View source for 8d5r


==Structure of Y430F D-ornithine/D-lysine decarboxylase complex with D-ornithine==
<StructureSection load='8d5r' size='340' side='right'caption='[[8d5r]], [[Resolution|resolution]] 1.44&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[8d5r]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8D5R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8D5R FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.44&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ORX:N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-ORNITHINE'>ORX</scene>, <scene name='pdbligand=PUT:1,4-DIAMINOBUTANE'>PUT</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8d5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8d5r OCA], [https://pdbe.org/8d5r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8d5r RCSB], [https://www.ebi.ac.uk/pdbsum/8d5r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8d5r ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DOKDC_SALTY 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).<ref>PMID:29024617</ref> <ref>PMID:30699288</ref> 
<div style="background-color:#fffaf0;">
== 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 lambda(max) = 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<ref>PMID:36265649</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8d5r" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
[[Category: Nguyen Hoang KN]]
[[Category: Phillips RS]]