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Protein

Histone deacetylase 1

Gene

HDAC1

Organism
Homo sapiens (Human)
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. Deacetylates SP proteins, SP1 and SP3, and regulates their function. Component of the BRG1-RB1-HDAC1 complex, which negatively regulates the CREST-mediated transcription in resting neurons. Upon calcium stimulation, HDAC1 is released from the complex and CREBBP is recruited, which facilitates transcriptional activation. Deacetylates TSHZ3 and regulates its transcriptional repressor activity. Deacetylates 'Lys-310' in RELA and thereby inhibits the transcriptional activity of NF-kappa-B. Deacetylates NR1D2 and abrogates the effect of KAT5-mediated relieving of NR1D2 transcription repression activity. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development. Involved in CIART-mediated transcriptional repression of the circadian transcriptional activator: CLOCK-ARNTL/BMAL1 heterodimer. Required for the transcriptional repression of circadian target genes, such as PER1, mediated by the large PER complex or CRY1 through histone deacetylation.7 Publications

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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

  • Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone. EC:3.5.1.98

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ 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 sitei1411

<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 processBiological rhythms, Transcription, Transcription regulation

Enzyme and pathway databases

BRENDA Comprehensive Enzyme Information System

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BRENDAi
3.5.1.98 2681

Reactome - a knowledgebase of biological pathways and processes

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Reactomei
R-HSA-1362277 Transcription of E2F targets under negative control by DREAM complex
R-HSA-1362300 Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1
R-HSA-1538133 G0 and Early G1
R-HSA-193670 p75NTR negatively regulates cell cycle via SC1
R-HSA-201722 Formation of the beta-catenin:TCF transactivating complex
R-HSA-2122947 NOTCH1 Intracellular Domain Regulates Transcription
R-HSA-2173795 Downregulation of SMAD2/3:SMAD4 transcriptional activity
R-HSA-2173796 SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription
R-HSA-2644606 Constitutive Signaling by NOTCH1 PEST Domain Mutants
R-HSA-2894862 Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants
R-HSA-3214815 HDACs deacetylate histones
R-HSA-3769402 Deactivation of the beta-catenin transactivating complex
R-HSA-427389 ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression
R-HSA-427413 NoRC negatively regulates rRNA expression
R-HSA-4551638 SUMOylation of chromatin organization proteins
R-HSA-4641265 Repression of WNT target genes
R-HSA-539107 Activation of E2F1 target genes at G1/S
R-HSA-6804758 Regulation of TP53 Activity through Acetylation
R-HSA-73762 RNA Polymerase I Transcription Initiation
R-HSA-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
R-HSA-8943724 Regulation of PTEN gene transcription
R-HSA-9018519 Estrogen-dependent gene expression
R-HSA-9022538 Loss of MECP2 binding ability to 5mC-DNA
R-HSA-9022692 Regulation of MECP2 expression and activity
R-HSA-9022699 MECP2 regulates neuronal receptors and channels
R-HSA-9022702 MECP2 regulates transcription of neuronal ligands
R-HSA-983231 Factors involved in megakaryocyte development and platelet production

SABIO-RK: Biochemical Reaction Kinetics Database

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SABIO-RKi
Q13547

SIGNOR Signaling Network Open Resource

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SIGNORi
Q13547

<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_and_taxonomy_section">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 1 (EC:3.5.1.98)
Short name:
HD1
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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:HDAC1
Synonyms:RPD3L1
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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>OrganismiHomo sapiens (Human)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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 identifieri9606 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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
  • UP000005640 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">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 1

Organism-specific databases

Eukaryotic Pathogen Database Resources

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EuPathDBi
HostDB:ENSG00000116478.11

Human Gene Nomenclature Database

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HGNCi
HGNC:4852 HDAC1

Online Mendelian Inheritance in Man (OMIM)

