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Literature summary extracted from

  • Decroos, C.; Christianson, D.W.
    Design, synthesis, and evaluation of polyamine deacetylase inhibitors, and high-resolution crystal structures of their complexes with acetylpolyamine amidohydrolase (2015), Biochemistry, 54, 4692-4703 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
3.5.1.62 recombinant expression of His-tagged enzyme in Escherichia coli BL21(DE3) Mycoplana ramosa

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.5.1.62 purified enzyme in complex with 5 different inhibitors, sitting drop vapor diffusion method, mixing of 500 nl of 5-10 mg/ml of protein in 20 mM Tris, pH 8.0, 50 mM NaCl, 0.01% sodium azide, 0.5-2 mM ZnCl2, and 2.5 mM inhibitor, with 500 nl of precipitant solution containing 0.2 M LiNO3, or KNO3, or LiCL, and 20% w/v PEG 3350, and equilibration against 0.1 ml of precipitant solution reservoir, 2 days, 21°C, X-ray diffraction structure determination and analysis at 1.13-1.42 A resolution Mycoplana ramosa

Inhibitors

EC Number Inhibitors Comment Organism Structure
3.5.1.62 5-amino-N-hydroxypentanamide
-
 Mycoplana ramosa
3.5.1.62 5-[(3-aminopropyl)amino]pentane-1-thiol
-
 Mycoplana ramosa
3.5.1.62 6-amino-N-hydroxyhexanamide
-
 Mycoplana ramosa
3.5.1.62 6-[(3-aminopropyl)amino]-N-hydroxyhexanamide
-
 Mycoplana ramosa
3.5.1.62 7-amino-N-hydroxyheptanamide
-
 Mycoplana ramosa
3.5.1.62 7-[(3-aminopropyl)amino]-1,1,1-trifluoroheptan-2-one AAT, an analogue of N8-acetylspermidine Mycoplana ramosa
3.5.1.62 8-amino-N-hydroxyoctanamide
-
 Mycoplana ramosa
3.5.1.62 additional information design, synthesis, and evaluation of polyamine deacetylase inhibitors, and high-resolution crystal structures of their complexes with acetylpolyamine amidohydrolase, overview Mycoplana ramosa

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.5.1.62 Mg2+ required Mycoplana ramosa
3.5.1.62 Zn2+ dependent on Mycoplana ramosa

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.5.1.62 acetylcadaverine + H2O Mycoplana ramosa
-
 acetate + cadaverine
-
 ?
3.5.1.62 acetylputrescine + H2O Mycoplana ramosa
-
 acetate + putrescine
-
 ?
3.5.1.62 N1-acetylspermidine + H2O Mycoplana ramosa
-
 acetate + spermidine
-
 ?
3.5.1.62 N1-acetylspermine + H2O Mycoplana ramosa
-
 acetate + spermine
-
 ?
3.5.1.62 N8-acetylspermidine + H2O Mycoplana ramosa
-
 acetate + spermidine
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
3.5.1.62 Mycoplana ramosa Q48935
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
3.5.1.62 recombinant His-tagged enzyme from Escherichia coli BL21(DE3) by nickel affinity chromatography Mycoplana ramosa

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.5.1.62 acetylcadaverine + H2O
-
 Mycoplana ramosa acetate + cadaverine
-
 ?
3.5.1.62 acetylputrescine + H2O
-
 Mycoplana ramosa acetate + putrescine
-
 ?
3.5.1.62 BML-KI104 + H2O a commercial acetyllysine-fluorophore substrate. Deacetylation of the acetyllysine-fluorophore substrate is followed by cleavage of the lysine-fluorophore amide bond by a protease developer, resulting in a fluorescence shift Mycoplana ramosa acetate + ?
-
 ?
3.5.1.62 additional information the fluorophore Ac-Arg-His-Lys(Ac)-Lys(Ac)-aminomethylcoumarin is a poor substrate for APAH Mycoplana ramosa ?
-
 ?
3.5.1.62 N1-acetylspermidine + H2O
-
 Mycoplana ramosa acetate + spermidine
-
 ?
3.5.1.62 N1-acetylspermine + H2O
-
 Mycoplana ramosa acetate + spermine
-
 ?
3.5.1.62 N8-acetylspermidine + H2O
-
 Mycoplana ramosa acetate + spermidine
-
 ?

Synonyms

EC Number Synonyms Comment Organism
3.5.1.62 acetylpolyamine amidohydrolase
-
 Mycoplana ramosa
3.5.1.62 APAH
-
 Mycoplana ramosa
3.5.1.62 polyamine deacetylase
-
 Mycoplana ramosa

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
3.5.1.62 25
-
 assay at Mycoplana ramosa

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.5.1.62 8.2
-
 assay at Mycoplana ramosa

IC50 Value

EC Number IC50 Value IC50 Value Maximum Comment Organism Inhibitor Structure
3.5.1.62 0.000068
-
 pH 8.2, 25°C Mycoplana ramosa 7-amino-N-hydroxyheptanamide
3.5.1.62 0.00013
-
 pH 8.2, 25°C Mycoplana ramosa 6-amino-N-hydroxyhexanamide
3.5.1.62 0.00015
-
 pH 8.2, 25°C Mycoplana ramosa 8-amino-N-hydroxyoctanamide
3.5.1.62 0.00017
-
 pH 8.2, 25°C Mycoplana ramosa 5-amino-N-hydroxypentanamide
3.5.1.62 0.00027
-
 pH 8.2, 25°C Mycoplana ramosa 7-[(3-aminopropyl)amino]-1,1,1-trifluoroheptan-2-one
3.5.1.62 0.00039
-
 pH 8.2, 25°C Mycoplana ramosa 6-[(3-aminopropyl)amino]-N-hydroxyhexanamide
3.5.1.62 0.026
-
 pH 8.2, 25°C Mycoplana ramosa 5-[(3-aminopropyl)amino]pentane-1-thiol

General Information

EC Number General Information Comment Organism
3.5.1.62 evolution acetylpolyamine amidohydrolase (APAH) from Mycoplana ramosa is a zinc-dependent polyamine deacetylase that shares approximately 20% amino acid sequence identity with human histone deacetylases Mycoplana ramosa
3.5.1.62 additional information proposed mechanism of APAH, overview. The substrate binding mode is based on the complex of N8-acetylspermidine with the inactive mutant APAH H159A (PDB entry 3Q9C), and the binding of the tetrahedral intermediate is mimicked by the binding of trifluoromethylketone inhibitor 1 Mycoplana ramosa
3.5.1.62 physiological function polyamines are essential aliphatic polycations that bind to nucleic acids and accordingly are involved in a variety of cellular processes. Polyamine function can be regulated by acetylation and deacetylation, just as histone function can be regulated by lysine acetylation and deacetylation Mycoplana ramosa