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5x20
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 5x20 is ON HOLD until Jan 29 2019 Authors: Furukawa, N., Miyanaga, A., Wada, Y., Nakajima, M., Taguchi, H. Description: The ternary structure of D-...) |
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| - | '''Unreleased structure''' | ||
| - | The | + | ==The ternary structure of D-mandelate dehydrogenase with NADH and anilino(oxo)acetate== |
| + | <StructureSection load='5x20' size='340' side='right'caption='[[5x20]], [[Resolution|resolution]] 2.40Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[5x20]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterococcus_faecium_DO Enterococcus faecium DO]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X20 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X20 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]] 2.4Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AOT:2-OXIDANYLIDENE-2-PHENYLAZANYL-ETHANOIC+ACID'>AOT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5x20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x20 OCA], [https://pdbe.org/5x20 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x20 RCSB], [https://www.ebi.ac.uk/pdbsum/5x20 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x20 ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/Q3Y316_ENTFD Q3Y316_ENTFD] Catalyzes the NADPH-dependent reduction of ketopantoate into pantoic acid.[ARBA:ARBA00002919][RuleBase:RU362068] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Enterococcus faecium NAD-dependent d-mandelate dehydrogenase (d-ManDH) belongs to a ketopantoate reductase (KPR)-related d-2-hydroxyacid dehydrogenase family, and exhibits broad substrate specificity toward bulky hydrophobic 2-ketoacids, preferring C3-branched substrates. The ternary complex structure of d-ManDH with NADH and anilino(oxo)acetate (AOA) revealed that the substrate binding induces a shear motion of the N-terminal domain along the C-terminal domain, following the hinge motion induced by the NADH binding, and allows the bound NADH molecule to form favorable interactions with a 2-ketoacid substrate. d-ManDH possesses a sufficiently wide pocket that accommodates the C3 branched side chains of substrates like KPR, but unlike the pocket of KPR, the pocket of d-ManDH comprises an entirely hydrophobic surface and an expanded space, in which the AOA benzene is accommodated. The expanded space mostly comprises a mobile loop structure, which likely modulates the shape and size of the space depending on the substrate. | ||
| - | + | The ternary complex structure of d-mandelate dehydrogenase with NADH and anilino(oxo)acetate.,Furukawa N, Miyanaga A, Nakajima M, Taguchi H Biochem Biophys Res Commun. 2017 Mar 19. pii: S0006-291X(17)30552-1. doi:, 10.1016/j.bbrc.2017.03.088. PMID:28327357<ref>PMID:28327357</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: | + | <div class="pdbe-citations 5x20" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | |
| - | [[Category: | + | ==See Also== |
| - | [[Category: | + | *[[Mandelate dehydrogenase|Mandelate dehydrogenase]] |
| - | [[Category: | + | == References == |
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Enterococcus faecium DO]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Furukawa N]] | ||
| + | [[Category: Miyanaga A]] | ||
| + | [[Category: Nakajima M]] | ||
| + | [[Category: Taguchi H]] | ||
Current revision
The ternary structure of D-mandelate dehydrogenase with NADH and anilino(oxo)acetate
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