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MIMi
601241 gene

neXtProt; the human protein knowledge platform

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neXtProti
NX_Q13547

<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 Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi141H → A: Abolishes histone deacetylase activity. 1 Publication1
Mutagenesisi287F → Y: Abolishes interaction with CHFR; when associated with I-297. 1 Publication1
Mutagenesisi297M → I: Abolishes interaction with CHFR; when associated with Y-287. 1 Publication1
Mutagenesisi391 – 482Missing : Strongly decreases deacetylase activity, and disrupts interaction with NuRD and SIN3 complexes. Add BLAST92
Mutagenesisi421S → A: Strongly decreases deacetylase activity, and disrupts interaction with NuRD and SIN3 complexes. 1 Publication1
Mutagenesisi421S → D or E: Slightly decreases deacetylase activity. 1 Publication1
Mutagenesisi423S → A: Strongly decreases deacetylase activity, and disrupts interaction with NuRD and SIN3 complexes. 1 Publication1
Mutagenesisi423S → D or E: Decreases deacetylase activity. 1 Publication1
Mutagenesisi424E → A: Slightly decreases deacetylase activity, no effect on interaction with NuRD and SIN3 complexes. 1
Mutagenesisi425E → A: No effect on deacetylase activity, no effect on interaction with NuRD and SIN3 complexes. 1
Mutagenesisi426E → A: Decreases deacetylase activity, and disrupts interaction with NuRD and SIN3 complexes. 1

Organism-specific databases

DisGeNET

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DisGeNETi
3065

Open Targets

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OpenTargetsi
ENSG00000116478

The Pharmacogenetics and Pharmacogenomics Knowledge Base

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PharmGKBi
PA29226

Chemistry databases

ChEMBL database of bioactive drug-like small molecules

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ChEMBLi
CHEMBL325

Drug and drug target database

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DrugBanki
DB05015 Belinostat
DB05921 CRA-024781
DB05651 MGCD-0103
DB06603 Panobinostat
DB06176 Romidepsin
DB05223 SB939
DB02546 Vorinostat

IUPHAR/BPS Guide to PHARMACOLOGY

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GuidetoPHARMACOLOGYi
2658

Polymorphism and mutation databases

BioMuta curated single-nucleotide variation and disease association database

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BioMutai
HDAC1

Domain mapping of disease mutations (DMDM)

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DMDMi
2498443

<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.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001146871 – 482Histone deacetylase 1Add BLAST482

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei74N6-acetyllysine; alternateCombined sources1
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section describes <strong>covalent linkages</strong> of various types formed <strong>between two proteins (interchain cross-links)</strong> or <strong>between two parts of the same protein (intrachain cross-links)</strong>, except the disulfide bonds that are annotated in the <a href="http://www.uniprot.org/manual/disulfid">'Disulfide bond'</a> subsection.<p><a href='/help/crosslnk' target='_top'>More...</a></p>Cross-linki74Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateBy similarity
Modified residuei220N6-acetyllysineCombined sources1
Modified residuei261S-nitrosocysteineBy similarity1
Modified residuei273S-nitrosocysteineBy similarity1
Modified residuei393PhosphoserineCombined sources1
Modified residuei406PhosphoserineBy similarity1
Modified residuei409PhosphoserineCombined sources1
Modified residuei421Phosphoserine; by CK2Combined sources1 Publication1
Modified residuei423Phosphoserine; by CK2Combined sources1 Publication1
Modified residuei432N6-methylated lysine; by EHMT21 Publication1
Cross-linki438Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki444Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternate1 Publication
Cross-linki444Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Cross-linki456Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Cross-linki457Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki473Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Cross-linki476Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternate1 Publication
Cross-linki476Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Cross-linki480Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

Sumoylated on Lys-444 and Lys-476; which promotes enzymatic activity. Desumoylated by SENP1.3 Publications
Phosphorylation on Ser-421 and Ser-423 promotes enzymatic activity and interactions with NuRD and SIN3 complexes. Phosphorylated by CDK5.1 Publication
Ubiquitinated by CHFR, leading to its degradation by the proteasome. Ubiquitinated by KCTD11, leading to proteasomal degradation.2 Publications

Keywords - PTMi

Acetylation, Isopeptide bond, Methylation, Phosphoprotein, S-nitrosylation, Ubl conjugation

Proteomic databases

Encyclopedia of Proteome Dynamics

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EPDi
Q13547

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

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PaxDbi
Q13547

PeptideAtlas

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PeptideAtlasi
Q13547

PRoteomics IDEntifications database

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PRIDEi
Q13547

ProteomicsDB human proteome resource

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ProteomicsDBi
59529

Consortium for Top Down Proteomics

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TopDownProteomicsi
Q13547

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

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iPTMneti
Q13547

Comprehensive resource for the study of protein post-translational modifications (PTMs) in human, mouse and rat.

