6egr - Revision history

OCA at 07:51, 23 October 2019

OCA — Wed, 23 Oct 2019 07:51:07 GMT

←Older revision		Revision as of 07:51, 23 October 2019
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	==Crystal structure of Citrobacter freundii methionine gamma-lyase with V358Y replacement==		==Crystal structure of Citrobacter freundii methionine gamma-lyase with V358Y replacement==
-	<StructureSection load='6egr' size='340' side='right' caption='[[6egr]], [[Resolution\|resolution]] 1.45Å' scene=''>	+	<StructureSection load='6egr' size='340' side='right'caption='[[6egr]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6egr]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EGR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EGR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6egr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_freundii"_braak_1928 "bacterium freundii" braak 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EGR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EGR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AN672_11005, BED45_02240, BEH73_12300, CfB38_0199, HMPREF3212_02785, TO64_18625 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=546 "Bacterium freundii" Braak 1928])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methionine_gamma-lyase Methionine gamma-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.4.1.11 4.4.1.11] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methionine_gamma-lyase Methionine gamma-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.4.1.11 4.4.1.11] </span></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=6egr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6egr OCA], [http://pdbe.org/6egr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6egr RCSB], [http://www.ebi.ac.uk/pdbsum/6egr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6egr ProSAT]</span></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=6egr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6egr OCA], [http://pdbe.org/6egr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6egr RCSB], [http://www.ebi.ac.uk/pdbsum/6egr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6egr ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Methionine deprivation of cancer cells, which are deficient in methionine biosynthesis, has been envisioned as a therapeutic strategy to reduce cancer cell viability. Methionine gamma-lyase (MGL), an enzyme that degrades methionine, has been exploited to selectively remove the amino acid from cancer cell environment. In order to increase MGL catalytic activity, we performed sequence and structure conservation analysis of MGLs from various microorganisms. Whereas most of the residues in the active site and at the dimer interface were found to be conserved, residues located in the C-terminal flexible loop, forming a wall of the active site entry channel, were found to be variable. Therefore, we carried out site-saturation mutagenesis at four independent positions of the C-terminal flexible loop, P357, V358, P360 and A366 of MGL from Citrobacter freundii, generating libraries that were screened for activity. Among the active variants, V358Y exhibits a 1.9-fold increase in the catalytic rate and a 3-fold increase in KM, resulting in a catalytic efficiency similar to wild type MGL. V358Y cytotoxic activity was assessed towards a panel of cancer and nonmalignant cell lines and found to exhibit IC50 lower than the wild type. The comparison of the 3D-structure of V358Y MGL with other MGL available structures indicates that the C-terminal loop is either in an open or closed conformation that does not depend on the amino acid at position 358. Nevertheless, mutations at this position allosterically affects catalysis.
		+
		+	Engineering methionine gamma-lyase from Citrobacter freundii for anticancer activity.,Raboni S, Revtovich S, Demitri N, Giabbai B, Storici P, Cocconcelli C, Faggiano S, Rosini E, Pollegioni L, Galati S, Buschini A, Morozova E, Kulikova V, Nikulin A, Gabellieri E, Cioni P, Demidkina T, Mozzarelli A Biochim Biophys Acta Proteins Proteom. 2018 Dec;1866(12):1260-1270. doi:, 10.1016/j.bbapap.2018.09.011. Epub 2018 Sep 27. PMID:30268810<ref>PMID:30268810</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6egr" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacterium freundii braak 1928]]
		+	[[Category: Large Structures]]
	[[Category: Methionine gamma-lyase]]		[[Category: Methionine gamma-lyase]]
	[[Category: Demidkina, T V]]		[[Category: Demidkina, T V]]

