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Structural and Chemical Biology of Deacetylases for Carbohydrates, Proteins, Small Molecules and Histones

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Review

Structural and Chemical Biology of Deacetylases for Carbohydrates, Proteins, Small Molecules and Histones

Marco Bürger et al. Commun Biol.

Erratum in

Abstract

Deacetylation is the removal of an acetyl group and occurs on a plethora of targets and for a wide range of biological reasons. Several pathogens deacetylate their surface carbohydrates to evade immune response or to support biofilm formation. Furthermore, dynamic acetylation/deacetylation cycles govern processes from chromatin remodeling to posttranslational modifications that compete with phosphorylation. Acetylation usually occurs on nitrogen and oxygen atoms and are referred to as N- and O-acetylation, respectively. This review discusses the structural prerequisites that enzymes must have to catalyze the deacetylation reaction, and how they adapted by formation of specific substrate and metal binding sites.

Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Phylogenetic tree of the deacetylase families discussed in this review, showing NCBI reference sequences (RefSeq) accession numbers. Created with SeaView 4.5.4. All protein structures herein were visualized with CCP4mg. Proteins discussed in this review were taken to represent each family and are displayed showing their folds, PDB codes and annotations from the CAZy database (CE4, CE7, and CE9)
Fig. 2
Fig. 2
Overview of the diversity of deacetylase substrates discussed in this review. a Carbohydrates, b small molecules, and c amino acid residues. N-acetyl are highlighted in blue and O-acetyl in red, respectively. Chemical structures were drawn using ChemDraw (Perkin Elmer)
Fig. 3
Fig. 3
Deacetylases can be classified in three major groups, according to their catalytic sites. Exemplary active site arrangements and simple catalytic mechanisms of a de-N-acetylases (PDB code 4F9D), b de-O-acetylases (PDB code 3M81), and c class III HDACs (PDB code 4I5I). N-acetyl is highlighted in blue and O-acetyl in red, respectively. Typical catalytic site residues are shown with white carbon atoms and metal binding residues in a are shown with carbon atoms colored in gray
Fig. 4
Fig. 4
Deacetylases feature a signature binding groove with electronegative charge. af Protein surface representations of deacetylases with different substrate specificities. Electrostatic surface potentials are contoured from −12.8 kT e−1 (red) to +12.8 kT e−1 (blue). gk Divalent metal coordination by different deacetylases. Distances are in Å. l Dimeric composition and m metal binding sites (white) and substrate binding residues (green) of the N-acetylglucosamine-6-phosphate deacetylase from Bacillus subtilis
Fig. 5
Fig. 5
Some deacetylases achieve specificity through oligomerization. a Oligomerization properties of small molecule deacetylases highlighting the narrow tunnel entrance to the hexamer and b the active sites (yellow circle) positioned towards the inside of the substrate conduit (PDB code 1ODS). The electrostatic surface potential is contoured from −12.8 kT e−1 (red) to +12.8 kT e−1 (blue)

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