5x20: Difference between revisions

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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 entry 5x20 is ON HOLD  until Jan 29 2019
==The ternary structure of D-mandelate dehydrogenase with NADH and anilino(oxo)acetate==
<StructureSection load='5x20' size='340' side='right'caption='[[5x20]], [[Resolution|resolution]] 2.40&Aring;' 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]] 2.4&#8491;</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.


Authors: Furukawa, N., Miyanaga, A., Wada, Y., Nakajima, M., Taguchi, H.
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>


Description: The ternary structure of D-mandelate dehydrogenase with NADH and anilino(oxo)acetate
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Nakajima, M]]
<div class="pdbe-citations 5x20" style="background-color:#fffaf0;"></div>
[[Category: Taguchi, H]]
 
[[Category: Furukawa, N]]
==See Also==
[[Category: Wada, Y]]
*[[Mandelate dehydrogenase|Mandelate dehydrogenase]]
[[Category: Miyanaga, A]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Enterococcus faecium DO]]
[[Category: Large Structures]]
[[Category: Furukawa N]]
[[Category: Miyanaga A]]
[[Category: Nakajima M]]
[[Category: Taguchi H]]
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