Crystal structure of the hydroxylaminopurine resistance protein, YiiM, and its putative molybdenum cofactor-binding catalytic site

Byeol Namgung,Jee-Hyeon Kim,Wan Seok Song,Sung-Il Yoon

doi:10.1038/s41598-018-21660-y

Byeol Namgung, Jee-Hyeon Kim + Show 2 more

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https://doi.org/10.1038/s41598-018-21660-y

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Journal: Scientific Reports	Publication Date: Feb 19, 2018
Citations: 10	License type: open-access

Affiliation: Kangwon National University

Abstract

The molybdenum cofactor (Moco) is a molybdenum-conjugated prosthetic group that is ubiquitously found in plants, animals, and bacteria. Moco is required for the nitrogen-reducing reaction of the Moco sulfurase C-terminal domain (MOSC) family. Despite the biological significance of MOSC proteins in the conversion of prodrugs and resistance against mutagens, their structural features and Moco-mediated catalysis mechanism have not been described in detail. YiiM is a MOSC protein that is involved in reducing mutagenic 6-N-hydroxylaminopurine to nontoxic adenine in bacteria. Here, we report two crystal structures of YiiM: one from Gram-positive Geobacillus stearothermophilus (gsYiiM) and the other from Gram-negative Escherichia coli (ecYiiM). Although gsYiiM and ecYiiM differ in oligomerization state and protein stability, both consist of three structural modules (a β-barrel and two α-helix bundles) and feature a cavity surrounded by the three modules. The cavity is characterized by positive electrostatic potentials and high sequence conservation. Moreover, the ecYiiM cavity houses a phosphate group, which emulates a part of Moco, and contains a highly reactive invariant cysteine residue. We thus propose that the cavity is the catalytic site where Moco binds and the substrate is reduced. Moreover, our comparative structural analysis highlights the common but distinct structural features of MOSC proteins.

Highlights

Molybdenum in living organisms, except for that in nitrogenase, is usually bound to molybdopterin (MPT) to form a molybdenum cofactor (Moco) and exert catalytic activity[1,2]
Only several Moco sulfurase C-terminal domain (MOSC) family members, including human mitochondrial amidoxime reducing component and Escherichia coli YiiM and YcbX, have been functionally characterized. mARC, YiiM, and YcbX are involved in the reduction of N-hydroxylated substrates. mARC detoxifies mutagenic N-hydroxylated base analogs, such as 6-N-hydroxylaminopurine (HAP), and activates N-hydroxylated amidoxime prodrugs as a redox system in concert with NADH-cytochrome b5 reductase (Cytb5R) and cytochrome b5 (Cytb5)[5,6,7,8]
In analogy to nitrate reductase, electrons were proposed to flow from NADH to the mARC Moco through the Cytb5R flavin and Cytb[5] heme, resulting in mARC activation for the reduction of N-hydroxylated substrates[9]

Summary

Introduction

Molybdenum in living organisms, except for that in nitrogenase, is usually bound to molybdopterin (MPT) to form a molybdenum cofactor (Moco) and exert catalytic activity[1,2]. To provide insights into the catalytic mechanism of MOSC enzymes, we report two crystal structures of YiiM, one from Gram-positive Geobacillus stearothermophilus (gsYiiM) and the other from Gram-negative E. coli (ecYiiM).

Results

Conclusion