6G4B

Crystal structure of the omega transaminase from Pseudomonas jessenii in the apo form, crystallized from succinate

Summary for 6G4B

• Entry DOI: 10.2210/pdb6g4b/pdb
• Descriptor: Aspartate aminotransferase family protein, SUCCINIC ACID, GLYCEROL, ... (4 entities in total)
• Functional Keywords: transaminase, aminotransferase, pyridoxamine phosphate, plp-dependent, transferase
• Biological source: Pseudomonas sp
• Total number of polymer chains: 2
• Total formula weight: 101876.03

Authors

Rozeboom, H.J.,Janssen, D.B. (deposition date: 2018-03-27, release date: 2019-04-10, Last modification date: 2024-01-17)

Primary citation

Palacio, C.M.,Rozeboom, H.J.,Lanfranchi, E.,Meng, Q.,Otzen, M.,Janssen, D.B.
Biochemical properties of a Pseudomonas aminotransferase involved in caprolactam metabolism.
Febs J., 286:4086-4102, 2019

PubMed Abstract: The biodegradation of the nylon-6 precursor caprolactam by a strain of Pseudomonas jessenii proceeds via ATP-dependent hydrolytic ring opening to 6-aminohexanoate. This non-natural ω-amino acid is converted to 6-oxohexanoic acid by an aminotransferase (PjAT) belonging to the fold type I pyridoxal 5'-phosphate (PLP) enzymes. To understand the structural basis of 6-aminohexanoatate conversion, we solved different crystal structures and determined the substrate scope with a range of aliphatic and aromatic amines. Comparison with the homologous aminotransferases from Chromobacterium violaceum (CvAT) and Vibrio fluvialis (VfAT) showed that the PjAT enzyme has the lowest K values (highest affinity) and highest specificity constant (k /K ) with the caprolactam degradation intermediates 6-aminohexanoate and 6-oxohexanoic acid, in accordance with its proposed in vivo function. Five distinct three-dimensional structures of PjAT were solved by protein crystallography. The structure of the aldimine intermediate formed from 6-aminohexanoate and the PLP cofactor revealed the presence of a narrow hydrophobic substrate-binding tunnel leading to the cofactor and covered by a flexible arginine, which explains the high activity and selectivity of the PjAT with 6-aminohexanoate. The results suggest that the degradation pathway for caprolactam has recruited an aminotransferase that is well adapted to 6-aminohexanoate degradation. DATABASE: The atomic coordinates and structure factors P. jessenii 6-aminohexanoate aminotransferase have been deposited in the PDB as entries 6G4B (E∙succinate complex), 6G4C (E∙phosphate complex), 6G4D (E∙PLP complex), 6G4E (E∙PLP-6-aminohexanoate intermediate), and 6G4F (E∙PMP complex).

PubMed: 31162815
DOI: 10.1111/febs.14950

Experimental method

X-RAY DIFFRACTION (1.8 Å)