Crystal structures of MBP fusion proteins

Abstract

Although chaperone-assisted protein crystallization remains a comparatively rare undertaking, the number of crystal structures of polypeptides fused to maltose-binding protein (MBP) that have been deposited in the Protein Data Bank (PDB) has grown dramatically during the past decade. Altogether, 102 fusion protein structures were detected by Basic Local Alignment Search Tool (BLAST) analysis. Collectively, these structures comprise a range of sizes, space groups, and resolutions that are typical of the PDB as a whole. While most of these MBP fusion proteins were equipped with short inter-domain linkers to increase their rigidity, fusion proteins with long linkers have also been crystallized. In some cases, surface entropy reduction mutations in MBP appear to have facilitated the formation of crystals. A comparison of the structures of fused and unfused proteins, where both are available, reveals that MBP-mediated structural distortions are very rare.

Keywords: MBP fusion protein; chaperone-assisted crystallization; crystallization chaperone; crystallization tag; maltose-binding protein; surface entropy reduction mutagenesis.

Figure 1

Cumulative number of MBP fusion protein structures deposited in the PDB between 1999 and 2015.

Figure 2

Schematic diagram of a popular MBP fusion junction for crystallographic applications. See text for discussion.

Figure 3

General characteristics of MBP fusion proteins. (a) lengths of passenger proteins in intervals of amino acid residues. (b) Resolution of MBP fusion protein structures in Å (black bars, left ordinate scale) versus the sum total of all unique structures in the PDB (gray squares, right ordinate scale). (c) percentage of MBP fusion proteins crystallized in each of 16 different space groups (black) and percentage of all unique proteins in the PDB that have been crystallized in the same space groups (gray).

Figure 4

Conformational shifts observed in fused and unfused structures. (a) structural alignment of 3WAI (magenta) and 3WAJ (blue). (b) structural alignment of N‐terminal “mini domains” of AglB in 3WAI (magenta) and 3WAJ (blue). (c) structural alignment of MBP‐UBA3 from 2NVU (magenta) with unfused UBA3 from 3GZN (blue). (d,) structural alignment of the ubiquitin fold domains from fused (magenta) and unfused (blue) UBA3.