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 7
Structural comparisons between BcYkfC and the cyanobacterial NlpC/P60 endopeptidase AvPCP. (a) BcYkfC and AvPCP (PDB code 2hbw ; Xu et al., 2009

) are shown with the same orientation of their common SH3b1 and NlpC/P60 domains. The structurally equivalent residues in each are shown in red. (b) Stereoview of the C^α traces of the two proteins shown in (a) [the coloring is the same as in (a)]. (c) The S binding sites of the two proteins are nearly identical. The corresponding residues of AvPCP are labeled in parentheses. (d) Comparison of the active-site cavities and their environments. The catalytic cysteine is shown in white. A stick model of a docked murein tripeptide is shown in the active site of BcYkfC.

STRUCTURAL BIOLOGY
COMMUNICATIONS

ISSN: 2053-230X

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

doi:10.1107/S1744309110021214

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