Article

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.

Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
Acta Crystallographica Section F Structural Biology and Crystallization Communications (Impact Factor: 0.57). 10/2010; 66(Pt 10):1354-64. DOI: 10.1107/S1744309110021214
Source: PubMed

ABSTRACT Dipeptidyl-peptidase VI from Bacillus sphaericus and YkfC from Bacillus subtilis have both previously been characterized as highly specific γ-D-glutamyl-L-diamino acid endopeptidases. The crystal structure of a YkfC ortholog from Bacillus cereus (BcYkfC) at 1.8 Å resolution revealed that it contains two N-terminal bacterial SH3 (SH3b) domains in addition to the C-terminal catalytic NlpC/P60 domain that is ubiquitous in the very large family of cell-wall-related cysteine peptidases. A bound reaction product (L-Ala-γ-D-Glu) enabled the identification of conserved sequence and structural signatures for recognition of L-Ala and γ-D-Glu and, therefore, 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 the 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 residues interact with the free amine group of the alanine. This structural feature allows the definition of 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.

Download full-text

Full-text

Available from: Hsiu-Ju Chiu, Jul 05, 2015
0 Followers
 · 
118 Views
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The target range of a bacterial secretion system can be defined by effector substrate specificity or by the efficacy of effector delivery. Here, we report the crystal structure of Tse1, a type VI secretion (T6S) bacteriolytic amidase effector from Pseudomonas aeruginosa. Consistent with its role as a toxin, Tse1 has a more accessible active site than related housekeeping enzymes. The activity of Tse1 against isolated peptidoglycan shows its capacity to act broadly against Gram-negative bacteria and even certain Gram-positive species. Studies with intact cells indicate that Gram-positive bacteria can remain vulnerable to Tse1 despite cell wall modifications. However, interbacterial competition studies demonstrate that Tse1-dependent lysis is restricted to Gram-negative targets. We propose that the previously observed specificity for T6S against Gram-negative bacteria is a consequence of high local effector concentration achieved by T6S-dependent targeting to its site of action rather than inherent effector substrate specificity.
    Cell Reports 06/2012; 1(6):656-64. DOI:10.1016/j.celrep.2012.05.016 · 7.21 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Liganded structures can be instrumental in assigning function to uncharacterized proteins by revealing active sites, conserved residues, binding motifs, and substrate specificity. This introduction provides an overview and commentary on the value of liganded structures emerging from the JCSG structural genomics initiative.
    Acta Crystallographica Section F Structural Biology and Crystallization Communications 10/2010; 66(Pt 10):1306-8. DOI:10.1107/S1744309110035748 · 0.57 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: 9,10-Phenanthrenequinone (PQ) is harmful environmental pollutant that is detected in airborne particulates. The measurement of PQ in the air should be necessary to evaluate the potential adverse effects of PQ on human health. We have recently developed a determination method for PQ based on the fluorescence derivatization of PQ using benzaldehyde and ammonium acetate as a reagent. In this study, in order to obtain more sensitive and selective fluorescence derivatization reaction, we measured the fluorescence of the reaction mixture of PQ with 21 kinds of aromatic aldehydes in the presence of ammonium acetate. Among the tested aldehydes, 4-carbomethoxybenzaldehyde was found to be the best reagent in regard to fluorescence intensity and emission wavelength maximum. Based on the fluorescence derivatization with 4-carbomethoxybenzaldehyde, a highly sensitive chromatographic method was developed for the determination of PQ with the detection limit (S/N=3) of 1.2 fmol/injection.
    Talanta 07/2011; 85(1):809-12. DOI:10.1016/j.talanta.2011.03.085 · 3.51 Impact Factor