4zrd - Revision history

OCA at 15:46, 8 November 2023

2023-11-08T15:46:48Z

←Older revision		Revision as of 15:46, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4zrd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Malassezia_globosa_CBS_7966 Malassezia globosa CBS 7966]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZRD FirstGlance]. <br>		<table><tr><td colspan='2'>[[4zrd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Malassezia_globosa_CBS_7966 Malassezia globosa CBS 7966]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZRD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=4zrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zrd OCA], [https://pdbe.org/4zrd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zrd RCSB], [https://www.ebi.ac.uk/pdbsum/4zrd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zrd 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=4zrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zrd OCA], [https://pdbe.org/4zrd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zrd RCSB], [https://www.ebi.ac.uk/pdbsum/4zrd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zrd ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:38, 18 May 2023

2023-05-18T07:38:46Z

←Older revision		Revision as of 07:38, 18 May 2023
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	==Crystal structure of SMG1 F278N mutant==		==Crystal structure of SMG1 F278N mutant==
-	<StructureSection load='4zrd' size='340' side='right' caption='[[4zrd]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='4zrd' size='340' side='right'caption='[[4zrd]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4zrd]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Dandruff-associated_fungus Dandruff-associated fungus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZRD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4ZRD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4zrd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Malassezia_globosa_CBS_7966 Malassezia globosa CBS 7966]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZRD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MGL_0797 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=425265 Dandruff-associated fungus])</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=4zrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zrd OCA], [https://pdbe.org/4zrd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zrd RCSB], [https://www.ebi.ac.uk/pdbsum/4zrd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zrd 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=4zrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zrd OCA], [~~http~~://pdbe.org/4zrd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4zrd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4zrd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4zrd ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A8PUY1_MALGO A8PUY1_MALGO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4zrd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4zrd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Lipase 3D Structures\|Lipase 3D Structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Dandruff-associated fungus~~]]	+	[[Category: Large Structures]]
-	[[Category: Hou, S]]	+	[[Category: Malassezia globosa CBS 7966]]
-	[[Category: Liu, J]]	+	[[Category: Hou S]]
-	[[Category: Xu, H]]	+	[[Category: Liu J]]
-	[[Category: Xu, J]]	+	[[Category: Xu H]]
-	~~[[Category: Hydrolase]]~~	+	[[Category: Xu J]]
-	~~[[Category: Mono- and diacylglycerol lipase~~]]	+

OCA at 15:31, 16 November 2017

2017-11-16T15:31:12Z

←Older revision		Revision as of 15:31, 16 November 2017
Line 1:		Line 1:
		+
	==Crystal structure of SMG1 F278N mutant==		==Crystal structure of SMG1 F278N mutant==
	<StructureSection load='4zrd' size='340' side='right' caption='[[4zrd]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4zrd' size='340' side='right' caption='[[4zrd]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4zrd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZRD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZRD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4zrd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dandruff-associated_fungus Dandruff-associated fungus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZRD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZRD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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=4zrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zrd OCA], [http://pdbe.org/4zrd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zrd RCSB], [http://www.ebi.ac.uk/pdbsum/4zrd PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MGL_0797 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=425265 Dandruff-associated fungus])</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=4zrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zrd OCA], [http://pdbe.org/4zrd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zrd RCSB], [http://www.ebi.ac.uk/pdbsum/4zrd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zrd ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Dandruff-associated fungus]]
	[[Category: Hou, S]]		[[Category: Hou, S]]
	[[Category: Liu, J]]		[[Category: Liu, J]]

