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
Acta Crystallographica
Section F STRUCTURAL BIOLOGY COMMUNICATIONS

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Figure 3
Crystal structure of YkfC from B. cereus in complex with L-Ala-γ-D-Glu. (a) Ribbon representation of BcYkfC, highlighting its domain organization. SH3b1 is depicted in blue, SH3b2 in green and NlpC/P60 in red. The bound L-Ala-γ-D-Glu is shown as a stick model. (b) Ribbon representations of individual domains, showing the secondary-structure elements. (c) Molecular surface of YkfC colored by sequence conservation. The surface color gradient indicates the level of sequence conservation from the most conserved residues (deep red) to nonconserved residues (white).

STRUCTURAL BIOLOGY
COMMUNICATIONS

ISSN: 2053-230X

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

doi:10.1107/S1744309110021214

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