Accumulation of 2-deoxy-scyllo-inosamine by a 2-deoxystreptamine-requiring idiotroph of Micromonospora sagamiensis

Biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics

The 2-deoxystreptamine-containing aminoglycosides are an important class of clinically valuable antibiotics. A deep understanding of the biosynthesis of these natural products is required to enable efforts to rationally manipulate and engineer the biological production of novel aminoglycosides. This review discusses the development of our biosynthetic knowledge over the past half-century, with emphasis on the relatively recent contributions of molecular biology to the elucidation of these biosynthetic pathways.

Active Site Mapping of 2-Deoxy-scyllo-inosose Synthase, the Key Starter Enzyme for the Biosynthesis of 2-Deoxystreptamine. Mechanism-Based Inhibition and Identification of Lysine-141 as the Entrapped Nucleophile

A key enzyme in the biosynthesis of clinically important aminoglycoside antibiotics including neomycin, kanamycin, gentamicin, etc. is 2-deoxy-scyllo-inosose synthase (DOIS), which catalyzes the carbocycle formation from d-glucose-6-phosphate to 2-deoxy-scyllo-inosose (DOI). To clarify its precise reaction mechanism and crucial amino acid residues in the active site, we took advantage of a mechanism-based inhibitor carbaglucose-6-phosphate (pseudo-dl-glucose, C-6-P) with anticipation of its conversion to a reactive alpha,beta-unsaturated carbonyl intermediate. It turned out that C-6-P clearly showed time- and concentration-dependent inhibition against DOIS, and the molecular mass of the resulting modified-DOIS with C-6-P was 160 mass units larger than that of native DOIS. Thus, the expected alpha,beta-unsaturated intermediate appeared to trap a specific nucleophilic group in the active site through the Michael-type 1,4-addition. The covalently modified amino acid residue was determined to be Lys-141 by means of enzymatic digestion and subsequent LC/MS and LC/MS/MS of the digest. Also discussed are the role of Lys-141 in the substrate recognition and the reaction pathway and comparison with evolutionary related dehydroquinate synthase.

Importance of specific hydrogen-bond donor-acceptor interactions for the key carbocycle-forming reaction catalyzed by 2-deoxy-scyllo-inosose synthase in the biosynthesis of 2-deoxystreptamine-containing aminocyclitol antibiotics

A crucial enzyme in the biosynthesis of the 2-deoxystreptamine aglycon of clinically important aminocyclitol antibiotics is 2-deoxy-scyllo-inosose synthase (DOIS), which converts ubiquitous D-glucose 6-phosphate (G-6-P) into the specific carbocycle 2-deoxy-scyllo-inosose. Among all the oxygenated carbons of the substrate, C-1, -4, -5, and -6 are directly involved in the chemical transformation. To get insight into the roles of C-2 and C-3 hydroxy groups, 2-deoxy-2-fluoro-, 3-deoxy-3-fluoro-, 2-amino-2-deoxy-, and 3-amino-3-deoxy-D-glucose 6-phosphates (2-F-G-6-P, 3-F-G-6-P, 2-NH(2)-G-6-P, and 3-NH(2)-G-6-P, respectively) were subjected to the DOIS reaction as probe, since a fluorine substituent generally acts as a hydrogen-bond acceptor, and an ammonium functionality derived physiologically from an amino group as a hydrogen-bond donor. Among those tested, 2-F-G-6-P and 3-NH(2)-G-6-P were used as substrates by DOIS and were converted into the corresponding deoxyfluoro- and aminodeoxy-scyllo-inososes, respectively. In contrast, 3-F-G-6-P and 2-NH(2)-G-6-P were inactive in the cyclization reaction. Clearly, DOIS recognizes the G-6-P substrate through specific hydrogen-bonding interactions, i.e., through a hydrogen-donating group for C-2 and an accepting group for C-3 of the substrate. Modeling of DOIS based on the structure of evolutionary-related dehydroquinate synthase is also described.

Substrate specificity of 2-deoxy-scyllo-inosose synthase, the starter enzyme for 2-deoxystreptamine biosynthesis, toward deoxyglucose-6-phosphates and proposed mechanism

A crucial enzyme in the biosynthesis of the 2-deoxystreptamine aglycon of clinically important aminocyclitol antibiotics is 2-deoxy-scyllo-inosose synthase (DOIS), which is responsible for the initial carbocycle formation of 2-deoxy-scyllo-inosose (1) from D-glucose-6-phosphate (G-6-P) (2). To get more insight into the mechanism and substrate specificity, deoxy-D-glucose-6-phosphates (deoxy-G-6-P) were chemically synthesized and subjected to the reaction with DOIS. The enzyme appeared to use 2-deoxy- and 3-deoxy-G-6-P as substrates, both of which were converted into the corresponding dideoxy-scyllo-inosose products, but 4-deoxy-G-6-P failed in cyclization by DOIS. These results clearly support the proposed reaction mechanism involving the initial oxidation at C-4 of the G-6-P substrate. Another implication is the potential use of DOIS for the preparation of useful dideoxyinososes.