5x2x - Revision history

OCA at 07:53, 22 November 2023

OCA — Wed, 22 Nov 2023 07:53:28 GMT

←Older revision		Revision as of 07:53, 22 November 2023
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	<StructureSection load='5x2x' size='340' side='right'caption='[[5x2x]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5x2x' size='340' side='right'caption='[[5x2x]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x2x]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X2X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5X2X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x2x]] 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=5X2X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X2X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4LM:(2E)-2-{[(1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}BUT-2-ENOIC+ACID'>4LM</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>~~</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]] 2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x2v\|5x2v]], [[5x2w\|5x2w]], [[5x2y\|5x2y]], [[5x2z\|5x2z]], [[5x30\|5x30]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4LM:(2E)-2-{[(1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}BUT-2-ENOIC+ACID'>4LM</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5x2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x2x OCA], [~~http~~://pdbe.org/5x2x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5x2x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5x2x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5x2x ProSAT]</span></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=5x2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x2x OCA], [https://pdbe.org/5x2x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x2x RCSB], [https://www.ebi.ac.uk/pdbsum/5x2x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x2x ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/MEGL_PSEPU MEGL_PSEPU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Harada, S~~]]	+	[[Category: Pseudomonas putida]]
-	[[Category: ~~Sato, D~~]]	+	[[Category: Harada S]]
-	[[Category: ~~Shiba, T~~]]	+	[[Category: Sato D]]
-	[[Category: ~~Lyase]]~~	+	[[Category: Shiba T]]
-	~~[[Category: Pyridoxal 5'-phosphate~~]]	+

OCA at 07:23, 7 October 2020

OCA — Wed, 07 Oct 2020 07:23:34 GMT

←Older revision		Revision as of 07:23, 7 October 2020
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	==Crystal structure of Pseudomonas putida methionine gamma-lyase wild type with L-homocysteine intermediates==		==Crystal structure of Pseudomonas putida methionine gamma-lyase wild type with L-homocysteine intermediates==
-	<StructureSection load='5x2x' size='340' side='right' caption='[[5x2x]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5x2x' size='340' side='right'caption='[[5x2x]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x2x]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X2X OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5X2X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x2x]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X2X OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5X2X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4LM:(2E)-2-{[(1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}BUT-2-ENOIC+ACID'>4LM</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4LM:(2E)-2-{[(1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}BUT-2-ENOIC+ACID'>4LM</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x2v\|5x2v]], [[5x2w\|5x2w]], [[5x2y\|5x2y]], [[5x2z\|5x2z]], [[5x30\|5x30]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x2v\|5x2v]], [[5x2w\|5x2w]], [[5x2y\|5x2y]], [[5x2z\|5x2z]], [[5x30\|5x30]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5x2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x2x OCA], [http://pdbe.org/5x2x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x2x RCSB], [http://www.ebi.ac.uk/pdbsum/5x2x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x2x ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5x2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x2x OCA], [http://pdbe.org/5x2x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x2x RCSB], [http://www.ebi.ac.uk/pdbsum/5x2x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x2x ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5x2x" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5x2x" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Methionine gamma-lyase 3D structures\|Methionine gamma-lyase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Harada, S]]		[[Category: Harada, S]]
	[[Category: Sato, D]]		[[Category: Sato, D]]

OCA at 11:28, 16 November 2017

OCA — Thu, 16 Nov 2017 11:28:08 GMT

←Older revision		Revision as of 11:28, 16 November 2017
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	</div>		</div>
	<div class="pdbe-citations 5x2x" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5x2x" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Methionine gamma-lyase\|Methionine gamma-lyase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:52, 3 August 2017

OCA — Thu, 03 Aug 2017 10:52:15 GMT

←Older revision		Revision as of 10:52, 3 August 2017
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5x2x" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5x2x" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Methionine gamma-lyase\|Methionine gamma-lyase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:38, 12 April 2017

