5x7n: Difference between revisions
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==Crystal | ==Crystal structure of meso-diaminopimelate decarboxylase (DAPDC) from Corynebacterium glutamicum== | ||
<StructureSection load='5x7n' size='340' side='right' caption='[[5x7n]], [[Resolution|resolution]] 1.72Å' scene=''> | <StructureSection load='5x7n' size='340' side='right'caption='[[5x7n]], [[Resolution|resolution]] 1.72Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5x7n]] is a 2 chain structure. 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 [http:// | <table><tr><td colspan='2'>[[5x7n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Corgl Corgl]. 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 [http://proteopedia.org/fgij/fg.htm?mol=5X7N 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>, <scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr> | </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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5x7m|5x7m]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5x7m|5x7m]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lysA, Cgl1180, cg1334 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=196627 CORGL])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Diaminopimelate_decarboxylase Diaminopimelate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.20 4.1.1.20] </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_decarboxylase Diaminopimelate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.20 4.1.1.20] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http:// | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5x7n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x7n OCA], [http://pdbe.org/5x7n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x7n RCSB], [http://www.ebi.ac.uk/pdbsum/5x7n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x7n ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Corgl]] | |||
[[Category: Diaminopimelate decarboxylase]] | [[Category: Diaminopimelate decarboxylase]] | ||
[[Category: Large Structures]] | |||
[[Category: Kim, K J]] | [[Category: Kim, K J]] | ||
[[Category: Son, H F]] | [[Category: Son, H F]] | ||
[[Category: Decarboxylase]] | [[Category: Decarboxylase]] | ||
[[Category: Lyase]] | [[Category: Lyase]] | ||
Revision as of 12:46, 9 September 2020
Crystal structure of meso-diaminopimelate decarboxylase (DAPDC) from Corynebacterium glutamicumCrystal structure of meso-diaminopimelate decarboxylase (DAPDC) from Corynebacterium glutamicum
Structural highlights
Function[DCDA_CORGL] Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine.[HAMAP-Rule:MF_02120] Publication Abstract from PubMedl-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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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