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Figure 6
Models of substrate recognition by BcYkfC. (a) L-Ala-γ-D-Glu-DAP was docked into the active site of BcYkfC. The protein surface is colored according to a gradient in electrostatic potential from negative (red) to positive (blue) (MOE 2008.10; Chemical Computing Group Inc.). (b) Stereoview of the specific interactions (four polar, one nonpolar) of γ-D-Glu (cyan) in the context of the tripeptide by five residues of YkfC (Tyr226, Trp228, Asp237, Ser239 and Ser257). The protein residues are colored according to subsite (S1, orange; catalytic triad, magenta; S1′, green). (c) Sequence conservation of the active sites in NlpC/P60 domains based on 2277 NlpC/P60 domains with an intact catalytic dyad (Cys238 and His291) and a conserved Tyr226 (blue, S2; orange, S1; red, catalytic triad; green, S′ sites). (d) Sequence conservation of the active sites in the YkfC subfamily of NlpC/P60 enzymes based on 282 sequences selected based on the presence of a conserved aspartate residue at position 256 of BcYkfC. The conservation of this residue is highly correlated with a conserved tyrosine in the βD region of the SH3b domain (Tyr118 of BcYkfC); both of these residues interact with the free amine of L-Ala of the substrate.

ISSN: 2053-230X
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