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| | <StructureSection load='5gjm' size='340' side='right'caption='[[5gjm]], [[Resolution|resolution]] 2.91Å' scene=''> | | <StructureSection load='5gjm' size='340' side='right'caption='[[5gjm]], [[Resolution|resolution]] 2.91Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5gjm]] 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=5GJM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GJM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5gjm]] 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=5GJM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GJM 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></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]] 2.91Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5gjn|5gjn]], [[5gjo|5gjo]], [[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></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=5gjm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gjm OCA], [https://pdbe.org/5gjm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gjm RCSB], [https://www.ebi.ac.uk/pdbsum/5gjm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gjm 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=5gjm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gjm OCA], [http://pdbe.org/5gjm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gjm RCSB], [http://www.ebi.ac.uk/pdbsum/5gjm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gjm 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) is a crucial enzyme for acid stress resistance and is also utilized for the biosynthesis of cadaverine, a promising building block for bio-based polyamides. We determined the crystal structure of LDC from Selenomonas ruminantium (SrLDC). SrLDC functions as a dimer and each monomer consists of two distinct domains; a PLP-binding barrel domain and a sheet domain. We also determined the structure of SrLDC in complex with PLP and cadaverine and elucidated the binding mode of cofactor and substrate. Interestingly, compared with the apo-form of SrLDC, the SrLDC in complex with PLP and cadaverine showed a remarkable structural change at the PLP binding site. The PLP binding site of SrLDC contains the highly flexible loops with high b-factors and showed an open-closed conformational change upon the binding of PLP. In fact, SrLDC showed no LDC activity without PLP supplement, and we suggest that highly flexible PLP binding site results in low PLP affinity of SrLDC. In addition, other structurally homologous enzymes also contain the flexible PLP binding site, which indicates that high flexibility at the PLP binding site and low PLP affinity seems to be a common feature of these enzyme family.
Crystal Structure and Pyridoxal 5-Phosphate Binding Property of Lysine Decarboxylase from Selenomonas ruminantium.,Sagong HY, Son HF, Kim S, Kim YH, Kim IK, Kim KJ PLoS One. 2016 Nov 18;11(11):e0166667. doi: 10.1371/journal.pone.0166667., eCollection 2016. PMID:27861532[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Sagong HY, Son HF, Kim S, Kim YH, Kim IK, Kim KJ. Crystal Structure and Pyridoxal 5-Phosphate Binding Property of Lysine Decarboxylase from Selenomonas ruminantium. PLoS One. 2016 Nov 18;11(11):e0166667. doi: 10.1371/journal.pone.0166667., eCollection 2016. PMID:27861532 doi:http://dx.doi.org/10.1371/journal.pone.0166667
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