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Entry version 147 (12 Aug 2020)
Sequence version 1 (01 Nov 1996)
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Protein

HDA1 complex subunit 3

Gene

HDA3

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

Required for activity of HDA1 histone deacetylase complex. The HDA1 histone deacetylase complex is 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.2 Publications

Miscellaneous

Present with 1100 molecules/cell in log phase SD medium.1 Publication

<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, Repressor
Biological processTranscription, Transcription regulation

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
YEAST:G3O-34304-MONOMER

<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:
HDA1 complex subunit 3
Alternative name(s):
Histone deacetylase complex 1 subunit 3
<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:HDA3
Synonyms:PLO1
Ordered Locus Names:YPR179C
<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 XVI

Organism-specific databases

Eukaryotic Pathogen Database Resources

More...
EuPathDBi
FungiDB:YPR179C

Saccharomyces Genome Database

More...
SGDi
S000006383, HDA3

<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_00000839321 – 655HDA1 complex subunit 3Add BLAST655

Proteomic databases

MaxQB - The MaxQuant DataBase

More...
MaxQBi
Q06623

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

More...
PaxDbi
Q06623

PRoteomics IDEntifications database

More...
PRIDEi
Q06623

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
Q06623

<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 the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Heterodimer with HDA2.

Component of the HDA1 histone deacetylase complex composed of at least one HDA1 homodimer and one HDA2/HDA3 heterodimer.

Interacts with HDA1 and HDA3.

2 Publications

<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

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...
BioGRIDi
36351, 411 interactors

ComplexPortal: manually curated resource of macromolecular complexes

More...
ComplexPortali
CPX-1884, HDA1 complex

Database of interacting proteins

More...
DIPi
DIP-4636N

Protein interaction database and analysis system

More...
IntActi
Q06623, 7 interactors

Molecular INTeraction database

More...
MINTi
Q06623

STRING: functional protein association networks

More...
STRINGi
4932.YPR179C

Miscellaneous databases

RNAct, Protein-RNA interaction predictions for model organisms.

More...
RNActi
Q06623, 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

1655
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

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SMRi
Q06623

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
Q06623

<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

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and domains' section denotes the positions of regions of coiled coil within the protein.<p><a href='/help/coiled' target='_top'>More...</a></p>Coiled coili482 – 632Sequence analysisAdd BLAST151

<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

Belongs to the HDA2/3 family. HDA3 subfamily.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

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eggNOGi
ENOG502QT9V, Eukaryota

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_026579_0_0_1

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q06623

Identification of Orthologs from Complete Genome Data

More...
OMAi
SGDYWLP

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.40.50.12360, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR038609, HDA1_su2/3_sf
IPR021006, Hda2/3
IPR026216, HDA3

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF11496, HDA2-3, 1 hit

Protein Motif fingerprint database; a protein domain database

More...
PRINTSi
PR02093, HDA1SUBUNIT3

<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.

Q06623-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MDLLRILDTK PIPTIVDATT LGISGNTSGD YWLPTTMSLY QKELTDQIVS
60 70 80 90 100
LHYSDILRYF ETSHYKEDVI LESMKTMCLN GSLVATHPYL LIDHYMPKSL
110 120 130 140 150
ITRDVPAHLA ENSGKFSVLR DLINLVQEYE TETAIVCRPG RTMDLLEALL
160 170 180 190 200
LGNKVHIKRY DGHSIKSKQK ANDFSCTVHL FSSEGINFTK YPIKSKARFD
210 220 230 240 250
MLICLDTTVD TSQKDIQYLL QYKRERKGLE RYAPIVRLVA INSIDHCRLF
260 270 280 290 300
FGKKFDKNSR EYLENVTAAM VILRDRLGTL PPDLRPIYSQ KLHYLVEWLE
310 320 330 340 350
NPTVPWPLPD IYPLKQYTSM DVERSLLTEV HFKKSDDQLE DAFSNCSKKR
360 370 380 390 400
GRHGANKAAS STVAGIEDNI TPSFYSTKRL KNDYYTNPLK QDMTQLTGIT
410 420 430 440 450
TADNSSNVNY HLSSGIITHK LIQSMGEVYM DICVQKQELD DYSCLDDLQN
460 470 480 490 500
DHLKFFSNED EKIIKEYETV LRTNNENLNR SHELEVENNL KFSQIETLEK
510 520 530 540 550
DIETLKGSLM AQGETLSKLK DAFVKTDNVQ DEIEKEERVS VSRDTEKKYM
560 570 580 590 600
EQEIKRAVDA IRENEEETHK LNEKQNGLES ELKLKFEKSE ISTKELNEKI
610 620 630 640 650
GFLKKELKLE NDLNEELVGQ LSKTMDNLEN LTIPRVRTQN GNTKKKSRAK

KPGNV
Length:655
Mass (Da):75,463
Last modified:November 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:iCC8F8F73D6B78E45
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
U25842 Genomic DNA Translation: AAB68112.1
BK006949 Genomic DNA Translation: DAA11595.1

Protein sequence database of the Protein Information Resource

More...
PIRi
S59836

NCBI Reference Sequences

More...
RefSeqi
NP_015505.1, NM_001184276.1

Genome annotation databases

Ensembl fungal genome annotation project

More...
EnsemblFungii
YPR179C_mRNA; YPR179C; YPR179C

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
856309

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
sce:YPR179C

<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
U25842 Genomic DNA Translation: AAB68112.1
BK006949 Genomic DNA Translation: DAA11595.1
PIRiS59836
RefSeqiNP_015505.1, NM_001184276.1

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
3HGQX-ray3.00A/B/C/D6-333[»]
3HGTX-ray2.20A/B6-333[»]
SMRiQ06623
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi36351, 411 interactors
ComplexPortaliCPX-1884, HDA1 complex
DIPiDIP-4636N
IntActiQ06623, 7 interactors
MINTiQ06623
STRINGi4932.YPR179C

PTM databases

iPTMnetiQ06623

Proteomic databases

MaxQBiQ06623
PaxDbiQ06623
PRIDEiQ06623

Genome annotation databases

EnsemblFungiiYPR179C_mRNA; YPR179C; YPR179C
GeneIDi856309
KEGGisce:YPR179C

Organism-specific databases

EuPathDBiFungiDB:YPR179C
SGDiS000006383, HDA3

Phylogenomic databases

eggNOGiENOG502QT9V, Eukaryota
HOGENOMiCLU_026579_0_0_1
InParanoidiQ06623
OMAiSGDYWLP

Enzyme and pathway databases

BioCyciYEAST:G3O-34304-MONOMER

Miscellaneous databases

EvolutionaryTraceiQ06623

Protein Ontology

More...
PROi
PR:Q06623
RNActiQ06623, protein

Family and domain databases

Gene3Di3.40.50.12360, 1 hit
InterProiView protein in InterPro
IPR038609, HDA1_su2/3_sf
IPR021006, Hda2/3
IPR026216, HDA3
PfamiView protein in Pfam
PF11496, HDA2-3, 1 hit
PRINTSiPR02093, HDA1SUBUNIT3

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 nameiHDA3_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: Q06623
Secondary accession number(s): D6W4H9
<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 25, 2005
Last sequence update: November 1, 1996
Last modified: August 12, 2020
This is version 147 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 XVI
    Yeast (Saccharomyces cerevisiae) chromosome XVI: entries and gene names
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