3wqc: Difference between revisions
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==D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23== | ==D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23== | ||
<StructureSection load='3wqc' size='340' side='right' caption='[[3wqc]], [[Resolution|resolution]] 1.50Å' scene=''> | <StructureSection load='3wqc' size='340' side='right'caption='[[3wqc]], [[Resolution|resolution]] 1.50Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3wqc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WQC OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[3wqc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Delsh Delsh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WQC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WQC FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3wqd|3wqd]], [[3wqe|3wqe]], [[3wqf|3wqf]], [[3wqg|3wqg]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wqd|3wqd]], [[3wqe|3wqe]], [[3wqf|3wqf]], [[3wqg|3wqg]]</div></td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dthadh ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=518882 DELSH])</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Threo-3-hydroxy-D-aspartate_ammonia-lyase Threo-3-hydroxy-D-aspartate ammonia-lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.27 4.3.1.27] </span></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=3wqc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wqc OCA], [https://pdbe.org/3wqc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wqc RCSB], [https://www.ebi.ac.uk/pdbsum/3wqc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wqc ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
D-threo-3-Hydroxyaspartate dehydratase (D-THA DH) is a fold-type III pyridoxal 5'-phosphate-dependent enzyme, isolated from a soil bacterium of Delftia sp. HT23. It catalyzes the dehydration of D-threo-3-hydroxyaspartate (D-THA) and L-erythro-3-hydroxyaspartate (L-EHA). To elucidate the mechanism of substrate stereospecificity, crystal structures of D-THA DH were determined in complex with various ligands, such as an inhibitor (D-erythro-3-hydroxyaspartate (D-EHA)), a substrate (L-EHA), and the reaction intermediate (2-amino maleic acid). The C beta -OH of L-EHA occupied a position close to the active-site Mg2+, clearly indicating a possibility of metal-assisted C beta -OH elimination from the substrate. In contrast, the C beta -OH of an inhibitor was bound far from the active-site Mg2+. This suggests that the substrate specificity of D-THA DH is determined by the orientation of the C beta -OH at the active site, whose spatial arrangement is compatible with the 3R configuration of 3-hydroxyaspartate. We also report an optically pure synthesis of L-threo-3-hydroxyaspartate (L-THA) and D-EHA, promising intermediates for the synthesis of beta-benzyloxyaspartate, by using a purified D-THA DH as a biocatalyst for the resolution of racemic DL-threo-3-hydroxyaspartate (DL-THA) and DL-erythro-3-hydroxyaspartate (DL-EHA). Considering 50 % of the theoretical maximum, efficient yields of L-THA (38.9 %) and D-EHA (48.9 %) as isolated crystals were achieved with >99 % enantiomeric excess (e.e.). The results of nuclear magnetic resonance signals verified the chemical purity of the products. We were directly able to isolate analytically pure compounds by the recrystallization of acidified reaction mixtures (pH 2.0) and thus avoiding the use of environmentally harmful organic solvents for the chromatographic purification. | |||
Structural insights into the substrate stereospecificity of D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23: a useful enzyme for the synthesis of optically pure L-threo- and D-erythro-3-hydroxyaspartate.,Matsumoto Y, Yasutake Y, Takeda Y, Tamura T, Yokota A, Wada M Appl Microbiol Biotechnol. 2015 Feb 26. PMID:25715785<ref>PMID:25715785</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3wqc" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Delsh]] | |||
[[Category: Large Structures]] | |||
[[Category: Threo-3-hydroxy-D-aspartate ammonia-lyase]] | [[Category: Threo-3-hydroxy-D-aspartate ammonia-lyase]] | ||
[[Category: Matsumoto, Y]] | [[Category: Matsumoto, Y]] | ||
Latest revision as of 08:46, 3 August 2022
D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23
Structural highlights
Publication Abstract from PubMedD-threo-3-Hydroxyaspartate dehydratase (D-THA DH) is a fold-type III pyridoxal 5'-phosphate-dependent enzyme, isolated from a soil bacterium of Delftia sp. HT23. It catalyzes the dehydration of D-threo-3-hydroxyaspartate (D-THA) and L-erythro-3-hydroxyaspartate (L-EHA). To elucidate the mechanism of substrate stereospecificity, crystal structures of D-THA DH were determined in complex with various ligands, such as an inhibitor (D-erythro-3-hydroxyaspartate (D-EHA)), a substrate (L-EHA), and the reaction intermediate (2-amino maleic acid). The C beta -OH of L-EHA occupied a position close to the active-site Mg2+, clearly indicating a possibility of metal-assisted C beta -OH elimination from the substrate. In contrast, the C beta -OH of an inhibitor was bound far from the active-site Mg2+. This suggests that the substrate specificity of D-THA DH is determined by the orientation of the C beta -OH at the active site, whose spatial arrangement is compatible with the 3R configuration of 3-hydroxyaspartate. We also report an optically pure synthesis of L-threo-3-hydroxyaspartate (L-THA) and D-EHA, promising intermediates for the synthesis of beta-benzyloxyaspartate, by using a purified D-THA DH as a biocatalyst for the resolution of racemic DL-threo-3-hydroxyaspartate (DL-THA) and DL-erythro-3-hydroxyaspartate (DL-EHA). Considering 50 % of the theoretical maximum, efficient yields of L-THA (38.9 %) and D-EHA (48.9 %) as isolated crystals were achieved with >99 % enantiomeric excess (e.e.). The results of nuclear magnetic resonance signals verified the chemical purity of the products. We were directly able to isolate analytically pure compounds by the recrystallization of acidified reaction mixtures (pH 2.0) and thus avoiding the use of environmentally harmful organic solvents for the chromatographic purification. Structural insights into the substrate stereospecificity of D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23: a useful enzyme for the synthesis of optically pure L-threo- and D-erythro-3-hydroxyaspartate.,Matsumoto Y, Yasutake Y, Takeda Y, Tamura T, Yokota A, Wada M Appl Microbiol Biotechnol. 2015 Feb 26. PMID:25715785[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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