6XRC

Apo NIS synthetase DesD variant R306Q

Summary for 6XRC

• Entry DOI: 10.2210/pdb6xrc/pdb
• Related: 6NL2
• Descriptor: Desferrioxamine E biosynthesis protein DesD, GLYCEROL, ADENOSINE-5'-TRIPHOSPHATE, ... (5 entities in total)
• Functional Keywords: nis synthetase, catalytic variant, siderophore synthesis, biosynthetic protein
• Biological source: Streptomyces coelicolor
• Total number of polymer chains: 2
• Total formula weight: 136776.20

Authors

Hoffmann, K.M. (deposition date: 2020-07-11, release date: 2020-10-28, Last modification date: 2023-10-18)

Primary citation

Hoffmann, K.M.,Goncuian, E.S.,Karimi, K.L.,Amendola, C.R.,Mojab, Y.,Wood, K.M.,Prussia, G.A.,Nix, J.,Yamamoto, M.,Lathan, K.,Orion, I.W.
Cofactor Complexes of DesD, a Model Enzyme in the Virulence-related NIS Synthetase Family.
Biochemistry, 59:3427-3437, 2020

PubMed Abstract: The understudied nonribosomal-peptide-synthetase-independent siderophore (NIS) synthetase family has been increasingly associated with virulence in bacterial species due to its key role in the synthesis of hydroxamate and carboxylate "stealth" siderophores. We have identified a model family member, DesD, from , to structurally characterize using a combination of a wild-type and a Arg306Gln variant in , cofactor product AMP-bound, and cofactor reactant ATP-bound complexes. The kinetics in the family has been limited by solubility and reporter assays, so we have developed a label-free kinetics assay utilizing a single-injection isothermal-titration-calorimetry-based method. We report second-order rate constants that are 50 times higher than the previous estimations for DesD. Our Arg306Gln DesD variant was also tested under identical buffer and substrate conditions, and its undetectable activity was confirmed. These are the first reported structures for DesD, and they describe the critical cofactor coordination. This is also the first label-free assay to unambiguously determine the kinetics for an NIS synthetase.

PubMed: 32885650
DOI: 10.1021/acs.biochem.9b00899

Experimental method

X-RAY DIFFRACTION (2.45 Å)