7dzt - Revision history

OCA at 16:43, 29 November 2023

OCA — Wed, 29 Nov 2023 16:43:48 GMT

←Older revision		Revision as of 16:43, 29 November 2023
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	<StructureSection load='7dzt' size='340' side='right'caption='[[7dzt]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='7dzt' size='340' side='right'caption='[[7dzt]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7dzt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Bcc_58006 Bcc 58006~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DZT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DZT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7dzt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhizobacter_gummiphilus Rhizobacter gummiphilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DZT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DZT FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~A4W93_05950 (~~[~~https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=946333 BCC 58006])~~</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]] 2.35Å</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=7dzt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dzt OCA], [https://pdbe.org/7dzt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dzt RCSB], [https://www.ebi.ac.uk/pdbsum/7dzt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dzt 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=7dzt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dzt OCA], [https://pdbe.org/7dzt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dzt RCSB], [https://www.ebi.ac.uk/pdbsum/7dzt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dzt ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A1W6L588_9BURK A0A1W6L588_9BURK]
	<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: Bcc 58006]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Kim, K J~~]]	+	[[Category: Rhizobacter gummiphilus]]
-	[[Category: ~~Sagong, H Y~~]]	+	[[Category: Kim K-J]]
-	[[Category: ~~Hydrolase]]~~	+	[[Category: Sagong H-Y]]
-	~~[[Category: Pet hydrolase~~]]	+

OCA at 10:52, 16 February 2022

OCA — Wed, 16 Feb 2022 10:52:14 GMT

←Older revision		Revision as of 10:52, 16 February 2022
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	==Cyrstal structure of PETase from Rhizobacter gummiphilus==		==Cyrstal structure of PETase from Rhizobacter gummiphilus==
-	<StructureSection load='7dzt' size='340' side='right'caption='[[7dzt]]' scene=''>	+	<StructureSection load='7dzt' size='340' side='right'caption='[[7dzt]], [[Resolution\|resolution]] 2.35Å' 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=7DZT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DZT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7dzt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bcc_58006 Bcc 58006]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DZT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DZT 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=7dzt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dzt OCA], [https://pdbe.org/7dzt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dzt RCSB], [https://www.ebi.ac.uk/pdbsum/7dzt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dzt ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">A4W93_05950 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=946333 BCC 58006])</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=7dzt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dzt OCA], [https://pdbe.org/7dzt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dzt RCSB], [https://www.ebi.ac.uk/pdbsum/7dzt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dzt ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The development of a superb polyethylene terephthalate (PET) hydrolyzing enzyme requires an accurate understanding of the PET decomposition mechanism. However, studies on PET degrading enzymes, including the PET hydrolase from Ideonella sakaiensis (IsPETase), have not provided sufficient knowledge of the molecular mechanisms for the hardly accessible substrate. Here, we report a novel PET hydrolase from Rhizobacter gummiphilus (RgPETase), which has a hydrolyzing activity similar to IsPETase toward microcrystalline PET but distinct behavior toward low crystallinity PET film. Structural analysis of RgPETase reveals that the enzyme shares the key structural features of IsPETase for high PET hydrolysis activity but has distinguished structures at the surface-exposed regions. RgPETase shows a unique conformation of the wobbling tryptophan containing loop (WW-loop) and change of the electrostatic surface charge on the loop dramatically affects the PET-degrading activity. We further show that effect of the electrostatic surface charge to the activity varies depending on locations. This work provides valuable information underlying the uncovered PET decomposition mechanism.
		+
		+	Implications for the PET decomposition mechanism through similarity and dissimilarity between PETases from Rhizobacter gummiphilus and Ideonella sakaiensis.,Sagong HY, Son HF, Seo H, Hong H, Lee D, Kim KJ J Hazard Mater. 2021 Aug 15;416:126075. doi: 10.1016/j.jhazmat.2021.126075. Epub , 2021 May 11. PMID:34492896<ref>PMID:34492896</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7dzt" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bcc 58006]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kim K-J]]	+	[[Category: Kim, K J]]
-	[[Category: Sagong H-Y]]	+	[[Category: Sagong, H Y]]
		+	[[Category: Hydrolase]]
		+	[[Category: Pet hydrolase]]

OCA at 09:56, 7 July 2021

OCA — Wed, 07 Jul 2021 09:56:31 GMT

←Older revision		Revision as of 09:56, 7 July 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7dzt ~~is ON HOLD until Paper Publication~~	+	==Cyrstal structure of PETase from Rhizobacter gummiphilus==
-		+	<StructureSection load='7dzt' size='340' side='right'caption='[[7dzt]]' scene=''>
-	~~Authors~~: ~~Sagong~~, H.-Y., ~~Kim~~, K.-J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DZT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DZT FirstGlance]. <br>
-	~~Description: Cyrstal structure of PETase from Rhizobacter gummiphilus~~	+	</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=7dzt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dzt OCA], [https://pdbe.org/7dzt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dzt RCSB], [https://www.ebi.ac.uk/pdbsum/7dzt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dzt ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Kim, K.-J]]	+	__TOC__
-	[[Category: Sagong, H.-Y]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Kim K-J]]
		+	[[Category: Sagong H-Y]]

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

OCA — Wed, 03 Feb 2021 09:21:04 GMT

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

←Older revision

Revision as of 09:21, 3 February 2021

OCA: New page: '''Unreleased structure''' The entry 7dzt is ON HOLD until Paper Publication Authors: Sagong, H.-Y., Kim, K.-J. Description: Cyrstal structure of PETase from Rhizobacter gummiphilus [[...

OCA — Wed, 03 Feb 2021 09:21:03 GMT

New page: '''Unreleased structure''' The entry 7dzt is ON HOLD until Paper Publication Authors: Sagong, H.-Y., Kim, K.-J. Description: Cyrstal structure of PETase from Rhizobacter gummiphilus [[...

New page

'''Unreleased structure'''

The entry 7dzt is ON HOLD until Paper Publication

Authors: Sagong, H.-Y., Kim, K.-J.

Description: Cyrstal structure of PETase from Rhizobacter gummiphilus
[[Category: Unreleased Structures]]
[[Category: Kim, K.-J]]
[[Category: Sagong, H.-Y]]