A new method to investigate the catalytic mechanism of YhdE pyrophosphatase by using a pyrophosphate fluorescence probe.

Qingya Shen, Hongwei Tan, Guo-Wen Xing, Jimin Zheng, Zongchao Jia

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Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

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1citing papers in PubMed

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1 citing paper in PubMed.

Structural and dynamic properties of eutectic mixtures based on menthol and fatty acids derived from coconut oil: a MD simulation study.Scientific reports · 2022
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5 · Who and what money

Authors and funding

5 authors.

Qingya ShenCollege of Chemistry, Beijing Normal University, Beijing, 100875, China.

Hongwei TanCollege of Chemistry, Beijing Normal University, Beijing, 100875, China.

Guo-Wen XingCollege of Chemistry, Beijing Normal University, Beijing, 100875, China.

Jimin ZhengCollege of Chemistry, Beijing Normal University, Beijing, 100875, China. jimin_z@bnu.edu.cn.

Zongchao JiaDepartment of Biochemical and Molecular Science, Queen's University, Kingston, Ontario, K7L 3N6, Canada. jia@queensu.ca.ORCID 0000-0002-9322-9394

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

YhdE is a Maf (multicopy associated filamentation) proteins from Escherichia coli which exhibits pyrophosphatase activity towards selected nucleotides, although its catalytic mechanism remains unclear. Herein we used a novel fluorescence probe (4-isoACBA-Zn(II) complex) to characterize the enzymatic properties of YhdE and its mutant, establishing a new method for assaying pyrophosphatase catalytic function. Our results reveal for the first time that the new fluorescence sensor confers high sensitivity and specificity and pyrophosphate (PPi) is the direct catalytic product of YhdE. Crystal structures of a mutant in the active-site loop (YhdE_E33A) show conformational flexibility implicated in the catalytic mechanism of YhdE. ITC experiments and computational docking further reveal that Asp70 and substrate dTTP coordinate Mn

Indexed as

DiphosphatesFluorescent DyesCalorimetryCatalysisCatalytic DomainEnzyme AssaysEscherichia coli ProteinsHydrogen BondingHydrolysisKineticsMolecular ConformationMolecular Docking SimulationMolecular Dynamics SimulationProtein BindingPyrophosphatasesRecombinant ProteinsDiphosphatesdiphosphoric acidEscherichia coli ProteinsFluorescent DyesPyrophosphatasesRecombinant ProteinsYhdE protein, E coli

Identifiers

PMID28811554

DOI10.1038/s41598-017-08368-1

PMCPMC5557916

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