6P5Q

X-ray structure of Fe(II)-soaked UndA bound to lauric acid

Summary for 6P5Q

• Entry DOI: 10.2210/pdb6p5q/pdb
• Descriptor: UndA, LAURIC ACID, FE (III) ION, ... (5 entities in total)
• Functional Keywords: desaturase, iron, decarboxylase, fatty acid, oxidoreductase
• Biological source: Pseudomonas fluorescens
• Total number of polymer chains: 2
• Total formula weight: 71072.08

Authors

Rajakovich, L.J.,Mitchell, A.J.,Boal, A.K. (deposition date: 2019-05-30, release date: 2019-09-18, Last modification date: 2023-10-11)

Primary citation

Zhang, B.,Rajakovich, L.J.,Van Cura, D.,Blaesi, E.J.,Mitchell, A.J.,Tysoe, C.R.,Zhu, X.,Streit, B.R.,Rui, Z.,Zhang, W.,Boal, A.K.,Krebs, C.,Bollinger Jr., J.M.
Substrate-Triggered Formation of a Peroxo-Fe2(III/III) Intermediate during Fatty Acid Decarboxylation by UndA.
J.Am.Chem.Soc., 141:14510-14514, 2019

PubMed Abstract: The iron-dependent oxidase UndA cleaves one C3-H bond and the C1-C2 bond of dodecanoic acid to produce 1-undecene and CO. A published X-ray crystal structure showed that UndA has a heme-oxygenase-like fold, thus associating it with a structural superfamily that includes known and postulated non-heme diiron proteins, but revealed only a single iron ion in the active site. Mechanisms proposed for initiation of decarboxylation by cleavage of the C3-H bond using a monoiron cofactor to activate O necessarily invoked unusual or potentially unfeasible steps. Here we present spectroscopic, crystallographic, and biochemical evidence that the cofactor of Pf-5 UndA is actually a diiron cluster and show that binding of the substrate triggers rapid addition of O to the Fe(II/II) cofactor to produce a transient peroxo-Fe(III/III) intermediate. The observations of a diiron cofactor and substrate-triggered formation of a peroxo-Fe(III/III) intermediate suggest a small set of possible mechanisms for O, C3-H and C1-C2 activation by UndA; these routes obviate the problematic steps of the earlier hypotheses that invoked a single iron.

PubMed: 31487162
DOI: 10.1021/jacs.9b06093

Experimental method

X-RAY DIFFRACTION (1.86 Å)