7c3h: Difference between revisions
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The | ==Structure of L-lysine oxidase in complex with L-lysine== | ||
<StructureSection load='7c3h' size='340' side='right'caption='[[7c3h]], [[Resolution|resolution]] 1.70Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[7c3h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichoderma_viride Trichoderma viride]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7C3H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7C3H 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]] 1.7Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</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=7c3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7c3h OCA], [https://pdbe.org/7c3h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7c3h RCSB], [https://www.ebi.ac.uk/pdbsum/7c3h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7c3h ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A0G4DCU0_HYPRU A0A0G4DCU0_HYPRU] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
l-Lysine oxidase (LysOX) is a FAD-dependent homodimeric enzyme that catalyzes the oxidative deamination of l-lysine to produce alpha-keto-epsilon-aminocaproate with ammonia and hydrogen peroxide. LysOX shows strict substrate specificity for l-lysine, whereas most l-amino acid oxidases (LAAOs) exhibit broad substrate specificity for l-amino acids. Previous studies of LysOX showed that overall structural similarity to the well-studied snake venom LAAOs. However, the molecular mechanism of strict specificity for l-lysine was still unclear. We here determined the structure of LysOX in complex with l-lysine at 1.7 A resolution. The structure revealed that the hydrogen bonding network formed by D212, D315, and A440 with two water molecules is responsible for the recognition of the side chain amino group. In addition, a narrow hole formed by five hydrophobic residues in the active site contributes to strict substrate specificity. Mutation studies demonstrated that D212 and D315 are essential for l-lysine recognition, and the D212A/D315A double mutant LysOX showed different substrate specificity from LysOX. Moreover, the structural basis of the substrate specificity change has also been revealed by the structural analysis of the mutant variant and its substrate complexes. These results clearly explain the molecular mechanism of the strict specificity of LysOX and suggest that LysOX is a potential candidate for a template to design LAAOs specific to other l-amino acids. | |||
Structural basis of strict substrate recognition of l-lysine alpha-oxidase from Trichoderma viride.,Kondo H, Kitagawa M, Matsumoto Y, Saito M, Amano M, Sugiyama S, Tamura T, Kusakabe H, Inagaki K, Imada K Protein Sci. 2020 Sep 7. doi: 10.1002/pro.3946. PMID:32894626<ref>PMID:32894626</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 7c3h" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Trichoderma viride]] | |||
[[Category: Imada K]] | |||
[[Category: Kitagawa M]] | |||
[[Category: Kondo H]] | |||
[[Category: Sugiyama S]] | |||
Latest revision as of 18:54, 29 November 2023
Structure of L-lysine oxidase in complex with L-lysineStructure of L-lysine oxidase in complex with L-lysine
Structural highlights
FunctionPublication Abstract from PubMedl-Lysine oxidase (LysOX) is a FAD-dependent homodimeric enzyme that catalyzes the oxidative deamination of l-lysine to produce alpha-keto-epsilon-aminocaproate with ammonia and hydrogen peroxide. LysOX shows strict substrate specificity for l-lysine, whereas most l-amino acid oxidases (LAAOs) exhibit broad substrate specificity for l-amino acids. Previous studies of LysOX showed that overall structural similarity to the well-studied snake venom LAAOs. However, the molecular mechanism of strict specificity for l-lysine was still unclear. We here determined the structure of LysOX in complex with l-lysine at 1.7 A resolution. The structure revealed that the hydrogen bonding network formed by D212, D315, and A440 with two water molecules is responsible for the recognition of the side chain amino group. In addition, a narrow hole formed by five hydrophobic residues in the active site contributes to strict substrate specificity. Mutation studies demonstrated that D212 and D315 are essential for l-lysine recognition, and the D212A/D315A double mutant LysOX showed different substrate specificity from LysOX. Moreover, the structural basis of the substrate specificity change has also been revealed by the structural analysis of the mutant variant and its substrate complexes. These results clearly explain the molecular mechanism of the strict specificity of LysOX and suggest that LysOX is a potential candidate for a template to design LAAOs specific to other l-amino acids. Structural basis of strict substrate recognition of l-lysine alpha-oxidase from Trichoderma viride.,Kondo H, Kitagawa M, Matsumoto Y, Saito M, Amano M, Sugiyama S, Tamura T, Kusakabe H, Inagaki K, Imada K Protein Sci. 2020 Sep 7. doi: 10.1002/pro.3946. PMID:32894626[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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