Structure of Prokaryotic Polyamine Deacetylase Reveals Evolutionary Functional Relationships with Eukaryotic Histone Deacetylases,

Abstract

Polyamines are a ubiquitous class of polycationic small molecules that can influence gene expression by binding to nucleic acids. Reversible polyamine acetylation regulates nucleic acid binding and is required for normal cell cycle progression and proliferation. Here, we report the structures of Mycoplana ramosa acetylpolyamine amidohydrolase (APAH) complexed with a transition state analogue and a hydroxamate inhibitor, and an inactive mutant complexed with two acetylpolyamine substrates. The structure of APAH is the first of a histone deacetylase-like oligomer and reveals that an 18-residue insert in the L2 loop promotes dimerization and the formation of an 18-Å long “L”-shaped active site tunnel at the dimer interface, accessible only to narrow and flexible substrates. The importance of dimerization for polyamine deacetylase function leads to the suggestion that a comparable dimeric or double-domain histone deacetylase could catalyze polyamine deacetylation reactions in eukaryotes.

Design, Synthesis, and Evaluation of Polyamine Deacetylase Inhibitors, and High-Resolution Crystal Structures of Their Complexes with Acetylpolyamine Amidohydrolase

“…31 These differences give rise to alternative crystal symmetries. The coordination geometry of the active site Zn 2+ ion is also similar in each crystal form.…”

“…31,33 The IC 50 values for compounds 1, 2 , and 3 were reported previously. 33 Activity was measured using the commercially available Fluor-de-Lys deacetylase fluorogenic substrate (BML-KI104, Enzo Life Sciences).…”

“…31 HDAC8 was expressed from a pHD2-Xa-His plasmid (modified pET-20b plasmid) in Escherichia coli BL21(DE3) cells and purified using previously described procedures. 15,35 …”

“…29,30 Like the metal-dependent HDACs, APAH is a zinc metallohydrolase that adopts the α/β arginase fold. 31 However, APAHs are dimeric enzymes, as revealed by the crystal structures of APAH from M. ramosa and Burkholderia pseudomallei , 31,32 whereas HDACs such as HDAC8 are monomers. 12,13 Assembly of the APAH dimer results in a narrow “L”-shaped active site at the dimer interface that confers specifity for long, flexible, and positively charged acetylpolyamine substrates.…”

Antibiotic dialogues: induction of silent biosynthetic gene clusters by exogenous small molecules

“…The authors explained their results by citing a parallel to chromatin organization: the bacterial genome is compacted by nucleoidassociated proteins, RNAs and differential supercoiling, which could lead to differential compaction for certain genes. In addition, bacteria have their own versions of HDAC proteins (Lombardi et al 2011). The mechanism for how these bacterial HDAC-like enzymes function is still unclear, so the pathway for the epigenetic approach in bacteria ultimately awaits further clarification (Moore et al 2012).…”