7CL2

The crystal structure of KanJ

Summary for 7CL2

• Entry DOI: 10.2210/pdb7cl2/pdb
• Descriptor: Kanamycin B dioxygenase, NICKEL (II) ION, SULFATE ION, ... (5 entities in total)
• Functional Keywords: dioxygenase, kanamycin biosynthesis, oxidoreductase
• Biological source: Streptomyces kanamyceticus
• Total number of polymer chains: 6
• Total formula weight: 202737.43

Authors

Kitayama, Y.,Miyanaga, A.,Kudo, F.,Eguchi, T. (deposition date: 2020-07-20, release date: 2021-01-13, Last modification date: 2024-03-27)

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

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: 33403742
DOI: 10.1002/cbic.202000839

Experimental method

X-RAY DIFFRACTION (2 Å)