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![[Figure 3]](rr5233fig3mag.jpg)
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Figure 3
SH3 domain comparisons. (a) The overall fold of the TsGH24 fungal muramidase SH3-like domain shown in ice blue. Loops potentially involved in target recognition are coloured red for the RT loop, green for the n-Src loop and yellow for the distal loop, which are named according to the standard SH3 convention. Two disulfide bridges, which are a specific feature of the SH3-like domains of fungal muramidases identified in the present study, are shown in ball-and-stick representation. (b) Peptide-binding site: triglycine forms salt bridges to the main-chain O atom of Asp6, the N atom of His8 and the side chain of Arg10. Two triglycine molecules (green) from the different subunits in the asymmetric unit coordinate a zinc ion together with two His8 residues from different chains, thus forming crystal contacts. In addition, there are two ethylene glycol molecules from the crystallization conditions that further stabilize the crystal contacts. The peptides are in ball-and-stick representation, the protein in ice blue and ethylene glycol molecules in light brown in cylinder representation. (c, d, e) Topology schemes and (f, g, h) complexes of SH3-like domains with (poly)peptides: (c, f) the TsGH24 SH3-like domain in complex with triglycine, (d, g) the SH3b domain of lysostaphin from Staphylococcus simulans with pentaglycine (PDB entry 5leo, Table 2 ![[link]](../../../../../../logos/arrows/d_arr.gif){kind=small} ) and (e, h) the mouse Grb2 N-terminal domain with a decapeptide spanning both the canonical and bacterial binding sites (PDB entry 2gbq, Table 2). Proteins and ligands are shown as ribbons and cylinders, respectively. The long bending strand 2 in (g) is shown by two fragments of ribbon. (i) Cα traces of SH3-like domains (f, g, h) superposed using GESAMT (Krissinel, 2012) and (j) the corresponding sequence and secondary-structure alignments. Exact amino-acid matches are highlighted in red. The quality of 3D alignment is represented by symbols above the second and third amino-acid sequences. A plus sign means a Cα distance of less than 1.5 Å from the corresponding residue from the first sequence. A dot indicates that GESAMT treated the two residues as spatially aligned despite a greater distance. Strands in the secondary-structure alignment are numbered sequentially for the second structure and by correspondence in the first and the third structure. Colours and order are as in (c)–(h). The three-residue helical motifs following strand 8 are not labelled in (j) and are omitted in (c)–(e). The yellow lines in (c) and (j) show disulfide bonds. |
![[Figure 3]](rr5233fig3.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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