6ane - Revision history

OCA at 14:21, 4 October 2023

OCA — Wed, 04 Oct 2023 14:21:18 GMT

←Older revision		Revision as of 14:21, 4 October 2023
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	==Crystal Structure of Ideonella sakaiensis PET Hydrolase==		==Crystal Structure of Ideonella sakaiensis PET Hydrolase==
-	<StructureSection load='6ane' size='340' side='right' caption='[[6ane]], [[Resolution\|resolution]] 2.02Å' scene=''>	+	<StructureSection load='6ane' size='340' side='right'caption='[[6ane]], [[Resolution\|resolution]] 2.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ane]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Idesa Idesa~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ANE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6ANE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ane]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Ideonella_sakaiensis Ideonella sakaiensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ANE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ANE FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.02Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">ISF6_4831 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=1547922 IDESA])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>[http://en.wikipedia.org/wiki/Poly(ethylene_terephthalate)_hydrolase Poly(ethylene terephthalate) hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.101 3.1.1.101] </~~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=6ane FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ane OCA], [https://pdbe.org/6ane PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ane RCSB], [https://www.ebi.ac.uk/pdbsum/6ane PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ane 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=6ane FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ane OCA], [~~http~~://pdbe.org/6ane PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ane RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ane PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ane ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PETH_IDESA PETH_IDESA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Idesa~~]]	+	[[Category: Ideonella sakaiensis]]
-	[[Category: Galaz-Davison, P]]	+	[[Category: Large Structures]]
-	[[Category: Parra~~, L P~~]]	+	[[Category: Galaz-Davison P]]
-	[[Category: Ramirez-Sarmiento~~, C A~~]]	+	[[Category: Parra LP]]
-	[[Category: Sotomayor, M]]	+	[[Category: Ramirez-Sarmiento CA]]
-	~~[[Category: Ab hydrolase]]~~	+	[[Category: Sotomayor M]]
-	~~[[Category: Cutinase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Petase]]~~	+
-	~~[[Category: Plastic~~]]	+

OCA at 05:56, 25 April 2018

OCA — Wed, 25 Apr 2018 05:56:42 GMT

←Older revision		Revision as of 05:56, 25 April 2018
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	<StructureSection load='6ane' size='340' side='right' caption='[[6ane]], [[Resolution\|resolution]] 2.02Å' scene=''>		<StructureSection load='6ane' size='340' side='right' caption='[[6ane]], [[Resolution\|resolution]] 2.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ane]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ANE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ANE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ane]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Idesa Idesa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ANE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ANE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ISF6_4831 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1547922 IDESA])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Poly(ethylene_terephthalate)_hydrolase Poly(ethylene terephthalate) hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.101 3.1.1.101] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Poly(ethylene_terephthalate)_hydrolase Poly(ethylene terephthalate) hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.101 3.1.1.101] </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=6ane FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ane OCA], [http://pdbe.org/6ane PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ane RCSB], [http://www.ebi.ac.uk/pdbsum/6ane PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ane 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=6ane FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ane OCA], [http://pdbe.org/6ane PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ane RCSB], [http://www.ebi.ac.uk/pdbsum/6ane PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ane ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Idesa]]
	[[Category: Galaz-Davison, P]]		[[Category: Galaz-Davison, P]]
	[[Category: Parra, L P]]		[[Category: Parra, L P]]

OCA at 05:43, 18 April 2018

OCA — Wed, 18 Apr 2018 05:43:06 GMT

←Older revision		Revision as of 05:43, 18 April 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 6ane is ~~ON HOLD until Paper~~ Publication	+	==Crystal Structure of Ideonella sakaiensis PET Hydrolase==
		+	<StructureSection load='6ane' size='340' side='right' caption='[[6ane]], [[Resolution\|resolution]] 2.02Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6ane]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ANE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ANE FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Poly(ethylene_terephthalate)_hydrolase Poly(ethylene terephthalate) hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.101 3.1.1.101] </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=6ane FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ane OCA], [http://pdbe.org/6ane PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ane RCSB], [http://www.ebi.ac.uk/pdbsum/6ane PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ane ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Polyethylene terephthalate (PET) is one of the most-consumed synthetic polymers, with an annual production of 50 million tons. Unfortunately, PET accumulates as waste and is highly resistant to biodegradation. Recently, fungal and bacterial thermophilic hydrolases were found to catalyze PET hydrolysis with optimal activities at high temperatures. Strikingly, an enzyme from Ideonella sakaiensis, termed PETase, was described to efficiently degrade PET at room temperature, but the molecular basis of its activity is not currently understood. Here, a crystal structure of PETase was determined at 2.02 A resolution and employed in molecular dynamics simulations showing that the active site of PETase has higher flexibility at room temperature than its thermophilic counterparts. This flexibility is controlled by a novel disulfide bond in its active site, with its removal leading to destabilization of the catalytic triad and reduction of the hydrolase activity. Molecular docking of a model substrate predicts that PET binds to PETase in a unique and energetically favorable conformation facilitated by several residue substitutions within its active site when compared to other enzymes. These computational predictions are in excellent agreement with recent mutagenesis and PET film degradation analyses. Finally, we rationalize the increased catalytic activity of PETase at room temperature through molecular dynamics simulations of enzyme-ligand complexes for PETase and other thermophilic PET-degrading enzymes at 298, 323, and 353 K. Our results reveal that both the binding pose and residue substitutions within PETase favor proximity between the catalytic residues and the labile carbonyl of the substrate at room temperature, suggesting a more favorable hydrolytic reaction. These results are valuable for enabling detailed evolutionary analysis of PET-degrading enzymes and for rational design endeavors aiming at increasing the efficiency of PETase and similar enzymes toward plastic degradation.

-	~~Authors~~:	+	Active Site Flexibility as a Hallmark for Efficient PET Degradation by I. sakaiensis PETase.,Fecker T, Galaz-Davison P, Engelberger F, Narui Y, Sotomayor M, Parra LP, Ramirez-Sarmiento CA Biophys J. 2018 Mar 27;114(6):1302-1312. doi: 10.1016/j.bpj.2018.02.005. PMID:29590588<ref>PMID:29590588</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6ane" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Galaz-Davison, P]]
		+	[[Category: Parra, L P]]
		+	[[Category: Ramirez-Sarmiento, C A]]
		+	[[Category: Sotomayor, M]]
		+	[[Category: Ab hydrolase]]
		+	[[Category: Cutinase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Petase]]
		+	[[Category: Plastic]]

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

OCA — Wed, 27 Sep 2017 16:35:34 GMT

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

←Older revision

Revision as of 16:35, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 6ane is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 16:35:33 GMT

New page: '''Unreleased structure''' The entry 6ane is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6ane is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]