View source for 5gjn


==Crystal structure of Lysine decarboxylase from Selenomonas ruminantium in P43212 space group==
<StructureSection load='5gjn' size='340' side='right'caption='[[5gjn]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5gjn]] is a 1 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=5GJN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GJN 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&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=5gjn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gjn OCA], [https://pdbe.org/5gjn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gjn RCSB], [https://www.ebi.ac.uk/pdbsum/5gjn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gjn ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DCLO_SELRU DCLO_SELRU] 
<div style="background-color:#fffaf0;">
== 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<ref>PMID:27861532</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5gjn" style="background-color:#fffaf0;"></div>

==See Also==
*[[Ornithine decarboxylase|Ornithine decarboxylase]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Selenomonas ruminantium]]
[[Category: Kim K-J]]
[[Category: Sagong H-Y]]