Proposed docking interface between peptidoglycan and the target recognition domain of zoocin A.
A docking model is proposed for the target recognition domain of the lytic exoenzyme zoocin A with the peptidoglycan on the outer cell surface of sensitive bacterial strains. Solubilized fragments from such peptidoglycans perturb specific backbone and side chain amide resonances in the recombinant form of the domain designated rTRD as detected in two-dimensional (1)H-(15)N correlation NMR spectra. The affected residues comprise a shallow surface cleft on the protein surface near W115, N53, N117, and Q105 among others, which interacts with the peptide portion of the peptidoglycan. Calculations with AutoDock Vina provide models of the docking interface. There is approximate homology between the rTDR-peptidoglycan docking site and the antigen binding site of Fab antibodies with the immunoglobin fold. EDTA was also found to bind to rTRD, but at a site distinct from the proposed peptidoglycan docking site.
Department of Chemistry, University of Alabama, Tuscaloosa, AL 35487, United States.
Yinghua
Y
Chen
Robin S
RS
Simmonds
Russell
R
Timkovich
D000941:Antigens / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry*; D001665:Binding Sites; D003198:Computer Simulation; D007140:Immunoglobulin Fab Fragments / Q000737:chemistry; D008956:Models, Chemical; D019906:Nuclear Magnetic Resonance, Biomolecular; D010457:Peptidoglycan / Q000737:chemistry*; D017434:Protein Structure, Tertiary
D000941:Antigens; D001426:Bacterial Proteins; D007140:Immunoglobulin Fab Fragments; D010457:Peptidoglycan; C106076:ZooA protein, Streptococcus equi
Cell wall specificity; Exoenzyme; Nuclear magnetic resonance; Peptidoglycan; Streptococcus