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| | <StructureSection load='3wyc' size='340' side='right'caption='[[3wyc]], [[Resolution|resolution]] 2.07Å' scene=''> | | <StructureSection load='3wyc' size='340' side='right'caption='[[3wyc]], [[Resolution|resolution]] 2.07Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3wyc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_thermosphaericus Bacillus thermosphaericus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WYC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WYC FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3wyc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ureibacillus_thermosphaericus Ureibacillus thermosphaericus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WYC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WYC FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=NES:2-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-ETHANESULFONIC+ACID'>NES</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]] 2.07Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wyb|3wyb]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=NES:2-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-ETHANESULFONIC+ACID'>NES</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ddh ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=51173 Bacillus thermosphaericus])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Diaminopimelate_dehydrogenase Diaminopimelate dehydrogenase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=3wyc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wyc OCA], [https://pdbe.org/3wyc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wyc RCSB], [https://www.ebi.ac.uk/pdbsum/3wyc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wyc ProSAT]</span></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=3wyc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wyc OCA], [https://pdbe.org/3wyc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wyc RCSB], [https://www.ebi.ac.uk/pdbsum/3wyc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wyc ProSAT]</span></td></tr> |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/DAPDH_URETH DAPDH_URETH] |
| - | Crystal structures of the thermostable meso-diaminopimelate dehydrogenase (DAPDH) from Ureibacillus thermosphaericus were determined for the enzyme in the apo form and in complex with NADP(+) and N-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid. The main-chain coordinates of the enzyme showed notable similarity to those of Symbiobacterium thermophilum DAPDH. However, the subunit arrangement of U. thermosphaericus DAPDH (a dimer) was totally different from that of the S. thermophilum enzyme (a hexamer). Structural comparison with the dimeric enzyme from the mesophile Corynebacterium glutamicum revealed that the presence of large numbers of intrasubunit and intersubunit hydrophobic interactions, as well as the extensive formation of intersubunit ion-pair networks, were likely to be the main factors contributing to the higher thermostability of U. thermosphaericus DAPDH. This differs from S. thermophilum DAPDH, within which the unique hexameric assembly is likely to be responsible for its high thermostability. Analysis of the active site of U. thermosphaericus DAPDH revealed the key factors responsible for the marked difference in substrate specificity between DAPDH and the D-amino acid dehydrogenase recently created from DAPDH by introducing five point mutations [Akita et al. (2012). Biotechnol. Lett. 34, 1693-1699; 1701-1702].
| + | |
| - | | + | |
| - | Structural insight into the thermostable NADP(+)-dependent meso-diaminopimelate dehydrogenase from Ureibacillus thermosphaericus.,Akita H, Seto T, Ohshima T, Sakuraba H Acta Crystallogr D Biol Crystallogr. 2015 May;71(Pt 5):1136-46. doi:, 10.1107/S1399004715003673. Epub 2015 Apr 24. PMID:25945579<ref>PMID:25945579</ref>
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| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 3wyc" style="background-color:#fffaf0;"></div>
| + | |
| - | == References ==
| + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus thermosphaericus]] | |
| - | [[Category: Diaminopimelate dehydrogenase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Akita, H]] | + | [[Category: Ureibacillus thermosphaericus]] |
| - | [[Category: Ohshima, T]] | + | [[Category: Akita H]] |
| - | [[Category: Sakuraba, H]]
| + | [[Category: Ohshima T]] |
| - | [[Category: Oxidoreductase]] | + | [[Category: Sakuraba H]] |
| - | [[Category: Rossmann fold]] | + | |
