PDBsum entry 5af7

Hydrolase

PDB id: 5af7

Contents

Protein chains

390 a.a.

Ligands

FAD ×2

GOL ×2

Waters ×831

PDB id:

5af7

Name:

Hydrolase

Title:

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

Structure:

Acyl-coa dehydrogenase. Chain: a, b. Synonym: 3-sulfinopropionyl-coenzyme a desulfinase. Engineered: yes

Source:

Advenella mimigardefordensis dpn7. Organism_taxid: 1247726. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.89Å R-factor: 0.165 R-free: 0.202

Authors:

M.Cianci,M.Schuermann,R.Meijers,T.R.Schneider,A.Steinbuechel

Key ref:

M.Schürmann et al. (2015). 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 D Biol Crystallogr, 71, 1360-1372. PubMed id: 26057676 DOI: 10.1107/S1399004715006616

Date:

20-Jan-15 Release date: 03-Jun-15

Protein chains

K4L7X3  (K4L7X3_9BURK) -  3-sulfinopropanoyl-CoA desulfinase from Advenella mimigardefordensis (strain DSM 17166 / LMG 22922 / DPN7)

Seq: 401 a.a.

Struc: 390 a.a.

Enzyme reactions

• Enzyme class: E.C.3.13.1.4 - 3-sulfinopropanoyl-CoA desulfinase.
• Reaction: 3-sulfinopropanoyl-CoA + H2O = propanoyl-CoA + sulfite + H⁺
• Cofactor: FAD

FAD (Bound ligand (Het Group name = FAD) corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1107/S1399004715006616

Acta Crystallogr D Biol Crystallogr 71:1360-1372 (2015)

PubMed id: 26057676

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.

M.Schürmann, R.Meijers, T.R.Schneider, A.Steinbüchel, M.Cianci.

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.