

Protein family/group databases

ESTHERiyeast-hda1, Arb2_domain

PTM databases

iPTMnetiP53973

Proteomic databases

MaxQBiP53973
PaxDbiP53973
PRIDEiP53973

Genome annotation databases

EnsemblFungiiYNL021W_mRNA; YNL021W; YNL021W
GeneIDi855710
KEGGisce:YNL021W

Organism-specific databases

EuPathDBiFungiDB:YNL021W
SGDiS000004966, HDA1

Phylogenomic databases

eggNOGiKOG1343, Eukaryota
GeneTreeiENSGT00940000159563
HOGENOMiCLU_007727_4_0_1
InParanoidiP53973
KOiK11407
OMAiFQKIVMP

Enzyme and pathway databases

ReactomeiR-SCE-3214815, HDACs deacetylate histones
R-SCE-3371511, HSF1 activation
R-SCE-4551638, SUMOylation of chromatin organization proteins
R-SCE-5617833, Cilium Assembly

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P53973
RNActiP53973, protein

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
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

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiHDA1_YEAST
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P53973
Secondary accession number(s): D6W1F8
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: October 7, 2020
This is version 169 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Reference proteome

Documents

  1. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast chromosome XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names
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