9DQR

Crystal structure of HrmJ from Streptomyces sp. Ag109_G2-6 (HrmJ-ssa) complexed with vanadyl(IV)-oxo and succinate

Summary for 9DQR

• Entry DOI: 10.2210/pdb9dqr/pdb
• Descriptor: 2OG-Fe dioxygenase family protein, SUCCINIC ACID, oxovanadium(2+), ... (4 entities in total)
• Functional Keywords: hydroxylase, non-heme iron 2og enzyme, oxidoreductase
• Biological source: Streptomyces sp. Ag109_G2-6
• Total number of polymer chains: 2
• Total formula weight: 59061.59

Authors

Zheng, Y.-C.,Chang, W.-C. (deposition date: 2024-09-24, release date: 2025-02-12, Last modification date: 2025-03-05)

Primary citation

Zheng, Y.C.,Li, X.,Cha, L.,Paris, J.C.,Michael, C.,Ushimaru, R.,Ogasawara, Y.,Abe, I.,Guo, Y.,Chang, W.C.
Comparison of a Nonheme Iron Cyclopropanase with a Homologous Hydroxylase Reveals Mechanistic Features Associated with Distinct Reaction Outcomes.
J.Am.Chem.Soc., 147:6162-6170, 2025

PubMed Abstract: Despite the diversity of reactions catalyzed by mononuclear iron and 2-oxoglutarate-dependent enzymes, the factors that lead to diverse reaction outcomes beyond canonical hydroxylation remain elusive. Cyclopropanation reactions are of particular interest not only due to the prevalence of cyclopropane moieties in pharmaceuticals but also due to the chemistry that allows cyclopropanation to outcompete oxygen rebound. HrmJ is one such cyclopropanase from the biosynthetic pathway of hormaomycin; however, a homologue is herein discovered that instead catalyzes -hydroxylation of the same nitro enolate substrate. These enzymes were reconstituted with Mn(II) and V(IV)═O as mimics of the resting (Fe(II)) and reactive (Fe(IV)═O) intermediate states, respectively. Corresponding crystal structures of the cyclopropanase bound with a substrate imply H atom transfer via an offline π-pathway. In contrast, analogous structural analysis of the hydroxylase implies H atom abstraction likely proceeds through a σ-pathway. Preparation of isotopically labeled substrates and stopped-flow kinetic analyses indicate that while the hydrogen of C4 is abstracted in both enzymes, the Fe(IV)═O intermediate reacts ca. 17-fold faster in the active site of the hydroxylase, consistent with the mechanistic assignments. These results also support a correlation between the mechanism of H atom transfer and the subsequent fate of the substrate radical once generated. A subtle difference in substrate positioning not only affects the H atom abstraction pathway but also allows the nitro enolate moiety to intercept the resulting substrate radical in the active site of the cyclopropase, thereby facilitating intramolecular C-C bond formation in a stereoselective manner.

PubMed: 39901767
DOI: 10.1021/jacs.4c17741

Experimental method

X-RAY DIFFRACTION (2 Å)