7XXR

Orf1 R342A-glycylthricin complex

Summary for 7XXR

• Entry DOI: 10.2210/pdb7xxr/pdb
• Descriptor: N-formimidoyl fortimicin A synthase, FLAVIN-ADENINE DINUCLEOTIDE, [(2~{R},3~{R},4~{S},5~{R},6~{R})-6-[(~{E})-[(3~{a}~{S},7~{R},7~{a}~{S})-7-oxidanyl-4-oxidanylidene-3,3~{a},5,6,7,7~{a}-hexahydro-1~{H}-imidazo[4,5-c]pyridin-2-ylidene]amino]-5-(2-azanylethanoylamino)-2-(hydroxymethyl)-4-oxidanyl-oxan-3-yl] carbamate, ... (4 entities in total)
• Functional Keywords: oxidoreductase
• Biological source: Streptomyces luteocolor
• Total number of polymer chains: 8
• Total formula weight: 449470.02

Authors

Wang, Y.L.,Li, T.L. (deposition date: 2022-05-30, release date: 2023-05-31, Last modification date: 2023-11-29)

Primary citation

Wang, Y.L.,Chang, C.Y.,Hsu, N.S.,Lo, I.W.,Lin, K.H.,Chen, C.L.,Chang, C.F.,Wang, Z.C.,Ogasawara, Y.,Dairi, T.,Maruyama, C.,Hamano, Y.,Li, T.L.
N-Formimidoylation/-iminoacetylation modification in aminoglycosides requires FAD-dependent and ligand-protein NOS bridge dual chemistry.
Nat Commun, 14:2528-2528, 2023

PubMed Abstract: Oxidized cysteine residues are highly reactive and can form functional covalent conjugates, of which the allosteric redox switch formed by the lysine-cysteine NOS bridge is an example. Here, we report a noncanonical FAD-dependent enzyme Orf1 that adds a glycine-derived N-formimidoyl group to glycinothricin to form the antibiotic BD-12. X-ray crystallography was used to investigate this complex enzymatic process, which showed Orf1 has two substrate-binding sites that sit 13.5 Å apart unlike canonical FAD-dependent oxidoreductases. One site could accommodate glycine and the other glycinothricin or glycylthricin. Moreover, an intermediate-enzyme adduct with a NOS-covalent linkage was observed in the later site, where it acts as a two-scissile-bond linkage facilitating nucleophilic addition and cofactor-free decarboxylation. The chain length of nucleophilic acceptors vies with bond cleavage sites at either N-O or O-S accounting for N-formimidoylation or N-iminoacetylation. The resultant product is no longer sensitive to aminoglycoside-modifying enzymes, a strategy that antibiotic-producing species employ to counter drug resistance in competing species.

PubMed: 37137912
DOI: 10.1038/s41467-023-38218-w

Experimental method

X-RAY DIFFRACTION (2.4 Å)