Ligand binding at the A-cluster in full-length or truncated acetyl-CoA synthase studied by X-ray absorption spectroscopy.

Peer Schrapers,Holger Dobbek,Julia Ilina,Stefan Mebs,Michael Haumann,Jae-Hun Jeoung,Christina M Gregg,Holger Dau,Eugene A Permyakov

doi:10.1371/journal.pone.0171039

Peer Schrapers, Holger Dobbek + Show 7 more

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https://doi.org/10.1371/journal.pone.0171039

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Abstract

Bacteria integrate CO2 reduction and acetyl coenzyme-A (CoA) synthesis in the Wood-Ljungdal pathway. The acetyl-CoA synthase (ACS) active site is a [4Fe4S]-[NiNi] complex (A-cluster). The dinickel site structure (with proximal, p, and distal, d, ions) was studied by X-ray absorption spectroscopy in ACS variants comprising all three protein domains or only the C-terminal domain with the A-cluster. Both variants showed two square-planar Ni(II) sites and an OH- bound at Ni(II)p in oxidized enzyme and a H2O at Ni(I)p in reduced enzyme; a Ni(I)p-CO species was induced by CO incubation and a Ni(II)-CH3- species with an additional water ligand by a methyl group donor. These findings render a direct effect of the N-terminal and middle domains on the A-cluster structure unlikely.

Highlights

Carbon oxide (COx) conversion is a challenging task in renewable energy exploration, combating the atmospheric greenhouse effect, and chemical research aiming at new catalysts using abundant metal species [1, 2]
The three domains are connected by a flexible linker, which facilitates large-scale conformational changes leading to “open” or “closed” configurations of the enzyme in CO dehydrogenase (CODH)/CoFeSP/ acetyl-CoA synthase (ACS) protein complexes [14,15,16,17, 44, 45]
Our results suggest that the A-cluster structure and the ability for cofactor reduction, as well as for carbon monoxide and methyl ligand binding are unrelated to the presence of the N-terminal and middle domains in ACSCh

Summary

Introduction

Carbon oxide (COx) conversion is a challenging task in renewable energy exploration, combating the atmospheric greenhouse effect, and chemical research aiming at new catalysts using abundant metal species [1, 2]. Various enzymes are found, which catalyze efficient and reversible COx transformations at active sites binding nickel, iron, or molybdenum ions [3,4,5,6,7]. Several biological carbon dioxide (CO2) to biomass conversion pathways exist in prokaryotes and eukaryotes [8]. Various prokaryotes employ the Wood-Ljungdahl pathway to reductively form acetyl coenzyme-A [9, 10]. Carbon monoxide (CO) as obtained from CO2 reduction by CO dehydrogenase (CODH) is utilized in a reaction involving two enzymes, corrinoid iron-sulfur protein (CoFeSP) with a methyl group bound to the cobalt ion of its cobalamin cofactor and acetyl-CoA synthase (ACS), to produce acetyl-CoA, the central metabolic building block (Eq 1) [11,12,13,14].

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