5yb7: Difference between revisions
New page: '''Unreleased structure''' The entry 5yb7 is ON HOLD until Sep 03 2019 Authors: Description: Category: Unreleased Structures |
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The | ==L-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 - L-ornithine complex== | ||
<StructureSection load='5yb7' size='340' side='right'caption='[[5yb7]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5yb7]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp._AIU_813 Pseudomonas sp. AIU 813]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YB7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YB7 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]] 2Å</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=ORN:L-ORNITHINE'>ORN</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=5yb7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yb7 OCA], [https://pdbe.org/5yb7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yb7 RCSB], [https://www.ebi.ac.uk/pdbsum/5yb7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yb7 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/W6JQJ6_9PSED W6JQJ6_9PSED] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
l-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 (l-AAO/MOG) catalyzes both the oxidative deamination and oxidative decarboxylation of the alpha-group of l-Lys to produce a keto acid and amide, respectively. l-AAO/MOG exhibits limited specificity for l-amino acid substrates with a basic side chain. We previously determined its ligand-free crystal structure and identified a key residue for maintaining the dual activities. Here, we determined the structures of l-AAO/MOG complexed with l-Lys, l-ornithine, and l-Arg and revealed its substrate recognition. Asp238 is located at the ceiling of a long hydrophobic pocket and forms a strong interaction with the terminal, positively charged group of the substrates. A mutational analysis on the D238A mutant indicated that the interaction is critical for substrate binding but not for catalytic control between the oxidase/monooxygenase activities. The catalytic activities of the D238E mutant unexpectedly increased, while the D238F mutant exhibited altered substrate specificity to long hydrophobic substrates. In the ligand-free structure, there are two channels connecting the active site and solvent, and a short region located at the dimer interface is disordered. In the l-Lys complex structure, a loop region is displaced to plug the channels. Moreover, the disordered region in the ligand-free structure forms a short helix in the substrate complex structures and creates the second binding site for the substrate. It is assumed that the amino acid substrate enters the active site of l-AAO/MOG through this route. Database: The atomic coordinates and structure factors (codes 5YB6, 5YB7, and 5YB8) have been deposited in the Protein Data Bank (http://wwpdb.org/). EC numbers: 1.4.3.2 (l-amino acid oxidase), 1.13.12.2 (lysine 2-monooxygenase). | |||
Ligand complex structures of l-amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 and its conformational change.,Im D, Matsui D, Arakawa T, Isobe K, Asano Y, Fushinobu S FEBS Open Bio. 2018 Feb 8;8(3):314-324. doi: 10.1002/2211-5463.12387. eCollection, 2018 Mar. PMID:29511608<ref>PMID:29511608</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 5yb7" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Amino acid oxidase 3D structures|Amino acid oxidase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Pseudomonas sp. AIU 813]] | |||
[[Category: Arakawa T]] | |||
[[Category: Asano Y]] | |||
[[Category: Fushinobu S]] | |||
[[Category: Im D]] | |||
[[Category: Isobe K]] | |||
[[Category: Matsui D]] | |||
Latest revision as of 11:25, 22 November 2023
L-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 - L-ornithine complexL-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 - L-ornithine complex
Structural highlights
FunctionPublication Abstract from PubMedl-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 (l-AAO/MOG) catalyzes both the oxidative deamination and oxidative decarboxylation of the alpha-group of l-Lys to produce a keto acid and amide, respectively. l-AAO/MOG exhibits limited specificity for l-amino acid substrates with a basic side chain. We previously determined its ligand-free crystal structure and identified a key residue for maintaining the dual activities. Here, we determined the structures of l-AAO/MOG complexed with l-Lys, l-ornithine, and l-Arg and revealed its substrate recognition. Asp238 is located at the ceiling of a long hydrophobic pocket and forms a strong interaction with the terminal, positively charged group of the substrates. A mutational analysis on the D238A mutant indicated that the interaction is critical for substrate binding but not for catalytic control between the oxidase/monooxygenase activities. The catalytic activities of the D238E mutant unexpectedly increased, while the D238F mutant exhibited altered substrate specificity to long hydrophobic substrates. In the ligand-free structure, there are two channels connecting the active site and solvent, and a short region located at the dimer interface is disordered. In the l-Lys complex structure, a loop region is displaced to plug the channels. Moreover, the disordered region in the ligand-free structure forms a short helix in the substrate complex structures and creates the second binding site for the substrate. It is assumed that the amino acid substrate enters the active site of l-AAO/MOG through this route. Database: The atomic coordinates and structure factors (codes 5YB6, 5YB7, and 5YB8) have been deposited in the Protein Data Bank (http://wwpdb.org/). EC numbers: 1.4.3.2 (l-amino acid oxidase), 1.13.12.2 (lysine 2-monooxygenase). Ligand complex structures of l-amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 and its conformational change.,Im D, Matsui D, Arakawa T, Isobe K, Asano Y, Fushinobu S FEBS Open Bio. 2018 Feb 8;8(3):314-324. doi: 10.1002/2211-5463.12387. eCollection, 2018 Mar. PMID:29511608[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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