7f1u: Difference between revisions

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-'''Unreleased structure'''
-The entry 7f1u is ON HOLD
+==Crystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant with L-methionine intermediates==
+<StructureSection load='7f1u' size='340' side='right'caption='[[7f1u]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[7f1u]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F1U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F1U 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]] 2.4&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3LM:(2E)-2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]-4-(METHYLSULFANYL)BUT-2-ENOIC+ACID'>3LM</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</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=7f1u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f1u OCA], [https://pdbe.org/7f1u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f1u RCSB], [https://www.ebi.ac.uk/pdbsum/7f1u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f1u ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MEGL_PSEPU MEGL_PSEPU]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+l-Methionine gamma-lyse (MGL), a pyridoxal 5'-phosphate-dependent enzyme, catalyzes the alpha,gamma-elimination of l-methionine (l-Met) and l-homocysteine (l-Hcy) to produce alpha-keto acids, thiols, and ammonia. Previously, various mutant enzymes of Pseudomonas putida MGL (PpMGL) were prepared to identify a homocysteine (Hcy)-specific enzyme that would assist the diagnosis of homocystinuria. Among the mutat enzymes the Q349S mutant exhibited high degradation activity toward l-Hcy. In the present study, PpMGL Q349S was characterized; the results suggested that it could be applied to determine the amount of l-Hcy. Compared to the wild-type PpMGL, specific activities of the Q349S mutant with l-Hcy and l-Met were 1.5 and 0.7 times, respectively. Additionally, we confirmed that l-Hcy in plasma samples could be accurately detected using the Q349S mutant by preincubating it with cysteine desulfurase (CsdA). Furthermore, we determined the X-ray crystal structure of PpMGL Q349S l-Met or l-Hcy complexes Michaelis complex, germinal diamine, and external aldimine at 2.25-2.40 A. These 3D structures showed that the interaction partner of the beta-hydroxyl group of Thr355 in the wild-type PpMGL was changed to the carboxyl group of the Hcy-PLP external aldimine in the Q349S mutant. The interaction of Ser349 and Arg375 was different between l-Met and l-Hcy recognition, indicating that it was important for the recognition of the carboxyl group of the substrate.
-Authors: Okawa, A., Handa, H., Yasuda, E., Murota, M., Kudo, D., Tamura, T., Shiba, T., Inagaki, K.
+Characterization and application of l-methionine gamma-lyase Q349S mutant enzyme with an enhanced activity toward l-homocysteine.,Okawa A, Handa H, Yasuda E, Murota M, Kudo D, Tamura T, Shiba T, Inagaki K J Biosci Bioeng. 2022 Mar;133(3):213-221. doi: 10.1016/j.jbiosc.2021.11.008. Epub, 2021 Dec 23. PMID:34953671<ref>PMID:34953671</ref>
-Description: Crystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant ligand-free form.
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Murota, M]]
+<div class="pdbe-citations 7f1u" style="background-color:#fffaf0;"></div>
-[[Category: Kudo, D]]
-[[Category: Yasuda, E]]
+==See Also==
-[[Category: Tamura, T]]
+*[[Methionine gamma-lyase 3D structures|Methionine gamma-lyase 3D structures]]
-[[Category: Inagaki, K]]
+== References ==
-[[Category: Shiba, T]]
+<references/>
-[[Category: Handa, H]]
+__TOC__
-[[Category: Okawa, A]]
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Pseudomonas putida]]
+[[Category: Handa H]]
+[[Category: Inagaki K]]
+[[Category: Kudo D]]
+[[Category: Murota M]]
+[[Category: Okawa A]]
+[[Category: Shiba T]]
+[[Category: Tamura T]]
+[[Category: Yasuda E]]