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Information on EC 3.5.1.98 - histone deacetylase and Organism(s) Saccharomyces cerevisiae and UniProt Accession P32561

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EC Tree
     3 Hydrolases
         3.5 Acting on carbon-nitrogen bonds, other than peptide bonds
             3.5.1 In linear amides
                3.5.1.98 histone deacetylase
IUBMB Comments
A class of enzymes that remove acetyl groups from N6-acetyl-lysine residues on a histone. The reaction of this enzyme is opposite to that of EC 2.3.1.48, histone acetyltransferase. Histone deacetylases (HDACs) can be organized into three classes, HDAC1, HDAC2 and HDAC3, depending on sequence similarity and domain organization. Histone acetylation plays an important role in regulation of gene expression. In eukaryotes, HDACs play a key role in the regulation of transcription and cell proliferation . May be identical to EC 3.5.1.17, acyl-lysine deacylase.
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Saccharomyces cerevisiae
UNIPROT: P32561
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Word Map
The taxonomic range for the selected organisms is: Saccharomyces cerevisiae
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea
Reaction Schemes
hydrolysis of an N6-acetyl-lysine residue of a histone to yield a deacetylated histone
Synonyms
histone deacetylase, hdac1, hdac6, hdac2, hdac3, hdac4, hdac5, hdac8, hdac9, hdac7, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
class II Hda1 HDAC
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SYSTEMATIC NAME
IUBMB Comments
histone amidohydrolase
A class of enzymes that remove acetyl groups from N6-acetyl-lysine residues on a histone. The reaction of this enzyme is opposite to that of EC 2.3.1.48, histone acetyltransferase. Histone deacetylases (HDACs) can be organized into three classes, HDAC1, HDAC2 and HDAC3, depending on sequence similarity and domain organization. Histone acetylation plays an important role in regulation of gene expression. In eukaryotes, HDACs play a key role in the regulation of transcription and cell proliferation [4]. May be identical to EC 3.5.1.17, acyl-lysine deacylase.
CAS REGISTRY NUMBER
COMMENTARY hide
9076-57-7
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
additional information
?
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5
binding kinetics, assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
20
binding kinetics, assay at
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
sake strain Kyokai No 701 and diverse deletion mutants
UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
transcript levels of ILV2, ILV3 and ILV5 are elevated in Rpd3L-deficient strains (rpd3DELTA, ume1DELTA, dep1DELTA, and sds3DELTA) but not in Rpd3S-single deficient strain (rco1DELTA and eaf3DELTA) compared to wild-type K701. The transcript levels of ATF2, a minor alcohol acetyltransferase, are higher in the rpd3DELTA and ume1DELTA strains than in the parental strain. K701 rpd3DELTA and K701 hda1DELTA alter the response to oxygen of isoamyl acetate production
physiological function
HDAC genes are non-essential in yeast, functional analysis of genes, RPD3, HDA1, SIR2, and HST1 in the Sake yeast strain Kyokai No. 701 (K701). RPD3 and Hda1 are translation regulatory proteins and histone deacetylases. Rpd3L-dependent regulation of genes ILV2, ILV3 and ILV5. Rpd3 and Hda1 may regulate isoamyl acetate production via oxygen in a Rox1-independent manner. Yeast HDACs, and maybe also HAT and their regulatory subunits, are keys to determine fermentation characteristics, and these genes may be an important target for improvement of yeast strains used for alcoholic beverage production
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
malfunction
physiological function
additional information
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
59000
ARB2 domain, gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
2 * 24000, ARB2 domain, SDS-PAGE
additional information
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
H604A/H608A/R609A
site-directed mutagenesis, the mutant ARB2-M4 completely loses the binding ability to histone H3-H4, histone binding kinetics, overview
Q463A/D471A
site-directed mutagenesis, histone binding kinetics, overview
V481A/S482A/M483A/D484A
site-directed mutagenesis, histone binding kinetics, overview
Y468A/E472A
site-directed mutagenesis, histone binding kinetics, overview
additional information
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged wild-type and mutant ARB2 domains from Escherichia coli strain BL21(DE3) by nickel affinity chroatography and gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant expression of His-tagged wild-type and mutant ARB2 domains (residues Hda1457-698) in Escherichia coli strain BL21(DE3)
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
mutations of the SCF-CDC4 ubiquitin ligase complex suppress cell death by preventing the degradation of Msn2 and Msn4 transcription factors. Accumulation of transcription factors Msn2 and Msn4 leads to the induction of PNC1, which is an activator of the Sir2 histone acetylase
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Tomimoto, K.; Akao, T.; Fukuda, H.
Histone deacetylases in sake yeast affect fermentation characteristics
Biosci. Biotechnol. Biochem.
83
1498-1505
2019
Saccharomyces cerevisiae (P32561), Saccharomyces cerevisiae (P53973), Saccharomyces cerevisiae, Saccharomyces cerevisiae ATCC 204508 (P32561), Saccharomyces cerevisiae ATCC 204508 (P53973)
Manually annotated by BRENDA team
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
Sci. Rep.
6
33905
2016
Saccharomyces cerevisiae (P53973), Saccharomyces cerevisiae, Saccharomyces cerevisiae ATCC 204508 (P53973)
Manually annotated by BRENDA team