7f1p - Revision history

OCA at 17:07, 29 November 2023

OCA — Wed, 29 Nov 2023 17:07:59 GMT

←Older revision		Revision as of 17:07, 29 November 2023
Line 1:		Line 1:

	==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]]

OCA at 02:51, 21 April 2022

OCA — Thu, 21 Apr 2022 02:51:52 GMT

←Older revision		Revision as of 02:51, 21 April 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7f1p ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant ligand-free form.==
-		+	<StructureSection load='7f1p' size='340' side='right'caption='[[7f1p]]' scene=''>
-	~~Authors~~: ~~Okawa, A~~.~~, Handa, H~~.~~, Yasuda, E~~.~~, Murota, M~~., ~~Kudo, D~~., ~~Tamura, T~~., ~~Shiba, T~~., ~~Inagaki, K~~.	+	== 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>
-	~~Description~~: ~~Crystal structure of Pseudomonas putida methionine gamma~~-~~lyase Q349S mutant ligand-free form~~.	+	</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>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Murota, M~~]]	+	__TOC__
-	[[Category: ~~Kudo, D~~]]	+	</StructureSection>
-	[[Category: ~~Yasuda, E~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Tamura, T~~]]	+	[[Category: Handa H]]
-	[[Category: ~~Inagaki, K~~]]	+	[[Category: Inagaki K]]
-	[[Category: Shiba, T]]	+	[[Category: Kudo D]]
-	[[Category: ~~Handa, H~~]]	+	[[Category: Murota M]]
-	[[Category: ~~Okawa, A~~]]	+	[[Category: Okawa A]]
		+	[[Category: Shiba T]]
		+	[[Category: Tamura T]]
		+	[[Category: Yasuda E]]

OCA at 06:04, 25 June 2021

OCA — Fri, 25 Jun 2021 06:04:41 GMT

←Older revision		Revision as of 06:04, 25 June 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7f1p is ON HOLD	+	The entry 7f1p is ON HOLD until Paper Publication

	Authors: Okawa, A., Handa, H., Yasuda, E., Murota, M., Kudo, D., Tamura, T., Shiba, T., Inagaki, K.		Authors: Okawa, A., Handa, H., Yasuda, E., Murota, M., Kudo, D., Tamura, T., Shiba, T., Inagaki, K.

OCA: Protected "7f1p" [edit=sysop:move=sysop]

OCA — Thu, 17 Jun 2021 13:33:18 GMT

Protected "7f1p" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:33, 17 June 2021

OCA: New page: '''Unreleased structure''' The entry 7f1p is ON HOLD Authors: Okawa, A., Handa, H., Yasuda, E., Murota, M., Kudo, D., Tamura, T., Shiba, T., Inagaki, K. Description: Crystal structure ...

OCA — Thu, 17 Jun 2021 13:33:17 GMT

New page: '''Unreleased structure''' The entry 7f1p is ON HOLD Authors: Okawa, A., Handa, H., Yasuda, E., Murota, M., Kudo, D., Tamura, T., Shiba, T., Inagaki, K. Description: Crystal structure ...

New page

'''Unreleased structure'''

The entry 7f1p is ON HOLD

Authors: Okawa, A., Handa, H., Yasuda, E., Murota, M., Kudo, D., Tamura, T., Shiba, T., Inagaki, K.

Description: Crystal structure of Pseudomonas putida methionine gamma-lyase Q349S mutant ligand-free form.
[[Category: Unreleased Structures]]
[[Category: Murota, M]]
[[Category: Kudo, D]]
[[Category: Yasuda, E]]
[[Category: Tamura, T]]
[[Category: Inagaki, K]]
[[Category: Shiba, T]]
[[Category: Handa, H]]
[[Category: Okawa, A]]