Xu, Qingping, Abdubeck, Polat, Chen, Connie, Chiu, Michelle, Feuerhelm, Julie, Grant, Joanna, Klock, Heath, Knuth, Mark, Okach, Linda, Nigoghossian, Edward, Puckett, Christina, Wooten, Tiffany, Lesley, Scott and Stolz, Barbara (2010) GNF ID 100606: Crystal 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. Acta Crystallographica Section F: Structural Biology and Crystallization Communications, F66. pp. 1-11. ISSN 1744-3091

Abstract

Crystal structure of a highly specific γ-D-glutamyl-L-diamino acid endopeptidases YkfC from Bacillus cereus in complex with L-Ala-γ-D-Glu reveals structural basis for substrate specificity of NlpC/P60 family cysteine peptidases.
Dipeptidyl-peptidase VI of Bacillus sphaericus and YkfC of Bacillus subtilis were both characterized previously as highly specific γ-D-glutamyl-L-diamino acid endopeptidases. The crystal structure of a YkfC orthologue from Bacillus cereus (BcYkfC) at 1.8 Å resolution reveals that it contains two N-terminal, bacterial SH3 domains (SH3b) in addition to a C-terminal catalytic NlpC/P60 domain, which is ubiquitous in the very large family of cell-wall related, cysteine peptidases. A bound reaction product (L-Ala-γ-D-Glu) enables the identification of conserved sequence and structural signatures for recognition of L-Ala and γ-D-Glu, hence provides a clear framework for understanding the substrate specificity observed in dipeptidyl-peptidase VI, YkfC and other NlpC/P60 domains in general. The first SH3b domain plays an important role in defining substrate specificity by contributing to formation of the active site, such that only murein peptides with a free N-terminal alanine are allowed. A conserved tyrosine in the SH3b domain of the YkfC subfamily is correlated with the presence of a conserved acidic residue in the NlpC/P60 domain and both interact with the free amine group of the alanine. This structural feature allows us to define a subfamily of NlpC/P60 enzymes with the same N-terminal substrate requirements, including a previously characterized cyanobacterial L-alanine-γ-D-glutamate endopeptidase that contains the two key components, an NlpC/P60 domain attached to an SH3b domain, for assembly of a YkfC-like active site.

Item Type:	Article
Related URLs:	http://journals.iucr.org/f/
Additional Information:	grant requirement B. Stolz is NOT an author -- NVS contact person for GNF manuscript approval. This manuscript shall NOT be copied to the OAK internet.
Keywords:	γ-D-glutamyl-L-diamino acid endopeptidase, cell-wall recycling, NlpC/P60, SH3b, cysteine peptidase, enzyme specificity
Related URLs:	http://journals.iucr.org/f/
Date Deposited:	13 Oct 2015 13:16
Last Modified:	13 Oct 2015 13:16
URI:	https://oak.novartis.com/id/eprint/3113