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PhosphoSitePlusi
Q13547

SwissPalm database of S-palmitoylation events

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SwissPalmi
Q13547

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the ‘Expression’ section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms. By default, the information is derived from experiments at the mRNA level, unless specified ‘at protein level’. <br></br>Examples: <a href="http://www.uniprot.org/uniprot/P92958#expression">P92958</a>, <a href="http://www.uniprot.org/uniprot/Q8TDN4#expression">Q8TDN4</a>, <a href="http://www.uniprot.org/uniprot/O14734#expression">O14734</a><p><a href='/help/tissue_specificity' target='_top'>More...</a></p>Tissue specificityi

Ubiquitous, with higher levels in heart, pancreas and testis, and lower levels in kidney and brain.

Gene expression databases

Bgee dataBase for Gene Expression Evolution

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Bgeei
ENSG00000116478 Expressed in 238 organ(s), highest expression level in colonic mucosa

CleanEx database of gene expression profiles

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CleanExi
HS_HDAC1

ExpressionAtlas, Differential and Baseline Expression

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ExpressionAtlasi
Q13547 baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

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Genevisiblei
Q13547 HS

Organism-specific databases

Human Protein Atlas

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HPAi
CAB005017
CAB068191
HPA029693

<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_section">'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_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Part of the core histone deacetylase (HDAC) complex composed of HDAC1, HDAC2, RBBP4 and RBBP7. The core complex associates with MTA2, MBD2, MBD3, MTA1L1, CHD3 and CHD4 to form the nucleosome remodeling and histone deacetylation (NuRD) complex, or with SIN3, SAP18 and SAP30 to form the SIN3 HDAC complex. Component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B/BRAF35, KDM1A, RCOR1/CoREST and PHF21A/BHC80. The BHC complex may also contain ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I. Component of a mSin3A corepressor complex that contains SIN3A, SAP130, SUDS3/SAP45, ARID4B/SAP180, HDAC1 and HDAC2. Found in a trimeric complex with APBB1 and TSHZ3; the interaction between HDAC1 and APBB1 is mediated by TSHZ3. Component of a RCOR/GFI/KDM1A/HDAC complex. Part of a complex composed of TRIM28, HDAC1, HDAC2 and EHMT2. Part of a complex containing at least CDYL, MIER1, MIER2, HDAC1 and HDAC2. The large PER complex involved in the histone deacetylation is composed of at least HDAC1, PER2, SFPQ and SIN3A. Associates with the 9-1-1 complex; interacts with HUS1. Found in a complex with DNMT3A and HDAC7. Interacts with the non-histone region of H2AFY. Interacts with TRIM28; the interaction recruits HDAC1 to E2F1 and inhibits its acetylation. Interacts with SP1; the interaction deacetylates SP1 and regulates its transcriptional activity. Interacts with SP3; the interaction deacetylates SP3 and regulates its transcriptional activity. In vitro, C(18) ceramides increase this interaction and the subsequent SP3 deacetylation and SP3-mediated repression of the TERT promoter. Interacts with TSHZ3 (via N-terminus); the interaction is direct. Interacts with APEX1; the interaction is not dependent on the acetylated status of APEX1. Interacts with C10orf90/FATS (via its N-terminal); the interaction prevents binding of HDAC1 to CDKN1A/p21 and facilitates the acetylation and stabilization of CDKN1A/p21. Interacts with CDKN1A/p21. Interacts with CDK5 complexed to CDK5R1 (p25). Interacts directly with GFI1 and GFI1B. Interacts with NR1D2 (via C-terminus). Interacts with TSC22D3 isoform 1; this interaction affects HDAC1 activity on MYOG promoter and thus inhibits MYOD1 transcriptional activity. Interacts with BAZ2A/TIP5, BANP, BCL6, BCOR, BHLHE40/DEC1, BRMS1, BRMS1L, CBFA2T3, CHFR, CIART, CRY1, DAXX, DDIT3/CHOP, DDX5, DNMT1, E4F1, EP300, HCFC1, HDAC9, INSM1, NFE4, NR4A2/NURR1, MIER1, KDM4A, KDM5B, KLF1, MINT, NRIP1, PCAF, PHB2, PRDM6, PRDM16, RB1, RERE, SAMSN1, SAP30L, SETDB1, SMAD3, SMARCA4/BRG1, SMYD2, SUV39H1, TGIF, TGIF2, TRAF6, UHRF1, UHRF2, ZMYND15, ZNF431 and ZNF541. Interacts with KDM5A (By similarity). Interacts with DNTTIP1 (PubMed:25653165). Identified in a histone deacetylase complex that contains DNTTIP1, HDAC1 and ELMSAN1; this complex assembles into a tetramer that contains four copies of each protein chain (PubMed:25653165). Interacts with CCAR2 (PubMed:21030595). Interacts with PPHLN1 (PubMed:17963697). Found in a complex with YY1, SIN3A and GON4L (By similarity). Interacts with CHD4 (PubMed:27616479). Found in a complex composed of at least SINHCAF, SIN3A, HDAC1, SAP30, RBBP4, OGT and TET1. Interacts with SIN3A (By similarity). Interacts with DHX36; this interaction occurs in a RNA-dependent manner (PubMed:18279852). Interacts with ZBTB7A (PubMed:25514493). Interacts with SMAD4; positively regulated by ZBTB7A (PubMed:25514493).By similarity48 Publications