OCA — Wed, 12 Apr 2017 11:38:03 GMT

←Older revision		Revision as of 11:38, 12 April 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5x2x is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Pseudomonas putida methionine gamma-lyase wild type with L-homocysteine intermediates==
		+	<StructureSection load='5x2x' size='340' side='right' caption='[[5x2x]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5x2x]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X2X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X2X FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4LM:(2E)-2-{[(1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}BUT-2-ENOIC+ACID'>4LM</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x2v\|5x2v]], [[5x2w\|5x2w]], [[5x2y\|5x2y]], [[5x2z\|5x2z]], [[5x30\|5x30]]</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5x2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x2x OCA], [http://pdbe.org/5x2x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x2x RCSB], [http://www.ebi.ac.uk/pdbsum/5x2x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x2x ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Methionine gamma-lyse (MGL) catalyzes the alpha, gamma-elimination of l-methionine and its derivatives as well as the alpha, beta-elimination of l-cysteine and its derivatives to produce alpha-keto acids, volatile thiols, and ammonia. The reaction mechanism of MGL has been characterized by enzymological studies using several site-directed mutants. The Pseudomonas putida MGL C116H mutant showed drastically reduced degradation activity toward methionine while retaining activity toward homocysteine. To understand the underlying mechanism and to discern the subtle differences between these substrates, we analyzed the crystal structures of the reaction intermediates. The complex formed between the C116H mutant and methionine demonstrated that a loop structure (Ala51-Asn64) in the adjacent subunit of the catalytic dimer cannot approach the cofactor pyridoxal 5'-phosphate (PLP) because His116 disrupts the interaction of Asp241 with Lys240, and the liberated side chain of Lys240 causes steric hindrance with this loop. Conversely, in the complex formed between C116H mutant and homocysteine, the thiol moiety of the substrate conjugated with PLP offsets the imidazole ring of His116 via a water molecule, disrupting the interaction of His116 and Asp241 and restoring the interaction of Asp241 with Lys240. These structural data suggest that the Cys116 to His mutation renders the enzyme inactive toward the original substrate, but activity is restored when the substrate is homocysteine due to substrate-assisted catalysis.

-	~~Authors: Shiba, T~~., Sato, D., ~~Harada~~, S.	+	Structural and mechanistic insights into homocysteine degradation by a mutant of methionine gamma-lyase based on substrate-assisted catalysis.,Sato D, Shiba T, Yunoto S, Furutani K, Fukumoto M, Kudou D, Tamura T, Inagaki K, Harada S Protein Sci. 2017 Mar 22. doi: 10.1002/pro.3158. PMID:28329912<ref>PMID:28329912</ref>

-	~~Description: Crystal structure~~ of ~~Pseudomonas putida methionine gamma~~-~~lyase wild type with L~~-~~homocysteine intermediates~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5x2x" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Harada, S]]
	[[Category: Sato, D]]		[[Category: Sato, D]]
	[[Category: Shiba, T]]		[[Category: Shiba, T]]
-	[[Category: ~~Harada, S~~]]	+	[[Category: Lyase]]
		+	[[Category: Pyridoxal 5'-phosphate]]

OCA at 20:07, 15 March 2017

OCA — Wed, 15 Mar 2017 20:07:41 GMT

←Older revision		Revision as of 20:07, 15 March 2017
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	Description: Crystal structure of Pseudomonas putida methionine gamma-lyase wild type with L-homocysteine intermediates		Description: Crystal structure of Pseudomonas putida methionine gamma-lyase wild type with L-homocysteine intermediates
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Sato, D]]
	[[Category: Shiba, T]]		[[Category: Shiba, T]]
	[[Category: Harada, S]]		[[Category: Harada, S]]
-	[[Category: Sato, D]]

OCA: Protected "5x2x" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 15:40:56 GMT

Protected "5x2x" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:40, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5x2x is ON HOLD until Paper Publication Authors: Shiba, T., Sato, D., Harada, S. Description: Crystal structure of Pseudomonas putida methionine ga...

OCA — Thu, 09 Mar 2017 15:40:55 GMT

New page: '''Unreleased structure''' The entry 5x2x is ON HOLD until Paper Publication Authors: Shiba, T., Sato, D., Harada, S. Description: Crystal structure of Pseudomonas putida methionine ga...

New page

'''Unreleased structure'''

The entry 5x2x is ON HOLD until Paper Publication

Authors: Shiba, T., Sato, D., Harada, S.

Description: Crystal structure of Pseudomonas putida methionine gamma-lyase wild type with L-homocysteine intermediates
[[Category: Unreleased Structures]]
[[Category: Shiba, T]]
[[Category: Harada, S]]
[[Category: Sato, D]]