title: Functional annotation and structural characterization of a novel lactonase hydrolyzing D-xylono-1,4-lactone-5-phosphate and L-arabino-1,4-lactone-5-phosphate.
abstract: A novel lactonase from Mycoplasma synoviae 53 (MS53_0025) and Mycoplasma agalactiae PG2 (MAG_6390) was characterized by protein structure determination, molecular docking, gene context analysis, and library screening. The crystal structure of MS53_0025 was determined to a resolution of 2.06 Å. This protein adopts a typical amidohydrolase (β/α)8-fold and contains a binuclear zinc center located at the C-terminal end of the β-barrel. A phosphate molecule was bound in the active site and hydrogen bonds to Lys217, Lys244, Tyr245, Arg275, and Tyr278. Both docking and gene context analysis were used to narrow the theoretical substrate profile of the enzyme, thus directing empirical screening to identify that MS53_0025 and MAG_6390 catalyze the hydrolysis of d-xylono-1,4-lactone-5-phosphate (2) with kcat/Km values of 4.7 × 10(4) and 5.7 × 10(4) M(-1) s(-1) and l-arabino-1,4-lactone-5-phosphate (7) with kcat/Km values of 1.3 × 10(4) and 2.2 × 10(4) M(-1) s(-1), respectively. The identification of the substrate profile of these two phospho-furanose lactonases emerged only when all methods were integrated and therefore provides a blueprint for future substrate identification of highly related amidohydrolase superfamily members.
authors: Department of Pharmaceutical Chemistry, University of California, San Francisco , 1700 Fourth Street, San Francisco, California 94158-2330, United States.
authors: Magdalena
authors: M
authors: Korczynska
authors: Dao Feng
authors: DF
authors: Xiang
authors: Zhening
authors: Z
authors: Zhang
authors: Chengfu
authors: C
authors: Xu
authors: Tamari
authors: T
authors: Narindoshvili
authors: Siddhesh S
authors: SS
authors: Kamat
authors: Howard J
authors: HJ
authors: Williams
authors: Shawn S
authors: SS
authors: Chang
authors: Peter
authors: P
authors: Kolb
authors: Brandan
authors: B
authors: Hillerich
authors: J Michael
authors: JM
authors: Sauder
authors: Stephen K
authors: SK
authors: Burley
authors: Steven C
authors: SC
authors: Almo
authors: Subramanyam
authors: S
authors: Swaminathan
authors: Brian K
authors: BK
authors: Shoichet
authors: Frank M
authors: FM
authors: Raushel
mesh_terms: D000581:Amidohydrolases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D018360:Crystallography, X-Ray; D007783:Lactones / Q000737:chemistry* / Q000378:metabolism; D062105:Molecular Docking Simulation; D045805:Mycoplasma synoviae / Q000201:enzymology* / Q000235:genetics; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013403:Sugar Phosphates / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D007783:Lactones; D013403:Sugar Phosphates; C122021:arabinonolactone-5-phosphate; D000581:Amidohydrolases