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction_section%27">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="http://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated on a monthly basis. Each binary interaction is displayed on a separate line.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

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BioGridi
109315, 564 interactors

ComplexPortal: manually curated resource of macromolecular complexes

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ComplexPortali
CPX-3321 SIN3A histone deacetylase complex
CPX-3322 SIN3B histone deacetylase complex
CPX-3323 SIN3A histone deacetylase complex, ES cell-specific variant
CPX-880 MBD2/NuRD nucleosome remodeling and deacetylase complex
CPX-922 MBD3/NuRD nucleosome remodeling and deacetylase complex

CORUM comprehensive resource of mammalian protein complexes

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CORUMi
Q13547

Database of interacting proteins

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DIPi
DIP-24184N

Protein interaction database and analysis system

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IntActi
Q13547, 264 interactors

Molecular INTeraction database

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MINTi
Q13547

STRING: functional protein association networks

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STRINGi
9606.ENSP00000362649

Chemistry databases

BindingDB database of measured binding affinities

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BindingDBi
Q13547

<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

1482
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

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ProteinModelPortali
Q13547

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

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SMRi
Q13547

Database of comparative protein structure models

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ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

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MobiDBi
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>Regioni9 – 321Histone deacetylaseAdd BLAST313

<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

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eggNOGi
KOG1342 Eukaryota
COG0123 LUCA

Ensembl GeneTree

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GeneTreei
ENSGT00940000154301

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

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HOGENOMi
HOG000225180

The HOVERGEN Database of Homologous Vertebrate Genes

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HOVERGENi
HBG057112

InParanoid: Eukaryotic Ortholog Groups

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InParanoidi
Q13547

KEGG Orthology (KO)

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KOi
K06067

Identification of Orthologs from Complete Genome Data

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OMAi
FCTISAG

Database of Orthologous Groups

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OrthoDBi
EOG091G067J

Database for complete collections of gene phylogenies

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PhylomeDBi
Q13547

TreeFam database of animal gene trees

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TreeFami
TF106171

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

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Gene3Di
3.40.800.20, 1 hit

Integrated resource of protein families, domains and functional sites

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InterProi
View protein in InterPro
IPR000286 His_deacetylse
IPR003084 His_deacetylse_1
IPR023801 His_deacetylse_dom
IPR037138 His_deacetylse_dom_sf
IPR023696 Ureohydrolase_dom_sf

The PANTHER Classification System

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PANTHERi
PTHR10625 PTHR10625, 1 hit

Pfam protein domain database

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Pfami
View protein in Pfam
PF00850 Hist_deacetyl, 1 hit

PIRSF; a whole-protein classification database

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PIRSFi
PIRSF037913 His_deacetylse_1, 1 hit

Protein Motif fingerprint database; a protein domain database

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PRINTSi
PR01270 HDASUPER
PR01271 HISDACETLASE

Superfamily database of structural and functional annotation

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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_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequence (1+)i

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">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.

