8d5d | pdb_00008d5d

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

spinqualitylabelsall models 8d5d, resolution 1.54Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 8d5d is a 2 chain structure with sequence from Salmonella enterica subsp. enterica serovar Typhimurium. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: 5DK, DMS, GOL, NA Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function DOKDC_SALTY Catalyzes the decarboxylation of D-ornithine and D-lysine (PubMed:29024617, PubMed:30699288). Ornithine is likely the physiological substrate (PubMed:29024617). Has no detectable diaminopimelate decarboxylase activity in vitro (PubMed:29024617). Publication Abstract from PubMed 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 lambdamax = 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. The Y430F mutant of Salmonella d-ornithine/d-lysine decarboxylase has altered stereospecificity and a putrescine allosteric activation site.,Phillips RS, Nguyen Hoang KN Arch Biochem Biophys. 2022 Nov 30;731:109429. doi: 10.1016/j.abb.2022.109429., Epub 2022 Oct 18. PMID:36265649 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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