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Entry version 65 (08 May 2019)
Sequence version 1 (14 Dec 2011)
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Protein

Histone deacetylase

Gene

hda-3

Organism
Caenorhabditis elegans
Status
Unreviewed-Annotation score:

Annotation score:4 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

<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.UniRule annotation EC:3.5.1.98

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei98SubstrateUniRule annotation1
<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 sitei140Proton acceptorUniRule annotation1
Binding sitei148Substrate; via carbonyl oxygenUniRule annotation1
<p>This subsection of the ‘Function’ section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi175Divalent metal cationUniRule annotation1
Metal bindingi177Divalent metal cationUniRule annotation1
Metal bindingi263Divalent metal cationUniRule annotation1
Binding sitei302SubstrateUniRule annotation1

<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 regulatorUniRule annotation, HydrolaseUniRule annotationSAAS annotation
Biological processTranscription, Transcription regulationUniRule annotation
LigandMetal-bindingUniRule annotation

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-CEL-1538133 G0 and Early G1
R-CEL-201722 Formation of the beta-catenin:TCF transactivating complex
R-CEL-2173795 Downregulation of SMAD2/3:SMAD4 transcriptional activity
R-CEL-3214815 HDACs deacetylate histones
R-CEL-3769402 Deactivation of the beta-catenin transactivating complex
R-CEL-4551638 SUMOylation of chromatin organization proteins
R-CEL-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
R-CEL-8943724 Regulation of PTEN gene transcription
R-CEL-983231 Factors involved in megakaryocyte development and platelet production

<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 deacetylaseUniRule annotation (EC:3.5.1.98UniRule annotation)
<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:hda-3Imported
ORF Names:CELE_R06C1.1Imported, R06C1.1Imported
<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>OrganismiCaenorhabditis elegansImported
<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 identifieri6239 [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 lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditinaRhabditomorphaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
<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
  • UP000001940 <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 I

Organism-specific databases

WormBase

More...
WormBasei
R06C1.1 ; CE18116 ; WBGene00001836 ; hda-3

<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 & Seán O’Donoghue; Source: COMPARTMENTS

Keywords - Cellular componenti

NucleusUniRule annotation

<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

Proteomic databases

Encyclopedia of Proteome Dynamics

More...
EPDi
G5ECH0

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

More...
PaxDbi
G5ECH0

PeptideAtlas

More...
PeptideAtlasi
G5ECH0

<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

Gene expression databases

Bgee dataBase for Gene Expression Evolution

More...
Bgeei
WBGene00001836 Expressed in 5 organ(s), highest expression level in multi-cellular organism

<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

Protein-protein interaction databases

Protein interaction database and analysis system

More...
IntActi
G5ECH0, 3 interactors

Molecular INTeraction database

More...
MINTi
G5ECH0

STRING: functional protein association networks

More...
STRINGi
6239.R06C1.1.1

<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

3D structure databases

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

More...
SMRi
G5ECH0

Database of comparative protein structure models

More...
ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
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

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini27 – 317Hist_deacetylInterPro annotationAdd BLAST291

<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 histone deacetylase family. HD Type 1 subfamily.UniRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG1342 Eukaryota
COG0123 LUCA

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
G5ECH0

KEGG Orthology (KO)

More...
KOi
K06067

Identification of Orthologs from Complete Genome Data

More...
OMAi
CDIAINY

Database of Orthologous Groups

More...
OrthoDBi
732770at2759

Database for complete collections of gene phylogenies

More...
PhylomeDBi
G5ECH0

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
IPR000286 His_deacetylse
IPR003084 His_deacetylse_1
IPR023801 His_deacetylse_dom
IPR037138 His_deacetylse_dom_sf
IPR023696 Ureohydrolase_dom_sf

Pfam protein domain database

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

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF037913 His_deacetylse_1, 1 hit

Protein Motif fingerprint database; a protein domain database

More...
PRINTSi
PR01270 HDASUPER
PR01271 HISDACETLASE

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_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>Sequencei

<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.