This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All

Q13547-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MAQTQGTRRK VCYYYDGDVG NYYYGQGHPM KPHRIRMTHN LLLNYGLYRK
60 70 80 90 100
MEIYRPHKAN AEEMTKYHSD DYIKFLRSIR PDNMSEYSKQ MQRFNVGEDC
110 120 130 140 150
PVFDGLFEFC QLSTGGSVAS AVKLNKQQTD IAVNWAGGLH HAKKSEASGF
160 170 180 190 200
CYVNDIVLAI LELLKYHQRV LYIDIDIHHG DGVEEAFYTT DRVMTVSFHK
210 220 230 240 250
YGEYFPGTGD LRDIGAGKGK YYAVNYPLRD GIDDESYEAI FKPVMSKVME
260 270 280 290 300
MFQPSAVVLQ CGSDSLSGDR LGCFNLTIKG HAKCVEFVKS FNLPMLMLGG
310 320 330 340 350
GGYTIRNVAR CWTYETAVAL DTEIPNELPY NDYFEYFGPD FKLHISPSNM
360 370 380 390 400
TNQNTNEYLE KIKQRLFENL RMLPHAPGVQ MQAIPEDAIP EESGDEDEDD
410 420 430 440 450
PDKRISICSS DKRIACEEEF SDSEEEGEGG RKNSSNFKKA KRVKTEDEKE
460 470 480
KDPEEKKEVT EEEKTKEEKP EAKGVKEEVK LA
Length:482
Mass (Da):55,103
Last modified:November 1, 1997 - 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:i4D35B7C1ED7838D6
GO

<p>In eukaryotic reference proteomes, unreviewed entries that are likely to belong to the same gene are computationally mapped, based on gene identifiers from Ensembl, EnsemblGenomes and model organism databases.<p><a href='/help/gene_centric_isoform_mapping' target='_top'>More...</a></p>Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
Q5TEE2Q5TEE2_HUMAN
Histone deacetylase 1
HDAC1
211Annotation score:

Annotation score:1 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 Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti312W → R in BAA08909 (PubMed:8646880).Curated1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
U50079 mRNA Translation: AAC50475.1
D50405 mRNA Translation: BAA08909.1
BC000301 mRNA Translation: AAH00301.1

The Consensus CDS (CCDS) project

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CCDSi
CCDS360.1

NCBI Reference Sequences

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RefSeqi
NP_004955.2, NM_004964.2

UniGene gene-oriented nucleotide sequence clusters

More...
UniGenei
Hs.88556

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...
Ensembli
ENST00000373548; ENSP00000362649; ENSG00000116478

Database of genes from NCBI RefSeq genomes

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GeneIDi
3065

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
hsa:3065

<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
U50079 mRNA Translation: AAC50475.1
D50405 mRNA Translation: BAA08909.1
BC000301 mRNA Translation: AAH00301.1
CCDSiCCDS360.1
RefSeqiNP_004955.2, NM_004964.2
UniGeneiHs.88556

3D structure databases

Select the link destinations:

Protein Data Bank Europe

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PDBei

Protein Data Bank RCSB

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RCSB PDBi

Protein Data Bank Japan

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PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1TYImodel-A1-482[»]
4BKXX-ray3.00B1-482[»]
5ICNX-ray3.30B1-376[»]
ProteinModelPortaliQ13547
SMRiQ13547
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi109315, 564 interactors
ComplexPortaliCPX-3321 SIN3A histone deacetylase complex
CPX-3322 SIN3B histone deacetylase complex
CPX-3323 SIN3A histone deacetylase complex, ES cell-specific variant
CPX-880 MBD2/NuRD nucleosome remodeling and deacetylase complex
CPX-922 MBD3/NuRD nucleosome remodeling and deacetylase complex
CORUMiQ13547
DIPiDIP-24184N
IntActiQ13547, 264 interactors
MINTiQ13547
STRINGi9606.ENSP00000362649

Chemistry databases

BindingDBiQ13547
ChEMBLiCHEMBL325
DrugBankiDB05015 Belinostat
DB05921 CRA-024781
DB05651 MGCD-0103
DB06603 Panobinostat
DB06176 Romidepsin
DB05223 SB939
DB02546 Vorinostat
GuidetoPHARMACOLOGYi2658

PTM databases

iPTMnetiQ13547
PhosphoSitePlusiQ13547
SwissPalmiQ13547

Polymorphism and mutation databases

BioMutaiHDAC1
DMDMi2498443

Proteomic databases

EPDiQ13547
PaxDbiQ13547
PeptideAtlasiQ13547
PRIDEiQ13547
ProteomicsDBi59529
TopDownProteomicsiQ13547

Protocols and materials databases

The DNASU plasmid repository

More...
DNASUi
3065
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000373548; ENSP00000362649; ENSG00000116478
GeneIDi3065
KEGGihsa:3065

Organism-specific databases

Comparative Toxicogenomics Database

More...
CTDi
3065
DisGeNETi3065
EuPathDBiHostDB:ENSG00000116478.11

GeneCards: human genes, protein and diseases

More...
GeneCardsi
HDAC1
HGNCiHGNC:4852 HDAC1
HPAiCAB005017
CAB068191
HPA029693
MIMi601241 gene
neXtProtiNX_Q13547
OpenTargetsiENSG00000116478
PharmGKBiPA29226

GenAtlas: human gene database

More...
GenAtlasi
Search...

