3-Sulfinopropionyl-coenzyme A (3SP-CoA) desulfinase from Advenella mimigardefordensis DPN7(T): crystal structure and function of a desulfinase with an acyl-CoA dehydrogenase fold.

Rob Meijers,Michele Cianci,Marc Schürmann,Thomas R Schneider,Alexander Steinbüchel

doi:10.1107/s1399004715006616

Abstract

3-Sulfinopropionyl-coenzyme A (3SP-CoA) desulfinase (AcdDPN7; EC 3.13.1.4) was identified during investigation of the 3,3'-dithiodipropionic acid (DTDP) catabolic pathway in the betaproteobacterium Advenella mimigardefordensis strain DPN7(T). DTDP is an organic disulfide and a precursor for the synthesis of polythioesters (PTEs) in bacteria, and is of interest for biotechnological PTE production. AcdDPN7 catalyzes sulfur abstraction from 3SP-CoA, a key step during the catabolism of DTDP. Here, the crystal structures of apo AcdDPN7 at 1.89 Å resolution and of its complex with the CoA moiety from the substrate analogue succinyl-CoA at 2.30 Å resolution are presented. The apo structure shows that AcdDPN7 belongs to the acyl-CoA dehydrogenase superfamily fold and that it is a tetramer, with each subunit containing one flavin adenine dinucleotide (FAD) molecule. The enzyme does not show any dehydrogenase activity. Dehydrogenase activity would require a catalytic base (Glu or Asp residue) at either position 246 or position 366, where a glutamine and a glycine are instead found, respectively, in this desulfinase. The positioning of CoA in the crystal complex enabled the modelling of a substrate complex containing 3SP-CoA. This indicates that Arg84 is a key residue in the desulfination reaction. An Arg84Lys mutant showed a complete loss of enzymatic activity, suggesting that the guanidinium group of the arginine is essential for desulfination. AcdDPN7 is the first desulfinase with an acyl-CoA dehydrogenase fold to be reported, which underlines the versatility of this enzyme scaffold.

Highlights

Degradation of 3-sulfinopropionyl-coenzyme A (3SP-CoA) into sulfite and propionyl-CoA is the last step in the 3,30dithiodipropionic acid (DTDP) bacterial catabolic pathway (Fig. 1)
AcdDPN7 is the first desulfinase with an acyl-CoA dehydrogenase fold to be reported, which underlines the versatility of this enzyme scaffold
The crystal structure of 3-sulfinopropionyl-coenzyme A (3SP-CoA) desulfinase (AcdDPN7) from A. mimigardefordensis was solved by molecular replacement using the monomer of an acyl-CoA dehydrogenase (Acd) from T. thermophilus HB8, which shares 36% sequence identity (PDB entry 1ukw; RIKEN Structural Genomics/Proteomics Initiative, unpublished work), as a search model

Summary

Introduction

Degradation of 3-sulfinopropionyl-coenzyme A (3SP-CoA) into sulfite and propionyl-CoA is the last step in the 3,30dithiodipropionic acid (DTDP) bacterial catabolic pathway (Fig. 1). DTDP is an organic disulfide and a precursor for the synthesis of polythioesters (PTEs; Lutke-Eversloh & Steinbuchel, 2003). Elucidation of the degradation pathway of DTDP in Advenella mimigardefordensis strain DPN7T and identification of the genes involved has been performed with the aim of providing a strategy to engineer strains suitable for biotechnological PTE production (Schurmann et al, 2011, 2013; Wubbeler et al, 2008, 2010; Bruland et al, 2009). The isolation of a desulfinase (EC 3.13.1.4) catalyzing sulfur abstraction from 3SP-CoA during DTDP catabolism in the betaproteobacterium Advenella mimigardefordensis strain DPN7T was reported (Schurmann et al, 2013).

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Conclusion