title: Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition.
abstract: Peptidoglycan surrounds the bacterial cytoplasmic membrane to protect the cell against osmolysis. The biosynthesis of peptidoglycan, made of glycan strands crosslinked by short peptides, is the target of antibiotics like β-lactams and glycopeptides. Nascent peptidoglycan contains pentapeptides that are trimmed by carboxypeptidases to tetra- and tripeptides. The well-characterized DD-carboxypeptidases hydrolyze the terminal D-alanine from the stem pentapeptide to produce a tetrapeptide. However, few LD-carboxypeptidases that produce tripeptides have been identified, and nothing is known about substrate specificity in these enzymes. We report biochemical properties and crystal structures of the LD-carboxypeptidases LdcB from Streptococcus pneumoniae, Bacillus anthracis, and Bacillus subtilis. The enzymes are active against bacterial cell wall tetrapeptides and adopt a zinc-carboxypeptidase fold characteristic of the LAS superfamily. We have also solved the structure of S. pneumoniae LdcB with a product mimic, elucidating the residues essential for peptidoglycan recognition and the conformational changes that occur on ligand binding.
authors.affiliation: Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
authors.forename: Christopher N
authors.initials: CN
authors.lastname: Hoyland
authors.affiliation: Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK.
authors.forename: Christine
authors.initials: C
authors.lastname: Aldridge
authors.affiliation: Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Cleverley
authors.affiliation: Institut des Sciences de la Vie, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium.
authors.forename: Marie-Clémence
authors.initials: MC
authors.lastname: Duchêne
authors.affiliation: Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Structural Genomics of Infectious Diseases (CSGID).
authors.forename: George
authors.initials: G
authors.lastname: Minasov
authors.affiliation: Center for Structural Genomics of Infectious Diseases (CSGID); Department of Chemical Engineering and Applied Chemistry, 200 College Street, University of Toronto, Toronto, ON M5G 1L6, Canada.
authors.forename: Olena
authors.initials: O
authors.lastname: Onopriyenko
authors.affiliation: Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK.
authors.forename: Karzan
authors.initials: K
authors.lastname: Sidiq
authors.affiliation: Center for Structural Genomics of Infectious Diseases (CSGID); Department of Chemical Engineering and Applied Chemistry, 200 College Street, University of Toronto, Toronto, ON M5G 1L6, Canada.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Stogios
authors.affiliation: Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Structural Genomics of Infectious Diseases (CSGID).
authors.forename: Wayne F
authors.initials: WF
authors.lastname: Anderson
authors.affiliation: Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Daniel
authors.affiliation: Center for Structural Genomics of Infectious Diseases (CSGID); Department of Chemical Engineering and Applied Chemistry, 200 College Street, University of Toronto, Toronto, ON M5G 1L6, Canada.
authors.forename: Alexei
authors.initials: A
authors.lastname: Savchenko
authors.affiliation: Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK.
authors.forename: Waldemar
authors.initials: W
authors.lastname: Vollmer
authors.affiliation: Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK. Electronic address: r.lewis@ncl.ac.uk.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Lewis
mesh_terms: D000595:Amino Acid Sequence; D001408:Bacillus anthracis / Q000201:enzymology; D001412:Bacillus subtilis / Q000201:enzymology; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D002236:Carbohydrate Conformation; D002268:Carboxypeptidases / Q000737:chemistry* / Q000378:metabolism; D018360:Crystallography, X-Ray; D007700:Kinetics; D008958:Models, Molecular; D010457:Peptidoglycan / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013296:Streptococcus pneumoniae / Q000201:enzymology
chemical_list: D001426:Bacterial Proteins; D010457:Peptidoglycan; D002268:Carboxypeptidases; C021505:LD-carboxypeptidase