Phylogenomic databases

eggNOGiKOG1342 Eukaryota
COG0123 LUCA
GeneTreeiENSGT00940000154301
HOGENOMiHOG000225180
HOVERGENiHBG057112
InParanoidiQ13547
KOiK06067
OMAiFCTISAG
OrthoDBiEOG091G067J
PhylomeDBiQ13547
TreeFamiTF106171

Enzyme and pathway databases

BRENDAi3.5.1.98 2681
ReactomeiR-HSA-1362277 Transcription of E2F targets under negative control by DREAM complex
R-HSA-1362300 Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1
R-HSA-1538133 G0 and Early G1
R-HSA-193670 p75NTR negatively regulates cell cycle via SC1
R-HSA-201722 Formation of the beta-catenin:TCF transactivating complex
R-HSA-2122947 NOTCH1 Intracellular Domain Regulates Transcription
R-HSA-2173795 Downregulation of SMAD2/3:SMAD4 transcriptional activity
R-HSA-2173796 SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription
R-HSA-2644606 Constitutive Signaling by NOTCH1 PEST Domain Mutants
R-HSA-2894862 Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants
R-HSA-3214815 HDACs deacetylate histones
R-HSA-3769402 Deactivation of the beta-catenin transactivating complex
R-HSA-427389 ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression
R-HSA-427413 NoRC negatively regulates rRNA expression
R-HSA-4551638 SUMOylation of chromatin organization proteins
R-HSA-4641265 Repression of WNT target genes
R-HSA-539107 Activation of E2F1 target genes at G1/S
R-HSA-6804758 Regulation of TP53 Activity through Acetylation
R-HSA-73762 RNA Polymerase I Transcription Initiation
R-HSA-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
R-HSA-8943724 Regulation of PTEN gene transcription
R-HSA-9018519 Estrogen-dependent gene expression
R-HSA-9022538 Loss of MECP2 binding ability to 5mC-DNA
R-HSA-9022692 Regulation of MECP2 expression and activity
R-HSA-9022699 MECP2 regulates neuronal receptors and channels
R-HSA-9022702 MECP2 regulates transcription of neuronal ligands
R-HSA-983231 Factors involved in megakaryocyte development and platelet production
SABIO-RKiQ13547
SIGNORiQ13547

Miscellaneous databases

ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data

More...
ChiTaRSi
HDAC1 human

The Gene Wiki collection of pages on human genes and proteins

More...
GeneWikii
HDAC1

Database of phenotypes from RNA interference screens in Drosophila and Homo sapiens

More...
GenomeRNAii
3065

Protein Ontology

More...
PROi
PR:Q13547

The Stanford Online Universal Resource for Clones and ESTs

More...
SOURCEi
Search...

Gene expression databases

BgeeiENSG00000116478 Expressed in 238 organ(s), highest expression level in colonic mucosa
CleanExiHS_HDAC1
ExpressionAtlasiQ13547 baseline and differential
GenevisibleiQ13547 HS

Family and domain databases

Gene3Di3.40.800.20, 1 hit
InterProiView protein in InterPro
IPR000286 His_deacetylse
IPR003084 His_deacetylse_1
IPR023801 His_deacetylse_dom
IPR037138 His_deacetylse_dom_sf
IPR023696 Ureohydrolase_dom_sf
PANTHERiPTHR10625 PTHR10625, 1 hit
PfamiView protein in Pfam
PF00850 Hist_deacetyl, 1 hit
PIRSFiPIRSF037913 His_deacetylse_1, 1 hit
PRINTSiPR01270 HDASUPER
PR01271 HISDACETLASE
SUPFAMiSSF52768 SSF52768, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
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 nameiHDAC1_HUMAN
<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: Q13547
Secondary accession number(s): Q92534
<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_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: December 5, 2018
This is version 221 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 programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

<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, Complete proteome, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
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