3WVN
Complex structure of VinN with L-aspartate
Summary for 3WVN
| Entry DOI | 10.2210/pdb3wvn/pdb |
| Related | 3WV4 3WV5 |
| Descriptor | Non-ribosomal peptide synthetase, ASPARTIC ACID (3 entities in total) |
| Functional Keywords | five-layered alpha-beta-alpha-beta-alpha sandwich fold, ligase, atp binding |
| Biological source | Streptomyces halstedii |
| Total number of polymer chains | 2 |
| Total formula weight | 118090.01 |
| Authors | Miyanaga, A.,Cieslak, J.,Shinohara, Y.,Kudo, F.,Eguchi, T. (deposition date: 2014-05-30, release date: 2014-10-01, Last modification date: 2023-11-08) |
| Primary citation | Miyanaga, A.,Cieslak, J.,Shinohara, Y.,Kudo, F.,Eguchi, T. The crystal structure of the adenylation enzyme VinN reveals a unique beta-amino acid recognition mechanism J.Biol.Chem., 289:31448-31457, 2014 Cited by PubMed 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. PubMed: 25246523DOI: 10.1074/jbc.M114.602326 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.2 Å) |
Structure validation
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