7f1u: Difference between revisions
New page: '''Unreleased structure''' The entry 7f1u is ON HOLD Authors: Okawa, A., Handa, H., Yasuda, E., Murota, M., Kudo, D., Tamura, T., Shiba, T., Inagaki, K. Description: Crystal structure ... |
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==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]] 2.40Å' 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]] 2.4Å</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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 7f1u" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: | ==See Also== | ||
[[Category: | *[[Methionine gamma-lyase 3D structures|Methionine gamma-lyase 3D structures]] | ||
[[Category: | == References == | ||
[[Category: Shiba | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: | </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]] | |||
Latest revision as of 20:08, 29 November 2023
Crystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant with L-methionine intermediatesCrystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant with L-methionine intermediates
Structural highlights
FunctionPublication Abstract from PubMedl-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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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