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Integrative structural biology of the penicillin-binding protein-1 from Staphylococcus aureus, an essential component of the divisome machinery

DOI: 10.1016/j.csbj.2021.09.018 DOI Help

Authors: Siseth Martínez-Caballero (Institute of Physical Chemistry “Rocasolano”, CSIC,) , Kiran V. Mahasenan (University of Notre Dame) , Choon Kim (University of Notre Dame) , Rafael Molina (Institute of Physical Chemistry “Rocasolano”, CSIC) , Rhona Feltzer (University of Notre Dame) , Mijoon Lee (University of Notre Dame) , Renee Bouley (University of Notre Dame) , Dusan Hesek (University of Notre Dame) , Jed F. Fisher (University of Notre Dame) , Ines G. Munoz (Spanish National Cancer Research Center (CNIO)) , Mayland Chang (University of Notre Dame) , Shahriar Mobashery (University of Notre Dame) , Juan A. Hermoso (Institute of Physical Chemistry “Rocasolano”, CSIC)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Computational And Structural Biotechnology Journal , VOL 19 , PAGES 5392 - 5405

State: Published (Approved)
Published: October 2021

Open Access Open Access

Abstract: The penicillin-binding proteins are the enzyme catalysts of the critical transpeptidation crosslinking polymerization reaction of bacterial peptidoglycan synthesis and the molecular targets of the penicillin antibiotics. Here, we report a combined crystallographic, small-angle X-ray scattering (SAXS) in-solution structure, computational and biophysical analysis of PBP1 of Staphylococcus aureus (saPBP1), providing mechanistic clues about its function and regulation during cell division. The structure reveals the pedestal domain, the transpeptidase domain, and most of the linker connecting to the “penicillin-binding protein and serine/threonine kinase associated” (PASTA) domains, but not its two PASTA domains, despite their presence in the construct. To address this absence, the structure of the PASTA domains was determined at 1.5 Å resolution. Extensive molecular-dynamics simulations interpret the PASTA domains of saPBP1 as conformationally mobile and separated from the transpeptidase domain. This conclusion was confirmed by SAXS experiments on the full-length protein in solution. A series of crystallographic complexes with β-lactam antibiotics (as inhibitors) and penta-Gly (as a substrate mimetic) allowed the molecular characterization of both inhibition by antibiotics and binding for the donor and acceptor peptidoglycan strands. Mass-spectrometry experiments with synthetic peptidoglycan fragments revealed binding by PASTA domains in coordination with the remaining domains. The observed mobility of the PASTA domain in saPBP1 could play a crucial role for in vivo interaction with its glycosyltransferase partner in the membrane or with other components of the divisome machinery, as well as for coordination of transpeptidation and polymerization processes in the bacterial divisome.

Journal Keywords: Divisome; Staphylococcus aureus; X-ray crystal structure; SAXS in-solution structure; Molecular dynamics simulations; PBP1; PASTA domains; Antibiotics inhibition; Peptidoglycan binding

Diamond Keywords: Bacteria; Enzymes

Subject Areas: Biology and Bio-materials

Instruments: B21-High Throughput SAXS

Other Facilities: XALOC at ALBA

Added On: 28/10/2021 09:23


Discipline Tags:

Pathogens Antibiotic Resistance Infectious Diseases Health & Wellbeing Structural biology Drug Discovery Life Sciences & Biotech

Technical Tags:

Scattering Small Angle X-ray Scattering (SAXS)