OCA at 08:08, 10 October 2018

OCA — Wed, 10 Oct 2018 08:08:17 GMT

←Older revision		Revision as of 08:08, 10 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6egr ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of Citrobacter freundii methionine gamma-lyase with V358Y replacement==
-		+	<StructureSection load='6egr' size='340' side='right' caption='[[6egr]], [[Resolution\|resolution]] 1.45Å' scene=''>
-	~~Authors~~: ~~Revtovich, S~~.V.~~, Demitri, N~~., ~~Raboni~~, S., ~~Nikulin, A~~.D., ~~Morozova, E~~.A., ~~Demidkina~~, T.V., ~~Storici, P~~., ~~Mozzarelli, A~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6egr]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EGR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EGR FirstGlance]. <br>
-	~~Description: Crystal structure of Citrobacter freundii methionine gamma-lyase with V358Y replacement~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
-	[[Category: ~~Storici~~, P]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methionine_gamma-lyase Methionine gamma-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.4.1.11 4.4.1.11] </span></td></tr>
-	[[Category: ~~Morozova~~, ~~E.A~~]]	+	<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=6egr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6egr OCA], [http://pdbe.org/6egr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6egr RCSB], [http://www.ebi.ac.uk/pdbsum/6egr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6egr ProSAT]</span></td></tr>
-	[[Category: ~~Demidkina~~, ~~T.V~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Methionine gamma-lyase]]
		+	[[Category: Demidkina, T V]]
		+	[[Category: Demitri, N]]
		+	[[Category: Morozova, E A]]
	[[Category: Mozzarelli, A]]		[[Category: Mozzarelli, A]]
-	[[Category: ~~Demitri~~, N]]	+	[[Category: Nikulin, A D]]
	[[Category: Raboni, S]]		[[Category: Raboni, S]]
-	[[Category: Revtovich, S.V]]	+	[[Category: Revtovich, S V]]
-	[[Category: ~~Nikulin~~, ~~A.D~~]]	+	[[Category: Storici, P]]
		+	[[Category: Lyase]]

OCA at 08:15, 4 October 2017

OCA — Wed, 04 Oct 2017 08:15:48 GMT

←Older revision		Revision as of 08:15, 4 October 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6egr is ON HOLD	+	The entry 6egr is ON HOLD until Paper Publication

	Authors: Revtovich, S.V., Demitri, N., Raboni, S., Nikulin, A.D., Morozova, E.A., Demidkina, T.V., Storici, P., Mozzarelli, A.		Authors: Revtovich, S.V., Demitri, N., Raboni, S., Nikulin, A.D., Morozova, E.A., Demidkina, T.V., Storici, P., Mozzarelli, A.
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Storici, P]]		[[Category: Storici, P]]
		+	[[Category: Morozova, E.A]]
	[[Category: Demidkina, T.V]]		[[Category: Demidkina, T.V]]
		+	[[Category: Mozzarelli, A]]
	[[Category: Demitri, N]]		[[Category: Demitri, N]]
		+	[[Category: Raboni, S]]
	[[Category: Revtovich, S.V]]		[[Category: Revtovich, S.V]]
	[[Category: Nikulin, A.D]]		[[Category: Nikulin, A.D]]
-	[[Category: Morozova, E.A]]
-	[[Category: Mozzarelli, A]]
-	[[Category: Raboni, S]]

OCA: Protected "6egr" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 17:08:38 GMT

Protected "6egr" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:08, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 6egr is ON HOLD Authors: Revtovich, S.V., Demitri, N., Raboni, S., Nikulin, A.D., Morozova, E.A., Demidkina, T.V., Storici, P., Mozzarelli, A. Desc...

OCA — Wed, 27 Sep 2017 17:08:37 GMT

New page: '''Unreleased structure''' The entry 6egr is ON HOLD Authors: Revtovich, S.V., Demitri, N., Raboni, S., Nikulin, A.D., Morozova, E.A., Demidkina, T.V., Storici, P., Mozzarelli, A. Desc...

New page

'''Unreleased structure'''

The entry 6egr is ON HOLD

Authors: Revtovich, S.V., Demitri, N., Raboni, S., Nikulin, A.D., Morozova, E.A., Demidkina, T.V., Storici, P., Mozzarelli, A.

Description: Crystal structure of Citrobacter freundii methionine gamma-lyase with V358Y replacement
[[Category: Unreleased Structures]]
[[Category: Storici, P]]
[[Category: Demidkina, T.V]]
[[Category: Demitri, N]]
[[Category: Revtovich, S.V]]
[[Category: Nikulin, A.D]]
[[Category: Morozova, E.A]]
[[Category: Mozzarelli, A]]
[[Category: Raboni, S]]