9JM9 image
Deposition Date 2024-09-20
Release Date 2025-06-18
Last Version Date 2025-06-18
Entry Detail
PDB ID:
9JM9
Title:
NADP-dependent oxidoreductase complexed with NADP and substrate 3
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.38 Å
R-Value Free:
0.28
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 41 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:NADP-dependent oxidoreductase
Gene (Uniprot):GLE_3219
Chain IDs:A, B
Chain Length:354
Number of Molecules:2
Biological Source:Lysobacter enzymogenes
Primary Citation
Structural Basis for Medium-Chain Dehydrogenase/Reductase-Catalyzed Reductive Cyclization in Polycyclic Tetramate Macrolactam Biosynthesis.
J.Am.Chem.Soc. 147 19253 19261 (2025)
PMID: 40406958 DOI: 10.1021/jacs.5c04971

Abstact

Few enzymes are known to catalyze reductive cyclizations via nucleophile-mediated C-C bond formation. Medium-chain dehydrogenases/reductases (MDRs) typically function as dehydrogenases or reductases. However, a distinct subclass of MDRs involved in polycyclic tetramate macrolactam (PoTeM) biosynthesis catalyzes reductive cyclizations via hydride-mediated C-C bond formation. Here, we present the apo and substrate-bound structures of OX4 and CftD, two enzymes responsible for the third ring formation in PoTeMs biosynthesis. Structural and mutational analysis reveal a catalytic mechanism wherein OX4 initiates a NADPH-dependent 1,6-reduction, followed by cyclization to form the C11-C22 bond, water-mediated protonation of the C7-carbonyl oxygen, and a final tautomerization to produce the cyclized product. Precise substrate positioning and stabilization of the enolate intermediate by the conserved residue W260 are critical for catalysis. These findings represent the first structural and mechanistic understanding of this newly identified cyclase subgroup and offer promising new avenues for enzyme engineering and natural product biosynthesis.

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