8D5D

Structure of Y430F D-ornithine/D-lysine decarboxylase complex with D-arginine

Summary for 8D5D

• Entry DOI: 10.2210/pdb8d5d/pdb
• Descriptor: D-ornithine/D-lysine decarboxylase, DIMETHYL SULFOXIDE, (E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-arginine, ... (6 entities in total)
• Functional Keywords: pyridoxal-5'-phosphate, d-amino acid, decarboxylase, fold iii, lyase
• Biological source: Salmonella enterica subsp. enterica serovar Typhimurium
• Total number of polymer chains: 2
• Total formula weight: 109677.72

Authors

Phillips, R.S.,Nguyen Hoang, K.N. (deposition date: 2022-06-04, release date: 2022-11-16, Last modification date: 2023-10-18)

Primary citation

Phillips, R.S.,Nguyen Hoang, K.N.
The Y430F mutant of Salmonella d-ornithine/d-lysine decarboxylase has altered stereospecificity and a putrescine allosteric activation site.
Arch.Biochem.Biophys., 731:109429-109429, 2022

PubMed Abstract: Tyrosine-430 of d-ornithine/d-lysine decarboxylase (DOKDC) is located in the active site, and was suggested to be responsible for the D-stereospecificity of the enzyme. We have prepared the Y430F mutant form of Salmonella enterica serovar typhimurium DOKDC and evaluated its catalytic activity with D- and l-lysine and ornithine. The kinetic results show that the Y430F mutant has measurable decarboxylase activity with both D- and l-lysine and ornithine, which wild type DOKDC does not. Spectroscopic experiments show that these amino acids bind to form external aldimine complexes with the pyridoxal-5'-phosphate with λ = 425 nm. In addition, we have obtained crystal structures of Y430F DOKDC bound to HEPES, putrescine, d-ornithine, d-lysine, and d-arginine. The d-amino acids bind in the crystals to form equilibrium mixtures of gem-diamine and external aldimine complexes. Furthermore, the crystal structures reveal an unexpected allosteric product activator site for putrescine located on the 2-fold axis between the two active sites. Putrescine binds by donating hydrogen bonds from the ammonium groups to Asp-361 and Gln-358 in the specificity helix of both chains. Addition of 0.1-1 mM putrescine eliminates the lag in steady state kinetics and abolishes the sigmoid kinetics. The catalytic loop was modeled with AlphaFold2, and the model shows that Glu-181 can form additional hydrogen bonds with the bound putrescine, likely stabilizing the catalytic closed conformation.

PubMed: 36265649
DOI: 10.1016/j.abb.2022.109429

Experimental method

X-RAY DIFFRACTION (1.54 Å)