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| | <StructureSection load='5gjo' size='340' side='right'caption='[[5gjo]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='5gjo' size='340' side='right'caption='[[5gjo]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5gjo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"ancyromonas_ruminantium"_certes_1889 "ancyromonas ruminantium" certes 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GJO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GJO FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5gjo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Selenomonas_ruminantium Selenomonas ruminantium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GJO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GJO FirstGlance]. <br> |
| - | </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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.8Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5gjm|5gjm]], [[5gjn|5gjn]], [[5gjp|5gjp]]</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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ldc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=971 "Ancyromonas ruminantium" Certes 1889])</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=5gjo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gjo OCA], [https://pdbe.org/5gjo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gjo RCSB], [https://www.ebi.ac.uk/pdbsum/5gjo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gjo 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/Lysine_decarboxylase Lysine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.18 4.1.1.18] </span></td></tr> | + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5gjo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gjo OCA], [http://pdbe.org/5gjo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gjo RCSB], [http://www.ebi.ac.uk/pdbsum/5gjo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gjo ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/DCLO_SELRU DCLO_SELRU] |
| | <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: Ancyromonas ruminantium certes 1889]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Lysine decarboxylase]] | + | [[Category: Selenomonas ruminantium]] |
| - | [[Category: Kim, K J]] | + | [[Category: Kim K-J]] |
| - | [[Category: Sagong, H Y]] | + | [[Category: Sagong H-Y]] |
| - | [[Category: Barrel domain]]
| + | |
| - | [[Category: Lyase]]
| + | |
| Structural highlights
Function
DCLO_SELRU
Publication Abstract from PubMed
Lysine decarboxylase (LDC) catalyzes the decarboxylation of l-lysine to produce cadaverine, an important industrial platform chemical for bio-based polyamides. However, due to high flexibility at the pyridoxal 5-phosphate (PLP) binding site, use of the enzyme for cadaverine production requires continuous supplement of large amounts of PLP. In order to develop an LDC enzyme from Selenomonas ruminantium (SrLDC) with an enhanced affinity for PLP, we introduced an internal disulfide bond between Ala225 and Thr302 residues with a desire to retain the PLP binding site in a closed conformation. The SrLDCA225C/T302C mutant showed a yellow color and the characteristic UV/Vis absorption peaks for enzymes with bound PLP, and exhibited three-fold enhanced PLP affinity compared with the wild-type SrLDC. The mutant also exhibited a dramatically enhanced LDC activity and cadaverine conversion particularly under no or low PLP concentrations. Moreover, introduction of the disulfide bond rendered SrLDC more resistant to high pH and temperature. The formation of the introduced disulfide bond and the maintenance of the PLP binding site in the closed conformation were confirmed by determination of the crystal structure of the mutant. This study shows that disulfide bond-mediated spatial reconstitution can be a platform technology for development of enzymes with enhanced PLP affinity.
Lysine Decarboxylase with an Enhanced Affinity for Pyridoxal 5-Phosphate by Disulfide Bond-Mediated Spatial Reconstitution.,Sagong HY, Kim KJ PLoS One. 2017 Jan 17;12(1):e0170163. doi: 10.1371/journal.pone.0170163., eCollection 2017. PMID:28095457[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Sagong HY, Kim KJ. Lysine Decarboxylase with an Enhanced Affinity for Pyridoxal 5-Phosphate by Disulfide Bond-Mediated Spatial Reconstitution. PLoS One. 2017 Jan 17;12(1):e0170163. doi: 10.1371/journal.pone.0170163., eCollection 2017. PMID:28095457 doi:http://dx.doi.org/10.1371/journal.pone.0170163
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