title: The crystal structure of the adenylation enzyme VinN reveals a unique β-amino acid recognition mechanism.
abstract: Adenylation enzymes play important roles in the biosynthesis and degradation of primary and secondary metabolites. Mechanistic insights into the recognition of α-amino acid substrates have been obtained for α-amino acid adenylation enzymes. The Asp residue is invariant and is essential for the stabilization of the α-amino group of the substrate. In contrast, the β-amino acid recognition mechanism of adenylation enzymes is still unclear despite the importance of β-amino acid activation for the biosynthesis of various natural products. Herein, we report the crystal structure of the stand-alone adenylation enzyme VinN, which specifically activates (2S,3S)-3-methylaspartate (3-MeAsp) in vicenistatin biosynthesis. VinN has an overall structure similar to that of other adenylation enzymes. The structure of the complex with 3-MeAsp revealed that a conserved Asp(230) residue is used in the recognition of the β-amino group of 3-MeAsp similar to α-amino acid adenylation enzymes. A mutational analysis and structural comparison with α-amino acid adenylation enzymes showed that the substrate-binding pocket of VinN has a unique architecture to accommodate 3-MeAsp as a β-amino acid substrate. Thus, the VinN structure allows the first visualization of the interaction of an adenylation enzyme with a β-amino acid and provides new mechanistic insights into the selective recognition of β-amino acids in this family of enzymes.
authors.affiliation: From the Departments of Chemistry and.
authors.forename: Akimasa
authors.initials: A
authors.lastname: Miyanaga
authors.affiliation: Chemistry and Materials Science, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan.
authors.forename: Jolanta
authors.initials: J
authors.lastname: Cieślak
authors.affiliation: Chemistry and Materials Science, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Shinohara
authors.affiliation: From the Departments of Chemistry and.
authors.forename: Fumitaka
authors.initials: F
authors.lastname: Kudo
authors.affiliation: Chemistry and Materials Science, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan eguchi@cms.titech.ac.jp.
authors.forename: Tadashi
authors.initials: T
authors.lastname: Eguchi
mesh_terms: D000595:Amino Acid Sequence; D000617:Aminoglycosides / Q000737:chemistry*; D001426:Bacterial Proteins / Q000737:chemistry*; D018360:Crystallography, X-Ray; D004252:DNA Mutational Analysis; D004926:Escherichia coli / Q000378:metabolism; D006860:Hydrogen Bonding; D007769:Lactams / Q000737:chemistry*; D018942:Macrolides / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D016202:N-Methylaspartate / Q000737:chemistry; D009713:Nucleotidyltransferases / Q000737:chemistry*; D010802:Phylogeny; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011994:Recombinant Proteins / Q000737:chemistry; D017386:Sequence Homology, Amino Acid; D013302:Streptomyces / Q000201:enzymology*; D013379:Substrate Specificity
chemical_list: D000617:Aminoglycosides; D001426:Bacterial Proteins; D007769:Lactams; D018942:Macrolides; D011994:Recombinant Proteins; C082785:vicenistatin; D016202:N-Methylaspartate; D009713:Nucleotidyltransferases
keywords: Adenylation Enzyme; Antibiotics; Biosynthesis; Polyketide; Structural Biology; X-ray Crystallography; β-Amino Acid