4yrb: Difference between revisions

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~~'''Unreleased structure'''~~

~~The entry~~ 4yrb is ~~ON HOLD until Paper~~ Publication

==mouse TDH mutant R180K with NAD+ bound==

== Structural highlights ==

<table><tr><td colspan='2'>[[4yrb]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YRB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YRB 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]] 3.25Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=4yrb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yrb OCA], [https://pdbe.org/4yrb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yrb RCSB], [https://www.ebi.ac.uk/pdbsum/4yrb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yrb ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/TDH_MOUSE TDH_MOUSE]

== Publication Abstract from PubMed ==

Mouse l-threonine dehydrogenase (mTDH), which belongs to the short-chain dehydrogenase/reductase (SDR) superfamily and mediates threonine catabolism, plays pivotal roles in both powerful biosynthesis and signaling in mouse stem cells and has a regulatory residue Arg180. Here we determined three crystal structures of mTDH: wild-type (WT) in the apo form; in complex with NAD(+) and a substrate analog, glycerol, or with only NAD(+); as well as the R180K variant with NAD(+). This is the first description of a structure for mammalian SDR-type TDH. Structural comparison revealed the structural basis for SDR-type TDH catalysis remains strictly conserved in bacteria and mammals. Kinetic enzyme assays, and isothermal titration calorimetry (ITC) measurements indicated the R180K mutation has little effect on NAD(+) binding affinity, whereas affects the substrate's affinity for the enzyme. The crystal structure of R180K with NAD(+), biochemical and spectroscopic studies suggested that the R180K mutant should bind NAD(+) in a similar way and have a similar folding to the WT. However, the R180K variant may have difficulty adopting the closed form due to reduced interaction of residue 180 with a loop which connects a key position for mTDH switching between the closed and open forms in mTDH catalysis, and thereby exhibited a significantly decreased kcat/Km value toward the substrate, l-Thr. In sum, our results suggest that activity of GalE-like TDH can be regulated by remote interaction, such as hydrogen bonding and hydrophobic interaction around the Arg180 of mTDH.

~~Authors~~: He, C., ~~Li, F~~.

Structural insights on mouse l-threonine dehydrogenase: A regulatory role of Arg180 in catalysis.,He C, Huang X, Liu Y, Li F, Yang Y, Tao H, Han C, Zhao C, Xiao Y, Shi Y J Struct Biol. 2015 Dec;192(3):510-8. doi: 10.1016/j.jsb.2015.10.014. Epub 2015, Oct 19. PMID:26492815<ref>PMID:26492815</ref>

~~Description~~: ~~mouse TDH mutant R180K with NAD+ bound~~

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased~~ Structures]]

</div>

[[Category: ~~Li, F~~]]

[[Category: He, C]]

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Mus musculus]]

[[Category: He C]]

[[Category: Li F]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 4yrb is ON HOLD  until Paper Publication
+==mouse TDH mutant R180K with NAD+ bound==
+<StructureSection load='4yrb' size='340' side='right'caption='[[4yrb]], [[Resolution|resolution]] 3.25&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4yrb]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YRB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YRB 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]] 3.25&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=4yrb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yrb OCA], [https://pdbe.org/4yrb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yrb RCSB], [https://www.ebi.ac.uk/pdbsum/4yrb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yrb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TDH_MOUSE TDH_MOUSE]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Mouse l-threonine dehydrogenase (mTDH), which belongs to the short-chain dehydrogenase/reductase (SDR) superfamily and mediates threonine catabolism, plays pivotal roles in both powerful biosynthesis and signaling in mouse stem cells and has a regulatory residue Arg180. Here we determined three crystal structures of mTDH: wild-type (WT) in the apo form; in complex with NAD(+) and a substrate analog, glycerol, or with only NAD(+); as well as the R180K variant with NAD(+). This is the first description of a structure for mammalian SDR-type TDH. Structural comparison revealed the structural basis for SDR-type TDH catalysis remains strictly conserved in bacteria and mammals. Kinetic enzyme assays, and isothermal titration calorimetry (ITC) measurements indicated the R180K mutation has little effect on NAD(+) binding affinity, whereas affects the substrate's affinity for the enzyme. The crystal structure of R180K with NAD(+), biochemical and spectroscopic studies suggested that the R180K mutant should bind NAD(+) in a similar way and have a similar folding to the WT. However, the R180K variant may have difficulty adopting the closed form due to reduced interaction of residue 180 with a loop which connects a key position for mTDH switching between the closed and open forms in mTDH catalysis, and thereby exhibited a significantly decreased kcat/Km value toward the substrate, l-Thr. In sum, our results suggest that activity of GalE-like TDH can be regulated by remote interaction, such as hydrogen bonding and hydrophobic interaction around the Arg180 of mTDH.
-Authors: He, C., Li, F.
+Structural insights on mouse l-threonine dehydrogenase: A regulatory role of Arg180 in catalysis.,He C, Huang X, Liu Y, Li F, Yang Y, Tao H, Han C, Zhao C, Xiao Y, Shi Y J Struct Biol. 2015 Dec;192(3):510-8. doi: 10.1016/j.jsb.2015.10.014. Epub 2015, Oct 19. PMID:26492815<ref>PMID:26492815</ref>
-Description: mouse TDH mutant R180K with NAD+ bound
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Li, F]]
+<div class="pdbe-citations 4yrb" style="background-color:#fffaf0;"></div>
-[[Category: He, C]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Mus musculus]]
+[[Category: He C]]
+[[Category: Li F]]