HDA1 complex

GO:0070823 · Other · Multiprotein complex · Proposed

A tetrameric histone deacetylase complex that contains a Class II deacetylase catalytic subunit. In S. cerevisiae it is composed of two Hda1p subunits along with Hda2p and Hda3p. [GO:0070823]

Part of: GO:0000785 — chromatin (no local record)

UniProt location names: UniProt Consortium, CC BY 4.0. Reference label and route sources.

Components

Component	Type	Part of / acts on	Grounding	Genes	Stoichiometry	Essential	Role
Hda1 HDA1 catalytic subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	HDA1	2	UNKNOWN	Class II histone deacetylase catalytic constituent present as two Hda1p copies in the budding-yeast HDA1 complex. `GO:0070823` GO:0070823 defines the S. cerevisiae HDA1 complex as a tetrameric histone deacetylase complex containing two Hda1p subunits. `DOI:10.1073/pnas.081560698` Wu et al. 2001 reported HDA1 self-interaction and interaction with the Hda2-Hda3 subcomplex in a likely HDA1 tetramer. `DOI:10.1074/jbc.271.26.15837` Carmen et al. 1996 identified HDA1 as a subunit of the 350-kDa yeast HDA histone deacetylase complex.
Hda2 HDA1 subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	HDA2	1	UNKNOWN	Hda2p constituent of the HDA1 complex Hda2-Hda3 subcomplex that associates with Hda1p and is required for histone deacetylase activity. `GO:0070823` GO:0070823 defines the S. cerevisiae HDA1 complex as containing Hda2p. `DOI:10.1073/pnas.081560698` Wu et al. 2001 identified HDA2 in the HDA1 complex and described HDA1 interaction with the Hda2-Hda3 subcomplex.
Hda3 HDA1 subunit	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	HDA3	1	UNKNOWN	Hda3p constituent of the HDA1 complex Hda2-Hda3 subcomplex that associates with Hda1p and is required for histone deacetylase activity. `GO:0070823` GO:0070823 defines the S. cerevisiae HDA1 complex as containing Hda3p. `DOI:10.1073/pnas.081560698` Wu et al. 2001 identified HDA3 in the HDA1 complex and described HDA1 interaction with the Hda2-Hda3 subcomplex. `DOI:10.1074/jbc.271.26.15837` Carmen et al. 1996 identified HDA3 as a subunit of the 350-kDa yeast HDA histone deacetylase complex.

Taxonomic distribution

NCBITaxon:4932 Saccharomyces cerevisiae — COMMON: Budding yeast is the organism in which GO:0070823 defines the HDA1 complex as a tetramer containing Hda1p, Hda2p and Hda3p. [GO:0070823]

Canonical examples

NCBITaxon:4932 Saccharomyces cerevisiae — Wu et al. 2001 identified Hda2p and Hda3p in the budding-yeast HDA1 complex and found that Hda1p self-interacts and associates with the Hda2-Hda3 subcomplex. [DOI:10.1073/pnas.081560698]

Functions

histone deacetylase activity GO:0004407 — The HDA1 complex removes acetyl groups from histone lysine residues through the Hda1 Class II catalytic subunits together with Hda2p and Hda3p.
- GO:0070823 GO:0070823 defines the HDA1 complex as a histone deacetylase complex.
- GO:0004407 GO:0004407 is the Gene Ontology molecular-function term for histone deacetylase activity.
- DOI:10.1073/pnas.081560698 Wu et al. 2001 reported that mutations in any of HDA1, HDA2 or HDA3 disrupt HDA1 complex catalytic activity in vitro and in vivo.
- DOI:10.1074/jbc.271.26.15837 Carmen et al. 1996 purified the 350-kDa budding-yeast HDA histone deacetylase activity and assigned HDA1 and HDA3 as complex subunits.

Mechanism graphs

HDA1 complex carries yeast histone deacetylase activity (FUNCTION)

In Saccharomyces cerevisiae, two Hda1p copies and the Hda2p and Hda3p proteins form the HDA1 histone deacetylase complex.

Subject	Predicate	Object	Evidence
Hda1 HDA1 catalytic subunit	contributes to	HDA1 complex	`GO:0070823` GO:0070823 defines the HDA1 complex as containing two Hda1p subunits. `DOI:10.1073/pnas.081560698` Wu et al. 2001 reported HDA1 self-interaction and HDA1 complex membership.
Hda2 HDA1 subunit	contributes to	HDA1 complex	`GO:0070823` GO:0070823 defines the HDA1 complex as containing Hda2p. `DOI:10.1073/pnas.081560698` Wu et al. 2001 identified HDA2 in the HDA1 complex and assigned it to the Hda2-Hda3 subcomplex.
Hda3 HDA1 subunit	contributes to	HDA1 complex	`GO:0070823` GO:0070823 defines the HDA1 complex as containing Hda3p. `DOI:10.1073/pnas.081560698` Wu et al. 2001 identified HDA3 in the HDA1 complex and assigned it to the Hda2-Hda3 subcomplex. `DOI:10.1074/jbc.271.26.15837` Carmen et al. 1996 identified HDA3 as a subunit of the 350-kDa HDA complex.
HDA1 complex	supports	histone deacetylase activity	`GO:0070823` GO:0070823 defines HDA1 as a histone deacetylase complex. `GO:0004407` GO:0004407 is the molecular-function term for histone deacetylase activity. `DOI:10.1073/pnas.081560698` Wu et al. 2001 found that mutations in HDA1, HDA2 or HDA3 disrupted HDA1 catalytic activity.

Discussions

CURATION_TODO (OPEN): Resolve exact source-neutral family groundings for the Hda1, Hda2 and Hda3 constituents of the HDA1 complex. GO:0070823 defines budding-yeast Hda1p, Hda2p and Hda3p as the HDA1 complex constituents. Exact cross-eukaryotic InterPro, Pfam, NCBIfam or UniProt family boundaries for these HDA subunit classes need narrower curation before the component labels can be grounded.

Evidence

GO:0070823 Gene Ontology cellular-component term for the HDA1 complex.
GO:0000118 Gene Ontology cellular-component parent term for histone deacetylase complexes.
GO:0000785 — chromatin Gene Ontology cellular-component term for chromatin.
GO:0004407 Gene Ontology molecular-function term for histone deacetylase activity.
PMID:11287668 PubMed identifier for Wu et al. 2001, the PNAS HDA1 complex paper cited by GO:0070823.
DOI:10.1073/pnas.081560698 DOI for Wu et al. 2001, 'HDA2 and HDA3 are related proteins that interact with and are essential for the activity of the yeast histone deacetylase HDA1', verified through NCBI E-utilities.
PMID:8663039 PubMed identifier for Carmen et al. 1996, the JBC HDA complex subunit paper cited by GO:0070823.
DOI:10.1074/jbc.271.26.15837 DOI for Carmen et al. 1996, 'HDA1 and HDA3 are components of a yeast histone deacetylase (HDA) complex', verified through NCBI E-utilities.

Curation history

2026-09-26T03:20:53Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-09-26T03:21:58Z codex · EXPANDED_RECORD — Added HDA1 histone-deacetylase-complex parentage and chromatin parthood, Hda1/Hda2/Hda3 constituent rows, budding-yeast scope, histone deacetylase activity, GO/PubMed/DOI evidence, a nonmechanistic function graph, and a HDA1 subunit-grounding TODO.

Source: data/structures/other/hda1_complex.yaml