Structural and computational analysis of peptide recognition mechanism of class-C type penicillin binding protein, alkaline D-peptidase from Bacillus cereus DF4-B.

Shogo Nakano,Hiroaki Tokiwa,Hidenobu Komeda,Erika Ishitsubo,Nobuhiro Kawahara,Seiji Okazaki,Yasuhisa Asano

doi:10.1038/srep13836

Abstract

Alkaline D-peptidase from Bacillus cereus DF4-B, called ADP, is a D-stereospecific endopeptidase reacting with oligopeptides containing D-phenylalanine (D-Phe) at N-terminal penultimate residue. ADP has attracted increasing attention because it is useful as a catalyst for synthesis of D-Phe oligopeptides or, with the help of substrate mimetics, L-amino acid peptides and proteins. Structure and functional analysis of ADP is expected to elucidate molecular mechanism of ADP. In this study, the crystal structure of ADP (apo) form was determined at 2.1 Å resolution. The fold of ADP is similar to that of the class C penicillin-binding proteins of type-AmpH. Docking simulations and fragment molecular orbital analyses of two peptides, (D-Phe)4 and (D-Phe)2-(L-Phe)2, with the putative substrate binding sites of ADP indicated that the P1 residue of the peptide interacts with hydrophobic residues at the S1 site of ADP. Furthermore, molecular dynamics simulation of ADP for 50 nsec suggested that the ADP forms large cavity at the active site. Formation of the cavity suggested that the ADP has open state in the solution. For the ADP, having the open state is convenient to bind the peptides having bulky side chain, such as (D-Phe)4. Taken together, we predicted peptide recognition mechanism of ADP.

Highlights

Some penicillin-binding proteins (PBPs) take part in bacterial cell wall synthesis by catalyzing transglycosylation and transpeptidation of peptidoglycan[1]
The crystal structure of alkaline D-peptidase from Bacillus cereus DF4-B (ADP) consists of two subdomains: a five-stranded β -sheet flanked by three α -helices, and a cluster of mixed 310-helices and α -helices
Based on the crystal structure, our docking and molecular dynamics (MD) simulation analyses of ADP, and biochemical results obtained in previous studies[14], we propose a schematic model for recognition of the peptide ligands [(D-Phe)[4] and (D-Phe)2-(L-Phe)2] by ADP (Fig. 5)

Summary

Introduction

Some penicillin-binding proteins (PBPs) take part in bacterial cell wall synthesis by catalyzing transglycosylation and transpeptidation of peptidoglycan[1]. The dipeptides produced by the reaction always have D-Phe at the C-terminus[14] These results suggested that reactive peptides have D-Phe at the acyl donor site (P1; detailed explanations about the nomenclature of Schechter and Berger will be described later) and a hydrophobic residue at the acyl acceptor site (P1’). The OGp leaving group is recognized as D-Phe (P1) at S1 site of ADP, and enables ADP to mediate the acceptance of originally poorly reactive acyl moieties composed of L-amino acids. These special peptide esters are termed “substrate mimetics”. We propose a molecular mechanism by which ADP recognizes peptide ligands containing D-Phe

Methods

Results

Conclusion