Structure-guided insights into heterocyclic ring-cleavage catalysis of the non-heme Fe (II) dioxygenase NicX

Gongquan Liu, Yi-Lei Zhao, Fangyuan He, Peng Zhang, Xingyu Ouyang, Hongzhi Tang () and Ping Xu
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Gongquan Liu: Shanghai Jiao Tong University
Yi-Lei Zhao: Shanghai Jiao Tong University
Fangyuan He: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Peng Zhang: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Xingyu Ouyang: Shanghai Jiao Tong University
Hongzhi Tang: Shanghai Jiao Tong University
Ping Xu: Shanghai Jiao Tong University

Nature Communications, 2021, vol. 12, issue 1, 1-10

Abstract: Abstract Biodegradation of aromatic and heterocyclic compounds requires an oxidative ring cleavage enzymatic step. Extensive biochemical research has yielded mechanistic insights about catabolism of aromatic substrates; yet much less is known about the reaction mechanisms underlying the cleavage of heterocyclic compounds such as pyridine-ring-containing ones like 2,5-hydroxy-pyridine (DHP). 2,5-Dihydroxypyridine dioxygenase (NicX) from Pseudomonas putida KT2440 uses a mononuclear nonheme Fe(II) to catalyze the oxidative pyridine ring cleavage reaction by transforming DHP into N-formylmaleamic acid (NFM). Herein, we report a crystal structure for the resting form of NicX, as well as a complex structure wherein DHP and NFM are trapped in different subunits. The resting state structure displays an octahedral coordination for Fe(II) with two histidine residues (His265 and His318), a serine residue (Ser302), a carboxylate ligand (Asp320), and two water molecules. DHP does not bind as a ligand to Fe(II), yet its interactions with Leu104 and His105 function to guide and stabilize the substrate to the appropriate position to initiate the reaction. Additionally, combined structural and computational analyses lend support to an apical dioxygen catalytic mechanism. Our study thus deepens understanding of non-heme Fe(II) dioxygenases.

Date: 2021
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DOI: 10.1038/s41467-021-21567-9

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