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Literature summary extracted from

  • Shinsky, S.A.; Christianson, D.W.
    Polyamine deacetylase structure and catalysis prokaryotic acetylpolyamine amidohydrolase and eukaryotic HDAC10 (2018), Biochemistry, 57, 3105-3114 .
    View publication on PubMedView publication on EuropePMC

Application

EC Number Application Comment Organism
3.5.1.48 drug development HDAC10 is a biomarker and a target for the design of isozyme-selective inhibitors that will suppress autophagic responses to cancer chemotherapy, thereby rendering cancer cells more susceptible to cytotoxic drugs Homo sapiens
3.5.1.48 pharmacology HDAC10 isozyme-selective inhibitors will suppress autophagic responses to cancer chemotherapy, thereby rendering cancer cells more susceptible to cytotoxic drugs Homo sapiens

Inhibitors

EC Number Inhibitors Comment Organism Structure
3.5.1.48 7-[(3-aminopropyl)amino]-1,1,1-trifluoroheptan-2-one AAT, binds as a tetrahedral gem-diolate to both APAH (acetylpolyamine amidohydrolase, EC 3.5.1.62) and HDAC10, thereby mimicking the tetrahedral intermediate and its flanking transition states in catalysis Danio rerio
3.5.1.48 7-[(3-aminopropyl)amino]-1,1,1-trifluoroheptan-2-one AAT, binds as a tetrahedral gem-diolate to both APAH (acetylpolyamine amidohydrolase, EC 3.5.1.62) and HDAC10, thereby mimicking the tetrahedral intermediate and its flanking transition states in catalysis Homo sapiens
3.5.1.62 7-[(3-aminopropyl)amino]-1,1,1-trifluoroheptan-2-one AAT, binds as a tetrahedral gem-diolate to both APAH and HDAC10 (histone 10 deacetylase, EC 3.5.1.48), thereby mimicking the tetrahedral intermediate and its flanking transition states in catalysis Mycoplana ramosa

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.5.1.48 Zn2+ catalytic zinc ion Homo sapiens
3.5.1.48 Zn2+ catalytic zinc ion Danio rerio
3.5.1.62 Zn2+ catalytic zinc ion Mycoplana ramosa

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.5.1.48 N8-acetylspermidine + H2O Homo sapiens
-
 acetate + spermidine
-
 ?
3.5.1.48 N8-acetylspermidine + H2O Danio rerio
-
 acetate + spermidine
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
3.5.1.48 Danio rerio F1QCV2
-
-
3.5.1.48 Homo sapiens Q969S8
-
-
3.5.1.62 Mycoplana ramosa Q48935
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.5.1.48 additional information histone deacetylase 10 (HDAC10) from Danio rerio is a highly specific N8-acetylspermidine deacetylase. No activity with N1-acetylspermidine and N1-acetylspermine Danio rerio ?
-
 ?
3.5.1.48 additional information histone deacetylase 10 (HDAC10) from Homo sapiens is a highly specific N8-acetylspermidine deacetylase. No activity with N1-acetylspermidine and N1-acetylspermine Homo sapiens ?
-
 ?
3.5.1.48 N8-acetylspermidine + H2O
-
 Homo sapiens acetate + spermidine
-
 ?
3.5.1.48 N8-acetylspermidine + H2O
-
 Danio rerio acetate + spermidine
-
 ?
3.5.1.62 additional information acetylpolyamine amidohydrolase (APAH) from Mycoplana ramosa, is a broad-specificity polyamine deacetylase Mycoplana ramosa ?
-
 ?

