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| | ==Monomeric L-threonine 3-dehydrogenase from metagenome database (apo form)== | | ==Monomeric L-threonine 3-dehydrogenase from metagenome database (apo form)== |
| - | <StructureSection load='5y1d' size='340' side='right' caption='[[5y1d]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='5y1d' size='340' side='right'caption='[[5y1d]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5y1d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y1D FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5y1d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Uncultured_archaeon_MedDCM-OCT-S05-C57 Uncultured archaeon MedDCM-OCT-S05-C57]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y1D FirstGlance]. <br> |
| - | </td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5y1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y1d OCA], [http://pdbe.org/5y1d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y1d RCSB], [http://www.ebi.ac.uk/pdbsum/5y1d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y1d ProSAT]</span></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</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=5y1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y1d OCA], [https://pdbe.org/5y1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y1d RCSB], [https://www.ebi.ac.uk/pdbsum/5y1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y1d ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/D6PBM7_9ARCH D6PBM7_9ARCH] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Asano, Y]] | + | [[Category: Large Structures]] |
| - | [[Category: Ito, S]] | + | [[Category: Uncultured archaeon MedDCM-OCT-S05-C57]] |
| - | [[Category: Motoyama, T]] | + | [[Category: Asano Y]] |
| - | [[Category: Nakano, S]] | + | [[Category: Ito S]] |
| - | [[Category: Tokiwa, H]] | + | [[Category: Motoyama T]] |
| - | [[Category: Yamamoto, Y]] | + | [[Category: Nakano S]] |
| - | [[Category: Dehydrogenase]] | + | [[Category: Tokiwa H]] |
| - | [[Category: Nad+ binding protein]] | + | [[Category: Yamamoto Y]] |
| - | [[Category: Oxidoreductase]]
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| Structural highlights
Function
D6PBM7_9ARCH
Publication Abstract from PubMed
A short chain dehydrogenase like l-threonine 3-dehydrogenase (SDR-TDH) from metagenome data (mtTDH) was identified by database mining. Its enzymatic properties suggested that mtTDH has unique characteristics relative to other SDR-TDHs, including two mesophilic and thermophilic SDR-TDHs identified in this study. The activation energy of mtTDH was the lowest (29.6 kJ/mol) of those of the SDR-TDHs, indicating that it is a psychrophilic enzyme. Size-exclusion chromatography analysis revealed mtTDH is a monomer. Crystal structures of mtTDH in apo, binary, and two ternary complexes (l-Ser- and l-Thr-soaked forms) were determined at resolutions of 1.25-1.9 A. Structural and computational analysis revealed the molecular mechanism of switching between the open and closed states induced by substrate binding and product release. Furthermore, six residues and two water molecules at the active site contributing to product release were assigned. The residues could be categorized into two groups on the basis of the enzymatic properties of their variants: S111, Y136, and T177 and S74, T178, and D179. The former group appeared to affect l-Thr dehydrogenation directly, because the kcat value of their variants was >80-fold lower than that of wild-type mtTDH. On the other hand, the latter group contributes to switching between the open and closed states, which is important for the high substrate specificity of SDR-TDH for l-Thr: the kcat and Km toward l-Thr values of variants in these residues could not be determined because the initial velocity was unsaturated at high concentrations of l-Thr. On the basis of these findings, we proposed a product release mechanism for SDR-TDH associated with specific structural changes.
Product Release Mechanism Associated with Structural Changes in Monomeric l-Threonine 3-Dehydrogenase.,Motoyama T, Nakano S, Yamamoto Y, Tokiwa H, Asano Y, Ito S Biochemistry. 2017 Oct 31;56(43):5758-5770. doi: 10.1021/acs.biochem.7b00832., Epub 2017 Oct 19. PMID:28992410[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Motoyama T, Nakano S, Yamamoto Y, Tokiwa H, Asano Y, Ito S. Product Release Mechanism Associated with Structural Changes in Monomeric l-Threonine 3-Dehydrogenase. Biochemistry. 2017 Oct 31;56(43):5758-5770. doi: 10.1021/acs.biochem.7b00832., Epub 2017 Oct 19. PMID:28992410 doi:http://dx.doi.org/10.1021/acs.biochem.7b00832
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