View source for 3wbf


==Crystal Structure of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum co-crystallized with NADP+ and DAP==
<StructureSection load='3wbf' size='340' side='right'caption='[[3wbf]], [[Resolution|resolution]] 2.12&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3wbf]] 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=3WBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WBF 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]] 2.12&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=API:2,6-DIAMINOPIMELIC+ACID'>API</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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=3wbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wbf OCA], [https://pdbe.org/3wbf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wbf RCSB], [https://www.ebi.ac.uk/pdbsum/3wbf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wbf ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q67PI3_SYMTH Q67PI3_SYMTH] 
<div style="background-color:#fffaf0;">
== 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<ref>PMID:24339368</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3wbf" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Symbiobacterium thermophilum IAM 14863]]
[[Category: Guo RT]]
[[Category: Huang CH]]
[[Category: Li Z]]
[[Category: Liu WD]]
[[Category: Wu QQ]]
[[Category: Zhu DM]]