Subunits

EC Number Subunits Comment Organism
3.5.1.62 dimer alpha/beta fold. The quaternary structure, i.e. dimer assembly, provides the steric constriction that directs the polyamine substrate specificity of APAH Mycoplana ramosa

Synonyms

EC Number Synonyms Comment Organism
3.5.1.48 HDAC10
-
 Homo sapiens
3.5.1.48 HDAC10
-
 Danio rerio
3.5.1.48 histone deacetylase 10
-
 Homo sapiens
3.5.1.48 histone deacetylase 10
-
 Danio rerio
3.5.1.48 polyamine deacetylase
-
 Homo sapiens
3.5.1.48 polyamine deacetylase
-
 Danio rerio
3.5.1.62 acetylpolyamine amidohydrolase
-
 Mycoplana ramosa
3.5.1.62 APAH
-
 Mycoplana ramosa

General Information

EC Number General Information Comment Organism
3.5.1.48 evolution the enzyme adopts the characteristic arginase-deacetylase fold and employ a Zn2+-activated water molecule for catalysis. The active sites of HDAC10 and APAH (acetylpolyamine amidohydrolase, EC 3.5.1.62) are sterically constricted to enforce specificity for long, slender polyamine substrates and exclude bulky peptides and proteins containing acetyl-L-lysine. The tertiary structure (a unique 310 helix defined by the P(E,A)CE motif) provides the steric constriction that directs the polyamine substrate specificity of HDAC10. Structure and catalytic mechanism of polyamine deacetylases, comparison of HDAC and APAH, overview Homo sapiens
3.5.1.48 evolution the enzyme adopts the characteristic arginase-deacetylase fold and employ a Zn2+-activated water molecule for catalysis. The active sites of HDAC10 and APAH (acetylpolyamine amidohydrolase, EC 3.5.1.62) are sterically constricted to enforce specificity for long, slender polyamine substrates and exclude bulky peptides and proteins containing acetyl-L-lysine. The tertiary structure (a unique 310 helix defined by the P(E,A)CE motif) provides the steric constriction that directs the polyamine substrate specificity of HDAC10. Structure and catalytic mechanism of polyamine deacetylases, comparison of HDAC and APAH, overview Danio rerio
3.5.1.48 additional information nucleophilic attack of Zn2+-bound water at the amide carbonyl group polarized by Zn2+ and the catalytic tyrosine is facilitated by a general base. The Zn2+ ion, tyrosine, and tandem histidine residues contribute to transition state stabilization in each deacetylase. Collapse of the tetrahedral intermediate requires a proton donor, and the second histidine of the tandem pair must serve as the general acid due to its proximity to the leaving amino group. Structure-function analysis of substrate specificity, overview Homo sapiens
3.5.1.48 additional information nucleophilic attack of Zn2+-bound water at the amide carbonyl group polarized by Zn2+ and the catalytic tyrosine is facilitated by a general base. The Zn2+ ion, tyrosine, and tandem histidine residues contribute to transition state stabilization in each deacetylase. Collapse of the tetrahedral intermediate requires a proton donor, and the second histidine of the tandem pair must serve as the general acid due to its proximity to the leaving amino group. Structure-function analysis of substrate specificity, overview Danio rerio
3.5.1.48 physiological function HDAC10 and spermidine act as mediators of autophagy Homo sapiens
3.5.1.48 physiological function HDAC10 and spermidine act as mediators of autophagy Danio rerio
3.5.1.62 evolution the enzyme adopts the characteristic arginase-deacetylase fold and employ a Zn2+-activated water molecule for catalysis. The active sites of HDAC10 (histone 10 deacetylase, EC 3.5.1.48) and APAH are sterically constricted to enforce specificity for long, slender polyamine substrates and exclude bulky peptides and proteins containing acetyl-L-lysine. The quaternary structure, i.e., dimer assembly, provides the steric constriction that directs the polyamine substrate specificity of APAH. Structure and catalytic mechanism of polyamine deacetylases, comparison of HDAC and APAH, overview Mycoplana ramosa
3.5.1.62 additional information nucleophilic attack of Zn2+-bound water at the amide carbonyl group polarized by Zn2+ and the catalytic tyrosine is facilitated by a general base. The Zn2+ ion, tyrosine, and tandem histidine residues contribute to transition state stabilization in each deacetylase. Collapse of the tetrahedral intermediate requires a proton donor, and the second histidine of the tandem pair must serve as the general acid due to its proximity to the leaving amino group. Structure-function analysis of substrate specificity, overview Mycoplana ramosa