5gjp: Difference between revisions

Latest revision as of 11:33, 2 August 2023

Crystal structure of SrLDC in complex with PLP and Cadaverine

Structural highlights

5gjp is a 1 chain structure with sequence from Selenomonas ruminantium. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:	GOL, MG, N2P, NA, PGE, PLP
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

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:https://dx.doi.org/10.1371/journal.pone.0166667

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OCA

[1] 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:https://dx.doi.org/10.1371/journal.pone.0166667

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='5gjp' size='340' side='right'caption='[[5gjp]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5gjp]] is a 1 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=5GJP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GJP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5gjp]] 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=5GJP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GJP 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=N2P:PENTANE-1,5-DIAMINE'>N2P</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 2.5&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5gjm|5gjm]], [[5gjn|5gjn]], [[5gjo|5gjo]]</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=N2P:PENTANE-1,5-DIAMINE'>N2P</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=5gjp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gjp OCA], [https://pdbe.org/5gjp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gjp RCSB], [https://www.ebi.ac.uk/pdbsum/5gjp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gjp 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=5gjp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gjp OCA], [http://pdbe.org/5gjp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gjp RCSB], [http://www.ebi.ac.uk/pdbsum/5gjp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gjp ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/DCLO_SELRU DCLO_SELRU]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Ancyromonas ruminantium certes 1889]]
 [[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]]

5gjp: Difference between revisions

Latest revision as of 11:33, 2 August 2023

Crystal structure of SrLDC in complex with PLP and Cadaverine

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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