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Peptide transport in Bacillus subtilis – structure and specificity in the extracellular solute binding proteins OppA and DppE

DOI: 10.1099/mic.0.001274 DOI Help

Authors: Adam M. Hughes (University of York) , John F. Darby (University of York) , Eleanor J. Dodson (University of York) , Samuel J. Wilson (University of York) , Johan P. Turkenburg (University of York) , Gavin H. Thomas (University of York) , Anthony J. Wilkinson (University of York)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Microbiology , VOL 168

State: Published (Approved)
Published: December 2022
Diamond Proposal Number(s): 9948 , 13587

Open Access Open Access

Abstract: Peptide transporters play important nutritional and cell signalling roles in Bacillus subtilis, which are pronounced during stationary phase adaptations and development. Three high-affinity ATP-binding cassette (ABC) family transporters are involved in peptide uptake – the oligopeptide permease (Opp), another peptide permease (App) and a less well-characterized dipeptide permease (Dpp). Here we report crystal structures of the extracellular substrate binding proteins, OppA and DppE, which serve the Opp and Dpp systems, respectively. The structure of OppA was determined in complex with endogenous peptides, modelled as Ser-Asn-Ser-Ser, and with the sporulation-promoting peptide Ser-Arg-Asn-Val-Thr, which bind with Kd values of 0.4 and 2 µM, respectively, as measured by isothermal titration calorimetry. Differential scanning fluorescence experiments with a wider panel of ligands showed that OppA has highest affinity for tetra- and penta-peptides. The structure of DppE revealed the unexpected presence of a murein tripeptide (MTP) ligand, l-Ala-d-Glu-meso-DAP, in the peptide binding groove. The mode of MTP binding in DppE is different to that observed in the murein peptide binding protein, MppA, from Escherichia coli, suggesting independent evolution of these proteins from an OppA-like precursor. The presence of MTP in DppE points to a role for Dpp in the uptake and recycling of cell wall peptides, a conclusion that is supported by analysis of the genomic context of dpp, which revealed adjacent genes encoding enzymes involved in muropeptide catabolism in a gene organization that is widely conserved in Firmicutes.

Journal Keywords: sporulation; peptide transport; Bacillus subtilis; murein peptide; DppE; OppA

Diamond Keywords: Bacteria

Subject Areas: Biology and Bio-materials

Instruments: I02-Macromolecular Crystallography , I03-Macromolecular Crystallography , I04-Macromolecular Crystallography

Added On: 07/12/2022 08:26


Discipline Tags:

Structural biology Life Sciences & Biotech

Technical Tags:

Diffraction Macromolecular Crystallography (MX)