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Figure 4
Rounds of construct optimization for the HDAC4 histone deacetylase domain. (a) The construct boundaries of the original HDAC4 catalytic domain structure (PDB entry 2vqj, top) and the HDAC7 catalytic domain in PDB entry 3c0y (bottom) are shown. The HDAC7 numbering is aligned with the HDAC4 numbering. The first residue modelled in the original HDAC4 structure corresponds to the first residue modelled in the HDAC7 structure and was used as the starting point for the optimized HDAC4 construct (middle). The C-terminus of the optimized HDAC4 model was chosen based on the last residue visible in the HDAC7 structure. This shortened the new HDAC4 construct by about 20 residues compared with the original HDAC4 structure, and the new C-terminal boundary is highlighted in the cartoon representation of HDAC4 (PDB entry 2vqj). It was speculated that this truncation would help to generate an alternative crystal form with more favourable packing contacts. (b) Crystal structure of the new HDAC4 construct with bound ligand (PDB entry 4cbt). The new HDAC4 construct did result in an alternative crystal form. Here, close crystal contacts are observed between ligand (yellow) and Leu728 (magenta) at the terminus of a disordered loop in a neighbouring chain (blue). These contacts were thought to hinder co-crystallization with larger ligands. (c) In a second round of construct optimization, Leu728 was mutated to alanine (green) and the mutant readily crystallized in the presence of ligand in yet another crystal form devoid of packing interactions at the ligand-binding site (PDB entry 4cby). In addition, a loop that was disordered in the corresponding wild-type structure could be modelled into the electron density (orange). Figures were created with the CCP4mg molecular-graphics software (McNicholas et al., 2011BB39).

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ISSN: 2059-7983
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