| Aspect | Current understanding | Key supporting 2023–2024 sources (with DOI/URL) | Notes/quantitative details |
|---|---|---|---|
| Enzyme class / reaction | Rpd3 (UniProt P32561; YNL330C) is the budding yeast founding **class I, Zn²⁺-dependent histone deacetylase** that catalyzes hydrolytic removal of ε-N-acetyl groups from lysine residues on histones, functioning as the catalytic subunit of Sin3-associated HDAC complexes. It acts in both Rpd3S and Rpd3L chromatin complexes rather than as a free enzyme. (pqac-00000001, pqac-00000005, pqac-00000008) | Guan et al., 2023, **Nature**. DOI: 10.1038/s41586-023-06349-1. https://doi.org/10.1038/s41586-023-06349-1 (pqac-00000001); Patel et al., 2023, **Nat Commun**. DOI: 10.1038/s41467-023-38687-z. https://doi.org/10.1038/s41467-023-38687-z (pqac-00000005); Zhang et al., 2023, **Cell Research**. DOI: 10.1038/s41422-023-00884-2. https://doi.org/10.1038/s41422-023-00884-2 (pqac-00000008) | Active-site Zn²⁺ is structurally stabilized/coordinated by **D186, H188, D274** in the 2023 Rpd3S cryo-EM study. Rpd3L is ~**1.2 MDa**; Rpd3S is ~**0.6 MDa**. (pqac-00000008, pqac-00000002) |
| Rpd3S complex composition / stoichiometry / targeting logic | **Rpd3S** is the gene-body HDAC complex specialized for transcribed chromatin. Core composition: **Rpd3, Sin3, Ume1** plus chromatin-targeting subunits **Eaf3 and Rco1**. Recent structures show a stoichiometry of **1× Rpd3, 1× Sin3, 1× Ume1, 2× Eaf3, 2× Rco1** in the nucleosome-bound assembly. Recruitment/targeting is driven by multivalent readout of **H3K36me3** and **H3K4me0** together with nucleosomal/linker DNA contacts. Eaf3 chromodomain reads H3K36 methylation, while Rco1 PHD1 prefers unmodified H3K4, helping bias Rpd3S toward coding regions. (pqac-00000000, pqac-00000001, pqac-00000008, pqac-00000013) | Markert et al., 2023, **Nat Commun**. DOI: 10.1038/s41467-023-43968-8. https://doi.org/10.1038/s41467-023-43968-8 (supported through gathered summary context pqac-00000000); Guan et al., 2023. DOI: 10.1038/s41586-023-06349-1. https://doi.org/10.1038/s41586-023-06349-1 (pqac-00000001); Zhang et al., 2023. DOI: 10.1038/s41422-023-00884-2. https://doi.org/10.1038/s41422-023-00884-2 (pqac-00000008); Li et al., 2023, **Nat Struct Mol Biol**. DOI: 10.1038/s41594-023-01121-5. https://doi.org/10.1038/s41594-023-01121-5 (pqac-00000011) | Eaf3 CHD aromatic cage residues recognizing H3K36me3: **Y23, Y81, W84, W88**. Rco1 PHD1 binds H3(1–10) with **Kd ≈ 39 μM** and is destabilized by H3K4 methylation. The Sin3 scaffold and Rco1/Eaf3 also contact linker/nucleosomal DNA, enabling orientation over the nucleosome. (pqac-00000011, pqac-00000013, pqac-00000008) |
| Rpd3L complex composition / promoter targeting | **Rpd3L** is the larger promoter-proximal Sin3-associated deacetylase complex that performs localized deacetylation at or near recruitment sites of DNA-binding factors. It shares the catalytic/scaffold core (**Rpd3, Sin3, Ume1**) with Rpd3S but contains Rpd3L-specific accessory subunits such as **Pho23, Rxt2, Rxt3, Sap30, Sds3, Dep1** (and related promoter-recruitment factors noted in recent literature). Rpd3L is targeted primarily to **promoters**, often via transcription factors and/or promoter chromatin marks including **H3K4me3** readout by Pho23-linked mechanisms. (pqac-00000005, pqac-00000003, pqac-00000009, pqac-00000014) | Patel et al., 2023. DOI: 10.1038/s41467-023-38687-z. https://doi.org/10.1038/s41467-023-38687-z (pqac-00000005); Carrozza & Workman, 2024, **Cell Research**. DOI: 10.1038/s41422-023-00899-9. https://doi.org/10.1038/s41422-023-00899-9 (pqac-00000003); Dong et al., 2023, **Cell Research**. DOI: 10.1038/s41422-023-00869-1. https://doi.org/10.1038/s41422-023-00869-1 (pqac-00000009); Yague-Sanz, 2024, **Yeast**. DOI: 10.1002/yea.3921. https://doi.org/10.1002/yea.3921 (pqac-00000014) | Structural work indicates an asymmetric dimeric Rpd3L architecture with **two copies each of Rpd3, Sin3, and Ume1** in the core of the 12-subunit complex; one Rpd3 active site can be occluded by **Rxt2**, suggesting regulated catalytic access. (pqac-00000005) |
