9SCF

Fe(II)-2-oxoglutarate-dependent Pseudomonas savastanoi pv phaseolicola 1449B in complex with 2-oxoglutarate

Summary for 9SCF

• Entry DOI: 10.2210/pdb9scf/pdb
• Descriptor: 2-oxoglutarate-dependent ethylene/succinate-forming enzyme, MANGANESE (II) ION, 2-OXOGLUTARIC ACID, ... (4 entities in total)
• Functional Keywords: oxodoreductase, iron, oxidoreductase
• Biological source: Pseudomonas savastanoi
• Total number of polymer chains: 1
• Total formula weight: 38311.25

Authors

Sun, Y.,Dhingra, S.,Allen, M.,Brewitz, L.,Schofield, C.J. (deposition date: 2025-08-10, release date: 2026-03-18)

Primary citation

Sun, Y.,Dhingra, S.,Allen, M.D.,Cheng, E.S.Z.,Zhang, Z.,Schofield, C.J.,Brewitz, L.
Structural and Functional Validation of Pseudomonas Savastanoi Ethylene Forming Enzymes Reveals Flexibility in 2-Oxoglutarate Binding Mode and Conformation.
Chembiochem, 27:e202500702-e202500702, 2026

PubMed Abstract: Pseudomonas savastanoi pv. phaseolicola PK2 employs an Fe(II)-dependent ethylene/succinate-forming enzyme (PK2 PsEFE) to produce ethylene from 2-oxoglutarate (2OG). Here we report NMR-based assays showing that the putative P. savastanoi pv. glycinea PsEFE, which differs from PK2 PsEFE by a single residue, and the P. savastanoi pv.1449B PsEFE, which differs from PK2 PsEFE by 28 residues and a C-terminal 13-residue truncation, catalyze ethylene production from 2OG. Like the PK2 PsEFE, they catalyze oxidation of naturally occurring 2OG derivatives to give alcohol and diacid products. Crystallographic analysis demonstrates that the overall fold and active site of 1449B PsEFE is similar to that of PK2 PsEFE. Interestingly, 2OG was observed to adopt an atypical inverse metal ion binding mode in complex with 1449B PsEFE:Mn in which its 2-oxoacid group is positioned to interact with the guanidinium group of R277, but not the Mn ion, which substitutes for catalytically active Fe(II). Together with reported crystallographic results, this observation indicates that 2OG metal ion binding modes and conformations at the active sites of 2OG oxygenases can vary, possibly in a functionally or disease relevant manner.

PubMed: 41797450
DOI: 10.1002/cbic.202500702

Experimental method

X-RAY DIFFRACTION (1.65 Å)