7pz4 - Revision history

OCA at 13:11, 1 February 2024

OCA — Thu, 01 Feb 2024 13:11:22 GMT

←Older revision		Revision as of 13:11, 1 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7pz4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoascus_aurantiacus Thermoascus aurantiacus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PZ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PZ4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7pz4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoascus_aurantiacus Thermoascus aurantiacus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PZ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PZ4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKR:ACRYLIC+ACID'>AKR</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=HIC:4-METHYL-HISTIDINE'>HIC</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]] 1.85Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKR:ACRYLIC+ACID'>AKR</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=HIC:4-METHYL-HISTIDINE'>HIC</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=7pz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pz4 OCA], [https://pdbe.org/7pz4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pz4 RCSB], [https://www.ebi.ac.uk/pdbsum/7pz4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pz4 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=7pz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pz4 OCA], [https://pdbe.org/7pz4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pz4 RCSB], [https://www.ebi.ac.uk/pdbsum/7pz4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pz4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/G3XAP7_THEAU G3XAP7_THEAU]] Has endoglucanase activity on substrates containing beta-1,4 glycosidic bonds. Involved in the degradation of complex natural cellulosic substrates.[RuleBase:RU368122]	+	[https://www.uniprot.org/uniprot/G3XAP7_THEAU G3XAP7_THEAU] Has endoglucanase activity on substrates containing beta-1,4 glycosidic bonds. Involved in the degradation of complex natural cellulosic substrates.[RuleBase:RU368122]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 07:53, 21 September 2022

OCA — Wed, 21 Sep 2022 07:53:56 GMT

←Older revision		Revision as of 07:53, 21 September 2022
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	==Structure of an LPMO at 2.07x10^4 Gy==		==Structure of an LPMO at 2.07x10^4 Gy==
-	<StructureSection load='7pz4' size='340' side='right'caption='[[7pz4]]' scene=''>	+	<StructureSection load='7pz4' size='340' side='right'caption='[[7pz4]], [[Resolution\|resolution]] 1.85Å' 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=7PZ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PZ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7pz4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoascus_aurantiacus Thermoascus aurantiacus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PZ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PZ4 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=7pz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pz4 OCA], [https://pdbe.org/7pz4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pz4 RCSB], [https://www.ebi.ac.uk/pdbsum/7pz4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pz4 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKR:ACRYLIC+ACID'>AKR</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=HIC:4-METHYL-HISTIDINE'>HIC</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=7pz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pz4 OCA], [https://pdbe.org/7pz4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pz4 RCSB], [https://www.ebi.ac.uk/pdbsum/7pz4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pz4 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/G3XAP7_THEAU G3XAP7_THEAU]] Has endoglucanase activity on substrates containing beta-1,4 glycosidic bonds. Involved in the degradation of complex natural cellulosic substrates.[RuleBase:RU368122]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The recently discovered lytic polysaccharide monooxygenases (LPMOs) are Cu-containing enzymes capable of degrading polysaccharide substrates oxidatively. The generally accepted first step in the LPMO reaction is the reduction of the active-site metal ion from Cu(2+) to Cu(+). Here we have used a systematic diffraction data collection method to monitor structural changes in two AA9 LPMOs, one from Lentinus similis (LsAA9_A) and one from Thermoascus auranti-acus (TaAA9_A), as the active-site Cu is photoreduced in the X-ray beam. For LsAA9_A, the protein produced in two different recombinant systems was crystallized to probe the effect of post-translational modifications and different crystallization conditions on the active site and metal photoreduction. We can recommend that crystallographic studies of AA9 LPMOs wishing to address the Cu(2+) form use a total X-ray dose below 3 x 10(4) Gy, while the Cu(+) form can be attained using 1 x 10(6) Gy. In all cases, we observe the transition from a hexa-coordinated Cu site with two solvent-facing ligands to a T-shaped geometry with no exogenous ligands, and a clear increase of the theta2 parameter and a decrease of the theta3 parameter by averages of 9.2 degrees and 8.4 degrees , respectively, but also a slight increase in thetaT. Thus, the theta2 and theta3 parameters are helpful diagnostics for the oxidation state of the metal in a His-brace protein. On binding of cello-oligosaccharides to LsAA9_A, regardless of the production source, the thetaT parameter increases, making the Cu site less planar, while the active-site Tyr-Cu distance decreases reproducibly for the Cu(2+) form. Thus, the thetaT increase found on copper reduction may bring LsAA9_A closer to an oligosaccharide-bound state and contribute to the observed higher affinity of reduced LsAA9_A for cellulosic substrates.
		+
		+	Changes in active-site geometry on X-ray photoreduction of a lytic polysaccharide monooxygenase active-site copper and saccharide binding.,Tandrup T, Muderspach SJ, Banerjee S, Santoni G, Ipsen JO, Hernandez-Rollan C, Norholm MHH, Johansen KS, Meilleur F, Lo Leggio L IUCrJ. 2022 Aug 17;9(Pt 5):666-681. doi: 10.1107/S2052252522007175. eCollection, 2022 Sep 1. PMID:36071795<ref>PMID:36071795</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7pz4" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Thermoascus aurantiacus]]
	[[Category: Ipsen JO]]		[[Category: Ipsen JO]]
	[[Category: Johansen KS]]		[[Category: Johansen KS]]

OCA at 04:47, 25 August 2022

OCA — Thu, 25 Aug 2022 04:47:50 GMT

←Older revision		Revision as of 04:47, 25 August 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7pz4 is ~~ON HOLD until Paper Publication~~	+	==Structure of an LPMO at 2.07x10^4 Gy==
-		+	<StructureSection load='7pz4' size='340' side='right'caption='[[7pz4]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PZ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PZ4 FirstGlance]. <br>
-	~~Description~~:	+	</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=7pz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pz4 OCA], [https://pdbe.org/7pz4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pz4 RCSB], [https://www.ebi.ac.uk/pdbsum/7pz4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pz4 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Ipsen JO]]
		+	[[Category: Johansen KS]]
		+	[[Category: Lo Leggio L]]
		+	[[Category: Muderspach SJ]]
		+	[[Category: Tandrup T]]

OCA at 12:00, 17 November 2021

OCA — Wed, 17 Nov 2021 12:00:49 GMT

←Older revision		Revision as of 12:00, 17 November 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7pz4 is ON HOLD	+	The entry 7pz4 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7pz4" [edit=sysop:move=sysop]

OCA — Wed, 20 Oct 2021 14:58:42 GMT

Protected "7pz4" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:58, 20 October 2021

OCA: New page: '''Unreleased structure''' The entry 7pz4 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 20 Oct 2021 14:58:41 GMT

New page: '''Unreleased structure''' The entry 7pz4 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7pz4 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]