Function and X-Ray crystal structure of Escherichia coli YfdE

Elwood A Mullins,Kelly L Sullivan,T Joseph Kappock,Valerie De Crécy-Lagard

doi:10.1371/journal.pone.0067901

Elwood A Mullins, Kelly L Sullivan + Show 2 more

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https://doi.org/10.1371/journal.pone.0067901

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Journal: PloS one	Publication Date: Jul 23, 2013
Citations: 74	License type: CC BY 4.0

Affiliation: Purdue University West Lafayette

Abstract

Many food plants accumulate oxalate, which humans absorb but do not metabolize, leading to the formation of urinary stones. The commensal bacterium Oxalobacter formigenes consumes oxalate by converting it to oxalyl-CoA, which is decarboxylated by oxalyl-CoA decarboxylase (OXC). OXC and the class III CoA-transferase formyl-CoA:oxalate CoA-transferase (FCOCT) are widespread among bacteria, including many that have no apparent ability to degrade or to resist external oxalate. The EvgA acid response regulator activates transcription of the Escherichia coli yfdXWUVE operon encoding YfdW (FCOCT), YfdU (OXC), and YfdE, a class III CoA-transferase that is 30% identical to YfdW. YfdW and YfdU are necessary and sufficient for oxalate-induced protection against a subsequent acid challenge; neither of the other genes has a known function. We report the purification, in vitro characterization, 2.1-Å crystal structure, and functional assignment of YfdE. YfdE and UctC, an orthologue from the obligate aerobe Acetobacter aceti, perform the reversible conversion of acetyl-CoA and oxalate to oxalyl-CoA and acetate. The annotation of YfdE as acetyl-CoA:oxalate CoA-transferase (ACOCT) expands the scope of metabolic pathways linked to oxalate catabolism and the oxalate-induced acid tolerance response. FCOCT and ACOCT active sites contain distinctive, conserved active site loops (the glycine-rich loop and the GNxH loop, respectively) that appear to encode substrate specificity.

Highlights

Humans cannot catabolize oxalate, which promotes calcium oxalate urinary stone formation and other maladies [1]
Dietary oxalate uptake is suppressed by commensal oxalate degraders like Oxalobacter formigenes [3,4], an anaerobic gut bacterium that derives energy and carbon from a concise oxalate catabolic pathway centered on oxalyl-CoA decarboxylase (OXC) [5]
The sequence similarity and syntenic relationship of yfdW and yfdE suggested that they might share an acyl-CoA substrate. This hypothesis was tested with functional gene expression studies of YfdE and UctC, a YfdE homologue from Acetobacter aceti. We demonstrate that these proteins have acetyl-CoA:oxalate CoAtransferase (ACOCT) activity, which allows a core metabolite to serve as an alternate source of oxalyl-CoA

Summary

Introduction

Humans cannot catabolize oxalate, which promotes calcium oxalate urinary stone formation and other maladies [1]. Dietary oxalate uptake is suppressed by commensal oxalate degraders like Oxalobacter formigenes [3,4], an anaerobic gut bacterium that derives energy and carbon from a concise oxalate catabolic pathway centered on oxalyl-CoA decarboxylase (OXC) [5]. Thiamin-dependent OXC converts oxalyl-CoA and a proton to formyl-CoA and CO2 [6,7] in a singular a-decarboxylation reaction that is specific for oxalyl-CoA [6,8]. The class III CoA-transferase [9] formyl-CoA:oxalate CoAtransferase (FCOCT, encoded by frc), regenerates oxalyl-CoA with concomitant production of formate (Figure 1) [10,11]. FCOCT and OXC raise cytoplasmic pH [12], and in combination with the electrogenic oxalate:formate antiporter OxlT, generate a proton gradient [5]

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