5Z83 image
Entry Detail
PDB ID:
5Z83
Keywords:
Title:
Crystal structure of GenB1 from Micromonospora echinospora in complex with PLP (internal aldimine)
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2018-01-30
Release Date:
2019-01-16
Method Details:
Experimental Method:
Resolution:
1.70 Å
R-Value Free:
0.19
R-Value Work:
0.15
R-Value Observed:
0.15
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:C-6' aminotransferase
Chain IDs:A, B
Chain Length:437
Number of Molecules:2
Biological Source:Micromonospora echinospora
Primary Citation
Complete reconstitution of the diverse pathways of gentamicin B biosynthesis.
Nat. Chem. Biol. 15 295 303 (2019)
PMID: 30643280 DOI: 10.1038/s41589-018-0203-4

Abstact

Gentamicin B (GB), a valuable starting material for the preparation of the semisynthetic aminoglycoside antibiotic isepamicin, is produced in trace amounts by the wild-type Micromonospora echinospora. Though the biosynthetic pathway to GB has remained obscure for decades, we have now identified three hidden pathways to GB production via seven hitherto unknown intermediates in M. echinospora. The narrow substrate specificity of a key glycosyltransferase and the C6'-amination enzymes, in combination with the weak and unsynchronized gene expression of the 2'-deamination enzymes, limits GB production in M. echinospora. The crystal structure of the aminotransferase involved in C6'-amination explains its substrate specificity. Some of the new intermediates displayed similar premature termination codon readthrough activity but with reduced toxicity compared to the natural aminoglycoside G418. This work not only led to the discovery of unknown biosynthetic routes to GB, but also demonstrated the potential to mine new aminoglycosides from nature for drug discovery.

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