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International Journal of Systematic and... Feb 2020Two Gram-staining-negative, facultatively anaerobic, motile, short clavate and flagellated marine bacteria, designated strains BEI233 and LJC006, were isolated from the...
Two Gram-staining-negative, facultatively anaerobic, motile, short clavate and flagellated marine bacteria, designated strains BEI233 and LJC006, were isolated from the East China Sea. On the basis of the results of 16S rRNA gene sequencing and multilocus sequence analysis, BEI233 and LJC006 should be assigned to the genus . The closest phylogenetic relatives of BEI233 are LMG 19158 (98.7 % 16S rRNA gene sequence pairwise similarity), DSM 14397 (98.5 %), KCTC 42287 (97.7 %), ATCC 35048 (97.3 %) and MD16 (96.5 %), whereas for LJC006 they were CAIM 518 (97.1 %), LMG 7894 (97.0%), JCM 16456 (96.9 %) and LMG 21346 (96.1 %). The growth of BEI233 occurred at 10-37 °C, pH 5.0-8.0 and with 1-7 % (w/v) NaCl, while the growth of LJC006 occurred at 10-37 °C, pH 6.0-9.0, and 0-8 % (w/v) NaCl. The predominant fatty acids (>10 %) were summed feature 3 (Cω7 or/and Cω6), C and summed feature 8 (Cω7 or/and Cω6), with different proportions. The DNA G+C contents of BEI233 and LJC006 are 42.41 mol% and 41.88 mol%, respectively. On the basis of the results of polyphasic analysis, BEI233 and LJC006 are considered to represent novel species of the genus for which the names sp. nov. and sp. nov. are proposed. The type strains are BEI233 (=JCM 32692=KCTC 62618) and LJC006 (=JCM 32693=KCTC 62620), respectively.
Topics: Bacterial Typing Techniques; Base Composition; China; DNA, Bacterial; Fatty Acids; Multilocus Sequence Typing; Nucleic Acid Hybridization; Phylogeny; RNA, Ribosomal, 16S; Seawater; Sequence Analysis, DNA; Vibrio
PubMed: 31702534
DOI: 10.1099/ijsem.0.003842 -
Computational and Structural... 2019Transaminases (TAs) reversibly catalyze the transfer reaction of an amino group between an amino group donor and an amino group acceptor, using pyridoxal 5'-phosphate... (Review)
Review
Transaminases (TAs) reversibly catalyze the transfer reaction of an amino group between an amino group donor and an amino group acceptor, using pyridoxal 5'-phosphate (PLP) as a cofactor. TAs are categorized according to the amino group position of the donor substrate and respective TAs recognize their own specific substrates. Over the past decade, a number of TA structures have been determined by X-ray crystallography. On the basis of the structural information, the detailed mechanism of substrate recognition by TAs has also been elucidated. In this review, fold type I TAs are addressed intensively. Comparative studies on structural differences between the apo and holo forms of fold type I TAs have demonstrated that regions containing the active site exhibit structural plasticity in the apo form, facilitating PLP insertion into the active site. In addition, given that TAs recognize two different kinds of substrates, they possess dual substrate specificity. It is known that spatial rearrangements of active site residues occur upon binding of the substrates. Intriguingly, positively charged residues are predominantly distributed at the active site cavity. The electric field generated by such charge distributions may attract negatively charged molecules, such as PLP and amino group acceptors, into the active site. Indeed, TAs show remarkable dynamics in diverse aspects. In this review, we describe the comprehensive working mechanism of fold type I TAs, with a focus on conformational changes.
PubMed: 31452855
DOI: 10.1016/j.csbj.2019.07.007 -
The FEBS Journal Oct 2019The biodegradation of the nylon-6 precursor caprolactam by a strain of Pseudomonas jessenii proceeds via ATP-dependent hydrolytic ring opening to 6-aminohexanoate. This...
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).
Topics: Amino Acid Sequence; Aminocaproic Acid; Bacterial Proteins; Caprolactam; Crystallography, X-Ray; Models, Molecular; Phylogeny; Pseudomonas; Pyridoxal Phosphate; Sequence Homology; Substrate Specificity; Transaminases
PubMed: 31162815
DOI: 10.1111/febs.14950