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Figure 1.
Figure 1. (A) A subset from the multiple sequence alignment of
the entire DUF896 (PF05979) protein domain family (Pfam release
22.0) generated using Clustal X. The alignment includes YnzC
from Bacillus subtilis plus representatives from the major
genera of firmicutes that possess this protein (Streptococcus,
Listeria, Staphylococcus, Lactobacillus, Clostridium). Amino
acid residues identical or similar in 80% of the entire family
are shown in red and blue, respectively. Complete protein
sequences were used in the alignment and the conserved residues
were colored using the BOXSHADE server. The sequence numbering
for YnzC from B. subtilis and the secondary structural elements
found in its solution NMR structure (PDB ID, 2HEP) are shown
above the alignment. (B) Stereoview of the ribbon representation
of the lowest energy conformers (lowest CNS energy) from the
final solution NMR structures of full length YnzC (green) and
the truncated YnzC-1-46 construct (red). The secondary
structural elements are labeled. (C) A view into the core of the
YnzC-1-46 structure showing key hydrophobic (gold), aromatic
(green) and polar (cyan) side chains that form the interface
between the two helices. (D) Electrostatic potential surface
diagrams of the interhelical surfaces made by helix 1 and 2 in
YnzC. For clarity, the unstructured C-terminal region of the
protein has been omitted and only the structured residues (1-42)
are shown. (E) ConSurf images of the same interhelical faces of
YnzC based on the multiple sequence alignment of the entire
DUF896 (PF05979) protein domain family. Residue coloring,
reflecting the degree of residue conservation over the entire
family, ranges from magenta (highly conserved) to cyan
(variable).
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