Structure of the γ-d-glutamyl-l-diamino acid endopeptidase YkfC from Bacillus cereus in complex with l-Ala-γ-d-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases

Xu, Q.; Abdubek, P.; Astakhova, T.; Axelrod, H.L.; Bakolitsa, C.; Cai, X.; Carlton, D.; Chen, C.; Chiu, H.-J.; Chiu, M.; Clayton, T.; Das, D.; Deller, M.C.; Duan, L.; Ellrott, K.; Farr, C.L.; Feuerhelm, J.; Grant, J.C.; Grzechnik, A.; Han, G.W.; Jaroszewski, L.; Jin, K.K.; Klock, H.E.; Knuth, M.W.; Kozbial, P.; Krishna, S.S.; Kumar, A.; Lam, W.W.; Marciano, D.; Miller, M.D.; Morse, A.T.; Nigoghossian, E.; Nopakun, A.; Okach, L.; Puckett, C.; Reyes, R.; Tien, H.J.; Trame, C.B.; van den Bedem, H.; Weekes, D.; Wooten, T.; Yeh, A.; Hodgson, K.O.; Wooley, J.; Elsliger, M.-A.; Deacon, A.M.; Godzik, A.; Lesley, S.A.; Wilson, I.A.

doi:10.1107/S1744309110021214

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.

STRUCTURAL BIOLOGY
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ISSN: 2053-230X

Volume 66| Part 10| July 2010| Pages 1354-1364

doi:10.1107/S1744309110021214

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