View source for 5gz3


==Structure of D-amino acid dehydrogenase in complex with NADP==
<StructureSection load='5gz3' size='340' side='right'caption='[[5gz3]], [[Resolution|resolution]] 1.59&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5gz3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ureibacillus_thermosphaericus Ureibacillus thermosphaericus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GZ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GZ3 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]] 1.59&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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=5gz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gz3 OCA], [https://pdbe.org/5gz3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gz3 RCSB], [https://www.ebi.ac.uk/pdbsum/5gz3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gz3 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DAPDH_URETH DAPDH_URETH] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A stable NADP+-dependent d-amino acid dehydrogenase (DAADH) was recently created from Ureibacillus thermosphaericusmeso-diaminopimelate dehydrogenase through site-directed mutagenesis. To produce a novel DAADH mutant with different substrate specificity, the crystal structure of apo-DAADH was determined at a resolution of 1.78 A, and the amino-acid residues responsible for the substrate specificity were evaluated using additional site-directed mutagenesis. By introducing a single D94A mutation, the enzyme's substrate specificity was dramatically altered; the mutant utilized d-phenylalanine as the most preferable substrate for oxidative deamination and had a specific activity of 5.33 mumol/min/mg at 50 degrees C, which was 54-fold higher than that of the parent DAADH. In addition, the specific activities of the mutant toward d-leucine, d-norleucine, d-methionine, d-isoleucine, and d-tryptophan were much higher (6-25 times) than those of the parent enzyme. For reductive amination, D94A exhibited extremely high specific activity with phenylpyruvate (16.1 mumol/min/mg at 50 degrees C). The structures of the D94A/Y224F double mutant in complex with NADP+ and in complex with both NADPH and 2-keto-6-aminocapronic acid (lysine oxo-analogue) were then determined at resolutions of 1.59 A and 1.74 A, respectively. The phenylpyruvate-binding model suggests the D94A mutation prevents the substrate phenyl group from sterically clashing with the side chain of Asp94. Structural comparison suggests that both the enlarged substrate-binding pocket and enhanced hydrophobicity of the pocket are mainly responsible for the high reactivity of D94A toward the hydrophobic d-amino acids with bulky side chains.IMPORTANCE In recently years, the potential uses for d-amino acid as source materials for industrial production of medicines, seasonings and agrochemicals have been growing. To date, several methods have been used for the production of d-amino acid, but all include tedious steps. The use of NAD(P)+-dependent d-amino acid dehydrogenase (DAADH) makes single step production of d-amino acids from oxo acid analogs and ammonia possible. We recently succeeded in creating a stable DAADH and demonstrated that it is applicable for one-step synthesis of d-amino acids such as d-leucine and d-isoleucine. As the next step, creation of an enzyme exhibiting different substrate specificity and higher catalytic efficiency is a key to the further development of d-amino acid production. In this study, we succeeded in creating a novel mutant exhibiting extremely high catalytic activity for phenylpyruvate amination. Structural insight into the mutant will be useful for further improvement of DAADHs.

Structure based engineering of an artificially generated NADP+-dependent d-amino acid dehydrogenase.,Hayashi J, Seto T, Akita H, Watanabe M, Hoshino T, Yoneda K, Ohshima T, Sakuraba H Appl Environ Microbiol. 2017 Mar 31. pii: AEM.00491-17. doi:, 10.1128/AEM.00491-17. PMID:28363957<ref>PMID:28363957</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5gz3" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Ureibacillus thermosphaericus]]
[[Category: Akita H]]
[[Category: Hayashi J]]
[[Category: Ohshima T]]
[[Category: Sakuraba H]]
[[Category: Seto T]]
[[Category: Yoneda K]]