7f1p
From Proteopedia
(Difference between revisions)
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==Crystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant ligand-free form.== | ==Crystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant ligand-free form.== | ||
- | <StructureSection load='7f1p' size='340' side='right'caption='[[7f1p]]' scene=''> | + | <StructureSection load='7f1p' size='340' side='right'caption='[[7f1p]], [[Resolution|resolution]] 2.40Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
- | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F1P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F1P FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7f1p]] 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=7F1P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F1P FirstGlance]. <br> |
- | </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=7f1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f1p OCA], [https://pdbe.org/7f1p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f1p RCSB], [https://www.ebi.ac.uk/pdbsum/7f1p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f1p ProSAT]</span></td></tr> | + | </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=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</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=7f1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f1p OCA], [https://pdbe.org/7f1p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f1p RCSB], [https://www.ebi.ac.uk/pdbsum/7f1p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f1p ProSAT]</span></td></tr> | ||
</table> | </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> | ||
+ | </div> | ||
+ | <div class="pdbe-citations 7f1p" style="background-color:#fffaf0;"></div> | ||
+ | |||
+ | ==See Also== | ||
+ | *[[Methionine gamma-lyase 3D structures|Methionine gamma-lyase 3D structures]] | ||
+ | == References == | ||
+ | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
+ | [[Category: Pseudomonas putida]] | ||
[[Category: Handa H]] | [[Category: Handa H]] | ||
[[Category: Inagaki K]] | [[Category: Inagaki K]] |
Current revision
Crystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant ligand-free form.
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Categories: Large Structures | Pseudomonas putida | Handa H | Inagaki K | Kudo D | Murota M | Okawa A | Shiba T | Tamura T | Yasuda E