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

Acta Crystallographica Section F
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Figure 4
Active site and recognition of L-Ala-γ-D-Glu by BcYkfC. (a) Stereoview of a 2F_o − F_c OMIT map, where L-Ala-γ-D-Glu and OCS238 were omitted from phasing/refinement, contoured at 1.5σ. (b) The extensive hydrogen-bond network in the active site of BcYkfC. Hydrogen bonds and distances are shown as dashed lines. (c) L-Ala-γ-D-Glu (stick representation; yellow C atoms) is located in the active site at the interface of the SH3b1 domain (blue) and the NlpC/P60 domain (red). (d) The interaction between L-Ala-γ-D-Glu and the active site of YkfC. This figure was generated using the program MOE 2008.10 (Chemical Computing Group Inc.).

STRUCTURAL BIOLOGY
COMMUNICATIONS

ISSN: 2053-230X

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

doi:10.1107/S1744309110021214

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