7CL5
The crystal structure of KanJ in complex with kanamycin B and N-oxalylglycine
Summary for 7CL5
| Entry DOI | 10.2210/pdb7cl5/pdb |
| Descriptor | Kanamycin B dioxygenase, NICKEL (II) ION, N-OXALYLGLYCINE, ... (5 entities in total) |
| Functional Keywords | dioxygenase, kanamycin biosynthesis, oxidoreductase |
| Biological source | Streptomyces kanamyceticus |
| Total number of polymer chains | 6 |
| Total formula weight | 205760.46 |
| Authors | Kitayama, Y.,Miyanaga, A.,Kudo, F.,Eguchi, T. (deposition date: 2020-07-20, release date: 2021-01-13, Last modification date: 2023-11-29) |
| Primary citation | Kudo, F.,Kitayama, Y.,Miyanaga, A.,Numakura, M.,Eguchi, T. Stepwise Post-glycosylation Modification of Sugar Moieties in Kanamycin Biosynthesis. Chembiochem, 22:1668-1675, 2021 Cited by PubMed Abstract: Kanamycin A is the major 2-deoxystreptamine (2DOS)-containing aminoglycoside antibiotic produced by Streptomyces kanamyceticus. The 2DOS moiety is linked with 6-amino-6-deoxy-d-glucose (6ADG) at O-4 and 3-amino-3-deoxy-d-glucose at O-6. Because the 6ADG moiety is derived from d-glucosamine (GlcN), deamination at C-2 and introduction of C-6-NH are required in the biosynthesis. A dehydrogenase, KanQ, and an aminotransferase, KanB, are presumed to be responsible for the introduction of C-6-NH , although the substrates have not been identified. Here, we examined the substrate specificity of KanQ to better understand the biosynthetic pathway. It was found that KanQ oxidized kanamycin C more efficiently than the 3''-deamino derivative. Furthermore, the substrate specificity of an oxygenase, KanJ, that is responsible for deamination at C-2 of the GlcN moiety was examined, and the crystal structure of KanJ was determined. It was found that C-6-NH is important for substrate recognition by KanJ. Thus, the modification of the GlcN moiety occurs after pseudo-trisaccharide formation, followed by the introduction of C-6-NH by KanQ/KanB and deamination at C-2 by KanJ. PubMed: 33403742DOI: 10.1002/cbic.202000839 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.5 Å) |
Structure validation
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