7cgv
From Proteopedia
(Difference between revisions)
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==Full consensus L-threonine 3-dehydrogenase, FcTDH-IIYM (NAD+ bound form)== | ==Full consensus L-threonine 3-dehydrogenase, FcTDH-IIYM (NAD+ bound form)== | ||
| - | <StructureSection load='7cgv' size='340' side='right'caption='[[7cgv]]' scene=''> | + | <StructureSection load='7cgv' size='340' side='right'caption='[[7cgv]], [[Resolution|resolution]] 2.38Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CGV OCA]. For a <b>guided tour on the structure components</b> use [ | + | <table><tr><td colspan='2'>[[7cgv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CGV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CGV FirstGlance]. <br> |
| - | </td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.38Å</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=7cgv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cgv OCA], [https://pdbe.org/7cgv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cgv RCSB], [https://www.ebi.ac.uk/pdbsum/7cgv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cgv ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Exponentially increasing protein sequence data enables artificial enzyme design using sequence-based protein design methods, including full-consensus protein design (FCD). The success of artificial enzyme design is strongly dependent on the nature of the sequences used. Hence, sequences must be selected from databases and curated libraries prepared to enable a successful design by FCD. In this study, we proposed a selection approach regarding several key residues as sequence motifs. We used l-threonine 3-dehydrogenase (TDH) as a model to test the validity of this approach. In the classification, four residues (143, 174, 188, and 214) were used as key residues. We classified thousands of TDH homologous sequences into five groups containing hundreds of sequences. Utilizing sequences in the libraries, we designed five artificial TDHs by FCD. Among the five, we successfully expressed four in soluble form. Biochemical analysis of artificial TDHs indicated that their enzymatic properties vary; half of the maximum measured enzyme activity (t1/2) and activation energies were distributed from 53 to 65 degrees C and from 38 to 125 kJ/mol, respectively. The artificial TDHs had unique kinetic parameters, distinct from one another. Structural analysis indicates that consensus mutations are mainly introduced in the secondary or outer shell. The functional diversity of the artificial TDHs is due to the accumulation of mutations that affect their physicochemical properties. Taken together, our findings indicate that our proposed approach can help generate artificial enzymes with unique enzymatic properties. | ||
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| + | Protein Sequence Selection Method That Enables Full Consensus Design of Artificial l-Threonine 3-Dehydrogenases with Unique Enzymatic Properties.,Motoyama T, Hiramatsu N, Asano Y, Nakano S, Ito S Biochemistry. 2020 Oct 13;59(40):3823-3833. doi: 10.1021/acs.biochem.0c00570., Epub 2020 Sep 25. PMID:32945652<ref>PMID:32945652</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7cgv" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| + | [[Category: Synthetic construct]] | ||
[[Category: Asano Y]] | [[Category: Asano Y]] | ||
[[Category: Hiramatsu N]] | [[Category: Hiramatsu N]] | ||
Current revision
Full consensus L-threonine 3-dehydrogenase, FcTDH-IIYM (NAD+ bound form)
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