OCA at 07:43, 16 December 2015

2015-12-16T07:43:18Z

←Older revision		Revision as of 07:43, 16 December 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of SMG1 F278N mutant==
		+	<StructureSection load='4zrd' size='340' side='right' caption='[[4zrd]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4zrd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZRD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZRD FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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=4zrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zrd OCA], [http://pdbe.org/4zrd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zrd RCSB], [http://www.ebi.ac.uk/pdbsum/4zrd PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Monoacylglycerol and diacylglycerol lipases are industrially interesting enzymes, due to the health benefits that arise from the consumption of diglycerides compared to the traditional triglyceride oils. Most lipases possess an alpha-helix (lid) directly over the catalytic pocket which regulates the activity of the enzyme. Generally, lipases exist in active and inactive conformations, depending on the positioning of this lid subdomain. However, lipase SMG1, a monoacylglycerol and diacylglycerol specific lipase, has an atypical activation mechanism. In the present study we were able to prove by crystallography, in silico analysis and activity tests that only two positions, residues 102 and 278, are responsible for a gating mechanism that regulates the active and inactive states of the lipase, and that no significant structural changes take place during activation except for oxyanion hole formation. The elucidation of the gating effect provided data enabling the rational design of improved lipases with 6-fold increase in the hydrolytic activity toward diacylglycerols, just by providing additional substrate stabilization with a single mutation (F278N or F278T). Due to the conservation of F278 among the monoacylglycerol and diacylglycerol lipases in the Rhizomucor miehei lipase-like family, the gating mechanism described herein might represent a general mechanism applicable to other monoacylglycerol and diacylglycerol lipases as well. DATABASE: Structural data are available in the Protein Data Bank under the accession numbers 4ZRE (F278D mutant) and 4ZRD (F278N mutant).

-	~~The entry 4zrd is ON HOLD until Paper Publication~~	+	Structure of product-bound SMG1 lipase: active site gating implications.,Guo S, Xu J, Pavlidis IV, Lan D, Bornscheuer UT, Liu J, Wang Y FEBS J. 2015 Sep 13. doi: 10.1111/febs.13513. PMID:26365206<ref>PMID:26365206</ref>

-	~~Authors: Xu~~, J.~~, Xu, H., Hou,~~ S.~~, Liu, J~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure of SMG1 F278N mutant~~	+	<div class="pdbe-citations 4zrd" style="background-color:#fffaf0;"></div>
-	~~[[Category: Unreleased Structures]]~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Hou, S]]		[[Category: Hou, S]]
		+	[[Category: Liu, J]]
	[[Category: Xu, H]]		[[Category: Xu, H]]
-	[[Category: Liu, J]]
	[[Category: Xu, J]]		[[Category: Xu, J]]
		+	[[Category: Hydrolase]]
		+	[[Category: Mono- and diacylglycerol lipase]]

OCA at 07:52, 9 September 2015

2015-09-09T07:52:47Z

←Older revision		Revision as of 07:52, 9 September 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4zrd is ON HOLD	+	The entry 4zrd is ON HOLD until Paper Publication

	Authors: Xu, J., Xu, H., Hou, S., Liu, J.		Authors: Xu, J., Xu, H., Hou, S., Liu, J.

OCA: Protected "4zrd" [edit=sysop:move=sysop]

2015-05-20T11:03:34Z

Protected "4zrd" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:03, 20 May 2015

OCA: New page: '''Unreleased structure''' The entry 4zrd is ON HOLD Authors: Xu, J., Xu, H., Hou, S., Liu, J. Description: Crystal structure of SMG1 F278N mutant Category: Unreleased Structures [...

2015-05-20T11:03:33Z

New page: '''Unreleased structure''' The entry 4zrd is ON HOLD Authors: Xu, J., Xu, H., Hou, S., Liu, J. Description: Crystal structure of SMG1 F278N mutant Category: Unreleased Structures [...

New page

'''Unreleased structure'''

The entry 4zrd is ON HOLD

Authors: Xu, J., Xu, H., Hou, S., Liu, J.

Description: Crystal structure of SMG1 F278N mutant
[[Category: Unreleased Structures]]
[[Category: Hou, S]]
[[Category: Xu, H]]
[[Category: Liu, J]]
[[Category: Xu, J]]