1. A B Supplementary figure 5
Model of the L. japonicus NFR5 LysM2 domain based on the crystal structure of the LysM domain
from the ykuD protein (Bielnicki et al, 2006).
(A) Surface representation of the NFR5 LysM2 model coloured according to residue type: Grey is
hydrophobic, yellow is polar, red is acidic and blue is basic.
(B) Superimposition of the NFR5 LysM2 model based on ykuD (green) with the NFR5 LysM2 model
based on MltD (magenta) (Bateman & Bycroft 2000). Sidechains of the aminoacids labelled on the surface representation are shown, except for F159, which is omitted for clarity. The main differences are in the loop between the two helices and the loop between helix2 and strand2.
The binding site proposed by the ykuD based model suggest interactions with amino acids Y114, L118,
D120, F120 and F159 as in the MltD based model. The binding site suggested by the two models are
comparable, the main difference is Y130 which turns away from the cleft in the ykuD based model.
The model was constructed as described for the model based on MltD in supplementary methods and
superimposition of the models was done in PyMol (DeLano, 2002) using both mainchain and sidechain atoms, the two models superimpose with RMSD = Å.
Bielnicki J, Devedjiev Y, Derewenda U, Dauter Z, Joachimiak A, Derewenda ZS (2006) B. subtilis ykuD Protein at 2.0 Å Resolution: Insights into the Structure and Function of a Novel, Ubiquitous Family of Bacterial Enzymes. PROTEINS: Structure, Function, and Bioinformatics 62: 144–151