title: The dimerization domain in DapE enzymes is required for catalysis.
abstract: The emergence of antibiotic-resistant bacterial strains underscores the importance of identifying new drug targets and developing new antimicrobial compounds. Lysine and meso-diaminopimelic acid are essential for protein production and bacterial peptidoglycan cell wall remodeling and are synthesized in bacteria by enzymes encoded within dap operon. Therefore dap enzymes may serve as excellent targets for developing a new class of antimicrobial agents. The dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) converts N-succinyl-L,L-diaminopimelic acid to L,L-diaminopimelic acid and succinate. The enzyme is composed of catalytic and dimerization domains, and belongs to the M20 peptidase family. To understand the specific role of each domain of the enzyme we engineered dimerization domain deletion mutants of DapEs from Haemophilus influenzae and Vibrio cholerae, and characterized these proteins structurally and biochemically. No activity was observed for all deletion mutants. Structural comparisons of wild-type, inactive monomeric DapE enzymes with other M20 peptidases suggest that the dimerization domain is essential for DapE enzymatic activity. Structural analysis and molecular dynamics simulations indicate that removal of the dimerization domain increased the flexibility of a conserved active site loop that may provide critical interactions with the substrate.
authors.affiliation: Center for Structural Genomics of Infectious Diseases, Computation Institute, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Boguslaw
authors.initials: B
authors.lastname: Nocek
authors.affiliation: The Department of Chemistry and Biochemistry, Loyola University-Chicago, Chicago, Illinois, United States of America.
authors.forename: Anna
authors.initials: A
authors.lastname: Starus
authors.affiliation: Center for Structural Genomics of Infectious Diseases, Computation Institute, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Magdalena
authors.initials: M
authors.lastname: Makowska-Grzyska
authors.affiliation: The Department of Chemistry and Biochemistry, Loyola University-Chicago, Chicago, Illinois, United States of America.
authors.forename: Blanca
authors.initials: B
authors.lastname: Gutierrez
authors.affiliation: The Department of Chemistry and Biochemistry, Loyola University-Chicago, Chicago, Illinois, United States of America.
authors.forename: Stephen
authors.initials: S
authors.lastname: Sanchez
authors.affiliation: The Midwest Center for Structural Genomics, Bioscience Division, Argonne National Laboratory, Lemont, Illinois, United States of America.
authors.forename: Robert
authors.initials: R
authors.lastname: Jedrzejczak
authors.affiliation: The Midwest Center for Structural Genomics, Bioscience Division, Argonne National Laboratory, Lemont, Illinois, United States of America.
authors.forename: Jamey C
authors.initials: JC
authors.lastname: Mack
authors.affiliation: The Department of Chemistry and Biochemistry, Loyola University-Chicago, Chicago, Illinois, United States of America.
authors.forename: Kenneth W
authors.initials: KW
authors.lastname: Olsen
authors.affiliation: Center for Structural Genomics of Infectious Diseases, Computation Institute, University of Chicago, Chicago, Illinois, United States of America; The Midwest Center for Structural Genomics, Bioscience Division, Argonne National Laboratory, Lemont, Illinois, United States of America.
authors.forename: Andrzej
authors.initials: A
authors.lastname: Joachimiak
authors.affiliation: Department of Chemistry, Marquette University, Milwaukee, Wisconsin, United States of America.
authors.forename: Richard C
authors.initials: RC
authors.lastname: Holz
mesh_terms: D000581:Amidohydrolases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D002384:Catalysis; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D016297:Mutagenesis, Site-Directed; D009154:Mutation; D014734:Vibrio cholerae / Q000201:enzymology
chemical_list: D000581:Amidohydrolases; D001426:Bacterial Proteins; C054685:N-succinyl-l,l-diaminopimelic acid desuccinylase