G5ECH0-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSLQHSKSRV SYYYDGDFGN FYYGQGHPMK PHRVRMTHSL IVNYGLYRKL
60 70 80 90 100
NVMRPARASF SEITRYHSDD YINFLRNVKS DNMSTFTDQM ARFSVGEDCP
110 120 130 140 150
VFDGMYEFCQ LSCGGSLAAA ARLNRQESEI AINWMGGLHH AKKSEASGFC
160 170 180 190 200
YSNDIVLAIL ELLKHHKRVL YIDIDVHHGD GVEEAFYTTD RVMTVSFHKH
210 220 230 240 250
GEYFPGTGDL KDVGAGSGKY YALNVPLRDG VDDVTYERIF RTIMGEVMAR
260 270 280 290 300
FQPEAVVLQC GADSLAGDRL GVFNLTTYGH GKCVEYMKSF NVPLLLVGGG
310 320 330 340 350
GYTIRNVSRC WLYETAIALN QEVSDDLPLH DYFDYFIPDY KLHIKPLAAL
360 370 380 390 400
SNFNTPEFID QTIVALLENL KQLPHVPSVQ MQSISTSCDS IVKTFDEKLI
410 420 430 440 450
RDHQNDDVRV TQFEEDVQVE DSAEFYDGQE PETKNIQSMK RHASPICAAQ
460
EEMKKNRIDG GENVA
Length:465
Mass (Da):52,709
Last modified:December 14, 2011 - 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:i325E71D5197012C5
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
BX284601 Genomic DNA Translation: CAB03224.1

Protein sequence database of the Protein Information Resource

More...
PIRi
T23963

NCBI Reference Sequences

More...
RefSeqi
NP_493026.1, NM_060625.4

Genome annotation databases

Ensembl metazoan genome annotation project

More...
EnsemblMetazoai
R06C1.1.1; R06C1.1.1; WBGene00001836
R06C1.1.2; R06C1.1.2; WBGene00001836

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
173074

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
cel:CELE_R06C1.1

<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
BX284601 Genomic DNA Translation: CAB03224.1
PIRiT23963
RefSeqiNP_493026.1, NM_060625.4

3D structure databases

SMRiG5ECH0
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiG5ECH0, 3 interactors
MINTiG5ECH0
STRINGi6239.R06C1.1.1

Proteomic databases

EPDiG5ECH0
PaxDbiG5ECH0
PeptideAtlasiG5ECH0

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiR06C1.1.1; R06C1.1.1; WBGene00001836
R06C1.1.2; R06C1.1.2; WBGene00001836
GeneIDi173074
KEGGicel:CELE_R06C1.1

Organism-specific databases

Comparative Toxicogenomics Database

More...
CTDi
173074
WormBaseiR06C1.1 ; CE18116 ; WBGene00001836 ; hda-3

Phylogenomic databases

eggNOGiKOG1342 Eukaryota
COG0123 LUCA
InParanoidiG5ECH0
KOiK06067
OMAiCDIAINY
OrthoDBi732770at2759
PhylomeDBiG5ECH0

Enzyme and pathway databases

ReactomeiR-CEL-1538133 G0 and Early G1
R-CEL-201722 Formation of the beta-catenin:TCF transactivating complex
R-CEL-2173795 Downregulation of SMAD2/3:SMAD4 transcriptional activity
R-CEL-3214815 HDACs deacetylate histones
R-CEL-3769402 Deactivation of the beta-catenin transactivating complex
R-CEL-4551638 SUMOylation of chromatin organization proteins
R-CEL-8936459 RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
R-CEL-8943724 Regulation of PTEN gene transcription
R-CEL-983231 Factors involved in megakaryocyte development and platelet production

Gene expression databases

BgeeiWBGene00001836 Expressed in 5 organ(s), highest expression level in multi-cellular organism

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
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 nameiG5ECH0_CAEEL
<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: G5ECH0
<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/TrEMBL: December 14, 2011
Last sequence update: December 14, 2011
Last modified: May 8, 2019
This is version 65 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 statusiUnreviewed (UniProtKB/TrEMBL)

<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

Complete proteome, Proteomics identificationCombined sources, Reference proteomeImported
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