8AY0

Crystal Structure of the peptide binding protein DppE from Bacillus subtilis in complex with murein tripeptide

Summary for 8AY0

• Entry DOI: 10.2210/pdb8ay0/pdb
• Descriptor: Dipeptide-binding protein DppE, L-ALA-GAMMA-D-GLU-MESO-DIAMINOPIMELIC ACID, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: peptide-binding protein, murein tripeptide, bacillus subtilis, transport protein
• Biological source: Bacillus subtilis
• Total number of polymer chains: 3
• Total formula weight: 181199.76

Authors

Hughes, A.M.,Dodson, E.J.,Wilkinson, A.J. (deposition date: 2022-09-01, release date: 2023-02-22, Last modification date: 2024-02-07)

Primary citation

Hughes, A.M.,Darby, J.F.,Dodson, E.J.,Wilson, S.J.,Turkenburg, J.P.,Thomas, G.H.,Wilkinson, A.J.
Peptide transport in Bacillus subtilis - structure and specificity in the extracellular solute binding proteins OppA and DppE.
Microbiology (Reading, Engl.), 168:-, 2022

PubMed Abstract: Peptide transporters play important nutritional and cell signalling roles in 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 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--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 , 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 , which revealed adjacent genes encoding enzymes involved in muropeptide catabolism in a gene organization that is widely conserved in .

PubMed: 36748525
DOI: 10.1099/mic.0.001274

Experimental method

X-RAY DIFFRACTION (1.51 Å)