4ZUM: Crystal Structure Of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa In Complex With A Trifluoromethylketone Inhibitor

Citation:
Abstract
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. Acetylpolyamine amidohydrolase (APAH) from Mycoplana ramosa is a zinc-dependent polyamine deacetylase that shares approximately 20% amino acid sequence identity with human histone deacetylases. We now report the X-ray crystal structures of APAH-inhibitor complexes in a new and superior crystal form that diffracts to very high resolution (1.1-1.4 A). Inhibitors include previously synthesized analogues of N(8)-acetylspermidine bearing trifluoromethylketone, thiol, and hydroxamate zinc-binding groups [Decroos, C., Bowman, C. M., and Christianson, D. W. (2013) Bioorg. Med. Chem. 21, 4530], and newly synthesized hydroxamate analogues of shorter, monoacetylated diamines, the most potent of which is the hydroxamate analogue of N-acetylcadaverine (IC50 = 68 nM). The high-resolution crystal structures of APAH-inhibitor complexes provide key inferences about the inhibition and catalytic mechanism of zinc-dependent deacetylases. For example, the trifluoromethylketone analogue of N(8)-acetylspermidine binds as a tetrahedral gem-diol that mimics the tetrahedral intermediate and its flanking transition states in catalysis. Surprisingly, this compound is also a potent inhibitor of human histone deacetylase 8 with an IC50 of 260 nM. Crystal structures of APAH-inhibitor complexes are determined at the highest resolution of any currently existing zinc deacetylase structure and thus represent the most accurate reference points for understanding structure-mechanism and structure-inhibition relationships in this critically important enzyme family.
PDB ID: 4ZUMDownload
MMDB ID: 131314
PDB Deposition Date: 2015/5/17
Updated in MMDB: 2017/09
Experimental Method:
x-ray diffraction
Resolution: 1.42  Å
Source Organism:
Similar Structures:
Biological Unit for 4ZUM: dimeric; determined by author and by software (PISA)
Molecular Components in 4ZUM
Label Count Molecule
Proteins (2 molecules)
2
Acetylpolyamine Aminohydrolase
Molecule annotation
Chemicals (14 molecules)
1
2
2
2
3
2
4
2
5
4
6
2
* Click molecule labels to explore molecular sequence information.

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