title: The Class D beta-lactamase family: residues governing the maintenance and diversity of function.
abstract: Class D β-lactamases, a major source of bacterial resistance to β-lactam antibiotic therapies, represent a distinct subset of the β-lactamase superfamily. They share a serine hydrolase mechanism with Classes A/C vs. Class B. Further understanding of their sequence-structure-function relationships would benefit efforts to design a new generation of antibiotics as well as to predict evolutionary mechanisms in response to such therapies. Here we describe analyses based on our high-resolution multiple sequence alignment and phylogenetic tree of ∼80 Class D β-lactamases that leverage several 3D structures of these enzymes. We observe several sequence clusters on the phylogenetic tree, some that are species specific while others include several species from α-, β- and γ-proteobacteria. Residues characteristic of a specific cluster were identified and shown to be located just outside the active site, possibly modulating the function of the catalytic residues to facilitate reactions with specific types of β-lactams. Most significant was the discovery of a likely disulfide bond in a large group composed of α-, β- and γ-proteobacteria that would contribute to enzyme stability and hence bacterial viability under antibiotic assault. A network of co-evolving residues was identified which suggested the importance of maintaining a surface for binding a highly conserved Phe69.
authors.affiliation: Department of Cell and Molecular Biology, Grand Valley State University, Henry Hall, 1 Campus Drive, Allendale, MI 49401, USA.
authors.forename: Agnieszka
authors.initials: A
authors.lastname: Szarecka
authors.forename: Kimberly R
authors.initials: KR
authors.lastname: Lesnock
authors.forename: Carlos A
authors.initials: CA
authors.lastname: Ramirez-Mondragon
authors.forename: Hugh B
authors.initials: HB
authors.lastname: Nicholas
authors.forename: Troy
authors.initials: T
authors.lastname: Wymore
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites; D002384:Catalysis; D004220:Disulfides / Q000737:chemistry / Q000378:metabolism; D019277:Entropy; D006860:Hydrogen Bonding; D008958:Models, Molecular; D010802:Phylogeny; D020560:Proteobacteria / Q000737:chemistry / Q000201:enzymology* / Q000235:genetics / Q000378:metabolism; D013329:Structure-Activity Relationship; D001618:beta-Lactamases / Q000737:chemistry* / Q000145:classification / Q000235:genetics / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D004220:Disulfides; D001618:beta-Lactamases