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| | ==Crystal Structures of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum== | | ==Crystal Structures of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum== |
| - | <StructureSection load='3wb9' size='340' side='right' caption='[[3wb9]], [[Resolution|resolution]] 1.93Å' scene=''> | + | <StructureSection load='3wb9' size='340' side='right'caption='[[3wb9]], [[Resolution|resolution]] 1.93Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3wb9]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Symth Symth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WB9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WB9 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3wb9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Symbiobacterium_thermophilum_IAM_14863 Symbiobacterium thermophilum IAM 14863]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WB9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WB9 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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]] 1.93Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3wbb|3wbb]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">meso-dapdh, STH1425 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=292459 SYMTH])</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=3wb9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wb9 OCA], [https://pdbe.org/3wb9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wb9 RCSB], [https://www.ebi.ac.uk/pdbsum/3wb9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wb9 ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_dehydrogenase Diaminopimelate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.16 1.4.1.16] </span></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=3wb9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wb9 OCA], [http://pdbe.org/3wb9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wb9 RCSB], [http://www.ebi.ac.uk/pdbsum/3wb9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wb9 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q67PI3_SYMTH Q67PI3_SYMTH] |
| | <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: Diaminopimelate dehydrogenase]] | + | [[Category: Large Structures]] |
| - | [[Category: Symth]] | + | [[Category: Symbiobacterium thermophilum IAM 14863]] |
| - | [[Category: Guo, R T]] | + | [[Category: Guo RT]] |
| - | [[Category: Huang, C H]] | + | [[Category: Huang CH]] |
| - | [[Category: Li, Z]] | + | [[Category: Li Z]] |
| - | [[Category: Liu, W D]] | + | [[Category: Liu WD]] |
| - | [[Category: Wu, Q Q]] | + | [[Category: Wu QQ]] |
| - | [[Category: Zhu, D M]] | + | [[Category: Zhu DM]] |
| - | [[Category: D-amino acid dehydrogenase]]
| + | |
| - | [[Category: Domain motion]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Thermo-stable]]
| + | |
| Structural highlights
Function
Q67PI3_SYMTH
Publication Abstract from PubMed
Wild-type meso-diaminopimelate dehydrogenase (DAPDH) is usually specific to the native substrate, meso-2,6-diaminopimelate. Recently, a DAPDH from Symbiobacterium thermophilum (StDAPDH) was found to exhibit expanded substrate specificity. As such, its crystal structures in apo form and in complex with NADP(+) and both NADPH and meso-DAP were investigated to reveal the structural basis of its unique catalytic properties. Structural analysis results show that StDAPDH should prefer an ordered kinetic catalytic mechanism. A second substrate entrance tunnel with Met152 at its bottleneck was found, through which pyruvate/D-alanine might bind and enter the catalytic cavity, providing some structural insights into its high activity toward pyruvate. The side chain of Met152 might interact with Asp92 and Asn253, thus affecting the domain motion and catalysis. These results offer useful information for understanding the unique catalytic properties of StDAPDH and guiding further engineering of this enzyme.
Structural and mutational studies on the unusual substrate specificity of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum.,Liu W, Li Z, Huang CH, Guo RT, Zhao L, Zhang D, Chen X, Wu Q, Zhu D Chembiochem. 2014 Jan 24;15(2):217-22. doi: 10.1002/cbic.201300691. Epub 2013 Dec, 11. PMID:24339368[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Liu W, Li Z, Huang CH, Guo RT, Zhao L, Zhang D, Chen X, Wu Q, Zhu D. Structural and mutational studies on the unusual substrate specificity of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum. Chembiochem. 2014 Jan 24;15(2):217-22. doi: 10.1002/cbic.201300691. Epub 2013 Dec, 11. PMID:24339368 doi:http://dx.doi.org/10.1002/cbic.201300691
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