8D5R

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

8D5R の概要

• エントリーDOI: 10.2210/pdb8d5r/pdb
• 分子名称: D-ornithine/D-lysine decarboxylase, DIMETHYL SULFOXIDE, N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-ORNITHINE, ... (9 entities in total)
• 機能のキーワード: pyridoxal-5'-phosphate, d-amino acid, decarboxylase, fold iii, lyase
• 由来する生物種: Salmonella enterica subsp. enterica serovar Typhimurium
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 109541.29

構造登録者

Phillips, R.S.,Nguyen Hoang, K.N. (登録日: 2022-06-06, 公開日: 2022-11-16, 最終更新日: 2024-10-23)

主引用文献

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

実験手法

X-RAY DIFFRACTION (1.44 Å)