| Known / assayed histone substrate sites and preferences | Recent structural/biochemical studies show that Rpd3S deacetylates multiple acetyl-lysine sites on **H3 and H4 tails**. Assayed H3 sites include **H3K9ac, H3K14ac, H3K18ac, H3K23ac, H3K27ac**; assayed H4 sites include **H4K5ac, H4K8ac, H4K12ac, H4K16ac**. Distinct catalytic states suggest context-dependent substrate use: some structures position Rpd3S for **H4-tail deacetylation**, whereas others capture an **H3-tail** entering the active site with **H3K18** poised for catalysis. (pqac-00000008, pqac-00000012, pqac-00000015) | Zhang et al., 2023. DOI: 10.1038/s41422-023-00884-2. https://doi.org/10.1038/s41422-023-00884-2 (pqac-00000008); Guan et al., 2023. DOI: 10.1038/s41586-023-06349-1. https://doi.org/10.1038/s41586-023-06349-1 (pqac-00000015); Carrozza & Workman, 2024. DOI: 10.1038/s41422-023-00899-9. https://doi.org/10.1038/s41422-023-00899-9 (pqac-00000012); Dong et al., 2023. DOI: 10.1038/s41422-023-00869-1. https://doi.org/10.1038/s41422-023-00869-1 (pqac-00000009) | In one cryo-EM state, **H3K18** is oriented toward catalytic Zn²⁺; **H3K9/H3K14** were not accommodated in that exact conformation, showing substrate-state dependence. Commentary summarizing biochemical assays notes lower enzyme amounts deacetylated **H3K23/H3K14** more efficiently than **H3K9/H3K18/H3K27**. Recent structures also indicate Rpd3S can sample multiple tails and catalytic modes. (pqac-00000008, pqac-00000012, pqac-00000009) |
| Mechanistic / structural highlights | 2023 cryo-EM studies transformed understanding of Rpd3 by revealing how noncatalytic subunits specify chromatin engagement. Sin3 wraps around catalytic Rpd3 and contributes key DNA-binding surfaces; Eaf3 and Rco1 form duplicated reader modules that contact histone marks and DNA. Rpd3S can adopt multiple nucleosome-binding states (“close,” “loose,” alternative deacetylation, linker-tightening), explaining how the enzyme reaches different histone tails and even engages neighboring nucleosomes. (pqac-00000008, pqac-00000011, pqac-00000013, pqac-00000016) | Zhang et al., 2023. DOI: 10.1038/s41422-023-00884-2. https://doi.org/10.1038/s41422-023-00884-2 (pqac-00000008); Li et al., 2023. DOI: 10.1038/s41594-023-01121-5. https://doi.org/10.1038/s41594-023-01121-5 (pqac-00000011); Guan et al., 2023. DOI: 10.1038/s41586-023-06349-1. https://doi.org/10.1038/s41586-023-06349-1 (pqac-00000013); Figure/context summary from Guan et al. overall model (pqac-00000016) | Structural details include: **3.7 Å** Rpd3S–nucleosome structure (pqac-00000008); **3.5 Å** alternative Rpd3S structures including linker-tightening states (pqac-00000009); **3.1 Å** nucleosome-bound structure in another study (from retrieved paper metadata underlying pqac-00000011). Eaf3 CHD makes aromatic-cage recognition of H3K36me3, while Rco1 PHD1 enforces H3K4me0 preference; Sin3 basic surfaces anchor DNA. (pqac-00000008, pqac-00000011, pqac-00000013) |
| Cellular localization on chromatin / biological role | Functional division of labor is now clear: **Rpd3S acts mainly across transcribed gene bodies**, where it is recruited cotranscriptionally via Set2-linked **H3K36me3** and associated with elongating RNAPII to restore a deacetylated chromatin state and suppress **cryptic/spurious intragenic transcription**. **Rpd3L acts mainly at promoters**, where it mediates localized repression or fine-tuning near recruitment sites of transcription factors and promoter marks. (pqac-00000003, pqac-00000009, pqac-00000010, pqac-00000014) | Carrozza & Workman, 2024. DOI: 10.1038/s41422-023-00899-9. https://doi.org/10.1038/s41422-023-00899-9 (pqac-00000003, pqac-00000010); Dong et al., 2023. DOI: 10.1038/s41422-023-00869-1. https://doi.org/10.1038/s41422-023-00869-1 (pqac-00000009); Yague-Sanz, 2024. DOI: 10.1002/yea.3921. https://doi.org/10.1002/yea.3921 (pqac-00000014) | Gene-body acetylation accumulates when Rpd3S is lost, consistent with its elongation-coupled deacetylase role. Rpd3S also shows possible **di-nucleosome preference** and linker-length dependence in recent work, supporting action on chromatin behind RNAPII rather than isolated peptides. (pqac-00000001, pqac-00000012) |


*Table: This table summarizes the current functional annotation of Saccharomyces cerevisiae Rpd3 (UniProt P32561), emphasizing 2023–2024 structural and mechanistic advances. It highlights catalytic activity, Rpd3S/Rpd3L complex biology, substrate specificity, chromatin localization, and key quantitative details useful for annotation.*