7d4d: Difference between revisions
New page: '''Unreleased structure''' The entry 7d4d is ON HOLD until Paper Publication Authors: Kitagawa, M., Ito, N., Matsumoto, Y., Inagaki, K., Imada, K. Description: Structure of L-lysine ox... |
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==Structure of L-lysine oxidase precursor in complex with L-lysine (1.24M)== | |||
<StructureSection load='7d4d' size='340' side='right'caption='[[7d4d]], [[Resolution|resolution]] 2.29Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[7d4d]] is a 1 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=7D4D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7D4D 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]] 2.29Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</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=7d4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d4d OCA], [https://pdbe.org/7d4d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d4d RCSB], [https://www.ebi.ac.uk/pdbsum/7d4d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d4d ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A0G4DCU0_HYPRU A0A0G4DCU0_HYPRU] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Harmuful proteins are usually synthesized as inactive precursors and are activated by proteolytic processing. l-Amino acid oxidase (LAAO) is a flavoenzyme that catalyzes the oxidative deamination of l-amino acid to produce a 2-oxo acid with ammonia and highly toxic hydrogen peroxide and, therefore, is expressed as a precursor. The LAAO precursor shows significant variation in size and the cleavage pattern for activation. However, the molecular mechanism of how the propeptide suppresses the enzyme activity remains unclear except for deaminating/decarboxylating Pseudomonasl-phenylalanine oxidase (PAO), which has a short N-terminal propeptide composed of 14 residues. Here we show the inactivation mechanism of the l-lysine oxidase (LysOX) precursor (prLysOX), which has a long N-terminal propeptide composed of 77 residues, based on the crystal structure at 1.97â¯A resolution. The propeptide of prLysOX indirectly changes the active site structure to inhibit the enzyme activity. prLysOX retains weak enzymatic activity with strict specificity for l-lysine and shows raised activity in acidic conditions. The structures of prLysOX crystals that soaked in a solution with various concentrations of l-lysine have revealed that prLysOX can adopt two conformations; one is the inhibitory form, and the other is very similar to mature LysOX. The propeptide region of the latter form is disordered, and l-lysine is bound to the latter form. These results indicate that prLysOX uses a different strategy from PAO to suppress the enzyme activity and suggest that prLysOX can be activated quickly in response to the environmental change without proteolytic processing. | |||
Structural basis of enzyme activity regulation by the propeptide of l-lysine alpha-oxidase precursor from Trichoderma viride.,Kitagawa M, Ito N, Matsumoto Y, Saito M, Tamura T, Kusakabe H, Inagaki K, Imada K J Struct Biol X. 2021 Jan 13;5:100044. doi: 10.1016/j.yjsbx.2021.100044. , eCollection 2021. PMID:33554108<ref>PMID:33554108</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 7d4d" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
[[Category: Inagaki | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: Matsumoto | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Trichoderma viride]] | |||
[[Category: Imada K]] | |||
[[Category: Inagaki K]] | |||
[[Category: Ito N]] | |||
[[Category: Kitagawa M]] | |||
[[Category: Matsumoto Y]] | |||
Latest revision as of 19:26, 29 November 2023
Structure of L-lysine oxidase precursor in complex with L-lysine (1.24M)Structure of L-lysine oxidase precursor in complex with L-lysine (1.24M)
Structural highlights
FunctionPublication Abstract from PubMedHarmuful proteins are usually synthesized as inactive precursors and are activated by proteolytic processing. l-Amino acid oxidase (LAAO) is a flavoenzyme that catalyzes the oxidative deamination of l-amino acid to produce a 2-oxo acid with ammonia and highly toxic hydrogen peroxide and, therefore, is expressed as a precursor. The LAAO precursor shows significant variation in size and the cleavage pattern for activation. However, the molecular mechanism of how the propeptide suppresses the enzyme activity remains unclear except for deaminating/decarboxylating Pseudomonasl-phenylalanine oxidase (PAO), which has a short N-terminal propeptide composed of 14 residues. Here we show the inactivation mechanism of the l-lysine oxidase (LysOX) precursor (prLysOX), which has a long N-terminal propeptide composed of 77 residues, based on the crystal structure at 1.97â¯A resolution. The propeptide of prLysOX indirectly changes the active site structure to inhibit the enzyme activity. prLysOX retains weak enzymatic activity with strict specificity for l-lysine and shows raised activity in acidic conditions. The structures of prLysOX crystals that soaked in a solution with various concentrations of l-lysine have revealed that prLysOX can adopt two conformations; one is the inhibitory form, and the other is very similar to mature LysOX. The propeptide region of the latter form is disordered, and l-lysine is bound to the latter form. These results indicate that prLysOX uses a different strategy from PAO to suppress the enzyme activity and suggest that prLysOX can be activated quickly in response to the environmental change without proteolytic processing. Structural basis of enzyme activity regulation by the propeptide of l-lysine alpha-oxidase precursor from Trichoderma viride.,Kitagawa M, Ito N, Matsumoto Y, Saito M, Tamura T, Kusakabe H, Inagaki K, Imada K J Struct Biol X. 2021 Jan 13;5:100044. doi: 10.1016/j.yjsbx.2021.100044. , eCollection 2021. PMID:33554108[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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