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Literature summary for 3.5.1.98 extracted from

  • Shen, H.; Zhu, Y.; Wang, C.; Yan, H.; Teng, M.; Li, X.
    Structural and histone binding ability characterization of the ARB2 domain of a histone deacetylase Hda1 from Saccharomyces cerevisiae (2016), Sci. Rep., 6, 33905 .
    View publication on PubMedView publication on EuropePMC
Search for more literature for 3.5.1.98

Cloned(Commentary)

Cloned (Comment) Organism
recombinant expression of His-tagged wild-type and mutant ARB2 domains (residues Hda1457-698) in Escherichia coli strain BL21(DE3) Saccharomyces cerevisiae

Crystallization (Commentary)

Crystallization (Comment) Organism
Hda1 ARB2 domain, native and selenomethionine-labebeed protein, hanging drop vapour diffusion method, from 0.1 M sodium acetate trihydrate, pH 4.6, and 2.0 M sodium formate, 12°C, 1 day, X-ray diffraction structure determination and analysis at 2.7 A resolution, molecular replacement method and modelling Saccharomyces cerevisiae

Protein Variants

Protein Variants Comment Organism
H604A/H608A/R609A site-directed mutagenesis, the mutant ARB2-M4 completely loses the binding ability to histone H3-H4, histone binding kinetics, overview Saccharomyces cerevisiae
additional information construction of four mutants, ARB2-M1 (residues Gln463, His467 and Asp471 mutated to Ala), ARB2-M2 (residues Tyr468 and Glu472 mutated to Ala), ARB2-M3 (residues Val481, Ser482, Met483 and Asp484 mutated to Ala) and ARB2-M4 (residues His604, His608 and Arg609 mutated to Ala). The binding affinity of mutants ARB2-M1, ARB2-M2, ARB2-M3 and ARB2-M4 to histone H2A-H2B dimer is 0.0204 mM, 0.0169 mM, 0.0277 mM, and 0.0174 mM, respectively. And the binding affinity of mutants ARB2-M1, ARB2-M2 and ARB2-M3 to histone H3-H4 tetramer is 0.00984 mM, 0.00693 mM, and 0.00819 mM, respectively. Mutant ARB2-M4 completely loses the binding ability to histone H3-H4 Saccharomyces cerevisiae
Q463A/D471A site-directed mutagenesis, histone binding kinetics, overview Saccharomyces cerevisiae
V481A/S482A/M483A/D484A site-directed mutagenesis, histone binding kinetics, overview Saccharomyces cerevisiae
Y468A/E472A site-directed mutagenesis, histone binding kinetics, overview Saccharomyces cerevisiae

Molecular Weight [Da]

Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
59000
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 ARB2 domain, gel filtration Saccharomyces cerevisiae

Organism

Organism UniProt Comment Textmining
Saccharomyces cerevisiae P53973
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Saccharomyces cerevisiae ATCC 204508 P53973
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Purification (Commentary)

Purification (Comment) Organism
recombinant His-tagged wild-type and mutant ARB2 domains from Escherichia coli strain BL21(DE3) by nickel affinity chroatography and gel filtration Saccharomyces cerevisiae

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
additional information the enzyme HDA1 recognizes both the H2A-H2B dimer and H3-H4 tetramer as substrates. The ARB2 domain binds to the reconstituted yeast histone H2A-H2B dimer and H3-H4 tetramer in vitro Saccharomyces cerevisiae ?
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additional information the enzyme HDA1 recognizes both the H2A-H2B dimer and H3-H4 tetramer as substrates. The ARB2 domain binds to the reconstituted yeast histone H2A-H2B dimer and H3-H4 tetramer in vitro Saccharomyces cerevisiae ATCC 204508 ?
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Subunits

Subunits Comment Organism
homodimer 2 * 24000, ARB2 domain, SDS-PAGE Saccharomyces cerevisiae
More the ARB2 domain of Hda1 exists as a homodimer. The ARB2 domain displays an alpha/beta sandwich architecture with an arm protruding outside. Two ARB2 domain molecules form a compact homodimer via the arm elements, and assemble as an inverse V shape, overall structure analysis, overview. Perturbation of the dimer interface abolishes the histone binding ability of the ARB2 domain. Hda1 consists of an N-terminal catalytic domain and a C-terminal non-catalytic domain (ARB2). The catalytic domain of Hda1 shows high sequence homology to the HDACs Saccharomyces cerevisiae

Synonyms

Synonyms Comment Organism
class II Hda1 HDAC
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 Saccharomyces cerevisiae
hda1
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 Saccharomyces cerevisiae
HDAC
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 Saccharomyces cerevisiae

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
20
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 binding kinetics, assay at Saccharomyces cerevisiae

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.5
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 binding kinetics, assay at Saccharomyces cerevisiae

General Information

General Information Comment Organism
evolution the protruded arm regions are conserved among the Hda1 homologies, and residues Ile512, Ile523 and Leu525 that play key role in the domain-domain interaction are relatively conserved. The ARB2 domain of Hda1 shows structural similarity to the alpha/beta fold hydrolases Saccharomyces cerevisiae
malfunction perturbation of the dimer interface abolishes the histone binding ability of the ARB2 domain Saccharomyces cerevisiae
additional information the ARB2 domain displays an alpha/beta sandwich architecture with an arm protruding outside. Two ARB2 domain molecules form a compact homodimer via the arm elements, and assemble as an inverse V shape. The pull-down and ITC results reveal that the ARB2 domain possesses the histone binding ability, recognizing both the H2A-H2B dimer and H3-H4 tetramer. the unique dimer architecture of the ARB2 domain coincides with the function for anchoring to histone. Hda1 consists of an N-terminal catalytic domain and a C-terminal non-catalytic domain (ARB2). The catalytic domain of Hda1 shows high sequence homology to the HDACs structures. Role of the C-terminal non-catalytic domain of Hda1 functioning in the deacetylation process, overview Saccharomyces cerevisiae
physiological function Hda1 is the catalytic core component of the H2B- and H3-specific histone deacetylase (HDAC) complex from Saccharomyces cerevisiae, which is involved in the epigenetic repression and plays a crucial role in transcriptional regulation and developmental events Saccharomyces cerevisiae