5AF7

3-Sulfinopropionyl-coenzyme A (3SP-CoA) desulfinase from Advenella mimigardefordensis DPN7T: crystal structure and function of a desulfinase with an acyl-CoA dehydrogenase fold. Native crystal structure

Summary for 5AF7

• Entry DOI: 10.2210/pdb5af7/pdb
• Descriptor: ACYL-COA DEHYDROGENASE, FLAVIN-ADENINE DINUCLEOTIDE, GLYCEROL, ... (4 entities in total)
• Functional Keywords: hydrolase, desulfinase, acyl-coa dehydrogenase, 3-sulfinopropionyl-coenzyme a, flavin adenine dinucleotide
• Biological source: Advenella mimigardefordensis DPN7
• Total number of polymer chains: 2
• Total formula weight: 88918.78

Authors

Cianci, M.,Schuermann, M.,Meijers, R.,Schneider, T.R.,Steinbuechel, A. (deposition date: 2015-01-20, release date: 2015-06-03, Last modification date: 2024-01-10)

Primary citation

Schurmann, M.,Meijers, R.,Schneider, T.R.,Steinbuchel, A.,Cianci, M.
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.
Acta Crystallogr.,Sect.D, 71:1360-, 2015

PubMed 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.

PubMed: 26057676
DOI: 10.1107/S1399004715006616

Experimental method

X-RAY DIFFRACTION (1.89 Å)