6NOR

Crystal structure of GenD2 from gentamicin A biosynthesis in complex with NAD

Summary for 6NOR

• Entry DOI: 10.2210/pdb6nor/pdb
• Descriptor: Putative NAD dependent dehydrogenase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE (3 entities in total)
• Functional Keywords: oxidoreductase, nad depedent enzyme, 3d swapping domain
• Biological source: Micromonospora echinospora
• Total number of polymer chains: 6
• Total formula weight: 236297.29

Authors

Araujo, N.C.,Bury, P.S.,Huang, F.,Leadlay, P.F.,Dias, M.V.B. (deposition date: 2019-01-16, release date: 2019-05-15, Last modification date: 2024-03-13)

Primary citation

de Araujo, N.C.,Bury, P.D.S.,Tavares, M.T.,Huang, F.,Parise-Filho, R.,Leadlay, P.,Dias, M.V.B.
Crystal Structure of GenD2, an NAD-Dependent Oxidoreductase Involved in the Biosynthesis of Gentamicin.
Acs Chem.Biol., 14:925-933, 2019

PubMed Abstract: Gentamicins are clinically relevant aminoglycoside antibiotics produced by several Micromonospora species. Gentamicins are highly methylated and functionalized molecules, and their biosynthesis include glycosyltransferases, dehydratase/oxidoreductases, aminotransferases, and methyltransferases. The biosynthesis of gentamicin A from gentamicin A2 involves three enzymatic steps that modify the hydroxyl group at position 3″ of the unusual garosamine sugar to provide its substitution for an amino group, followed by an N-methylation. The first of these reactions is catalyzed by GenD2, an oxidoreductase from the Gfo/Idh/MocA protein family, which reduces the hydroxyl at the C3″ of gentamicin A to produce 3''-dehydro-3''-oxo-gentamicin A2 (DOA2). In this work, we solved the structure of GenD2 in complex with NAD+. Although the structure of GenD2 has a similar fold to other members of the Gfo/Idh/MocA family, this enzyme has several new features, including a 3D-domain swapping of two β-strands that are involved in a novel oligomerization interface for this protein family. In addition, the active site of this enzyme also has several specialties which are possibly involved in the substrate specificity, including a number of aromatic residues and a negatively charged region, which is complementary to the polycationic aminoglycoside-substrate. Therefore, docking simulations provided insights into the recognition of gentamicin A2 and into the catalytic mechanism of GenD2. This is the first report describing the structure of an oxidoreductase involved in aminoglycoside biosynthesis and could open perspectives into producing new aminoglycoside derivatives by protein engineering.

PubMed: 30995396
DOI: 10.1021/acschembio.9b00115

Experimental method

X-RAY DIFFRACTION (2.402 Å)