View source for 5x7n


==Crystal structure of meso-diaminopimelate decarboxylase (DAPDC) from Corynebacterium glutamicum==
<StructureSection load='5x7n' size='340' side='right'caption='[[5x7n]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5x7n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_glutamicum_ATCC_13032 Corynebacterium glutamicum ATCC 13032]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X7N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X7N 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]] 1.72&#8491;</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>, <scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=5x7n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x7n OCA], [https://pdbe.org/5x7n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x7n RCSB], [https://www.ebi.ac.uk/pdbsum/5x7n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x7n ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DCDA_CORGL DCDA_CORGL] Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine.[HAMAP-Rule:MF_02120]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
l-lysine is an essential amino acid that is widely used as a food supplement for humans and animals. meso-Diaminopimelic acid decarboxylase (DAPDC) catalyzes the final step in the de novol-lysine biosynthetic pathway by converting meso-diaminopimelic acid (meso-DAP) into l-lysine by decarboxylation reaction. To elucidate its molecular mechanisms, we determined the crystal structure of DAPDC from Corynebacterium glutamicum (CgDAPDC). The PLP cofactor is bound at the center of the barrel domain and forms a Schiff base with the catalytic Lys75 residue. We also determined the CgDAPDC structure in complex with both pyridoxal 5'-phosphate (PLP) and the l-lysine product and revealed that the protein has an optimal substrate binding pocket to accommodate meso-DAP as a substrate. Structural comparison of CgDAPDC with other amino acid decarboxylases with different substrate specificities revealed that the position of the alpha15 helix in CgDAPDC and the residues located on the helix are crucial for determining the substrate specificities of the amino acid decarboxylases.

Structural basis for substrate specificity of meso-diaminopimelic acid decarboxylase from Corynebacterium glutamicum.,Son HF, Kim KJ Biochem Biophys Res Commun. 2018 Jan 8;495(2):1815-1821. doi:, 10.1016/j.bbrc.2017.11.097. Epub 2017 Dec 9. PMID:29233695<ref>PMID:29233695</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5x7n" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Corynebacterium glutamicum ATCC 13032]]
[[Category: Large Structures]]
[[Category: Kim K-J]]
[[Category: Son H-F]]