7t5c - Revision history

OCA at 09:42, 25 October 2023

OCA — Wed, 25 Oct 2023 09:42:49 GMT

←Older revision		Revision as of 09:42, 25 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7t5c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Neurospora_crassa Neurospora crassa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7T5C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7T5C FirstGlance]. <br>		<table><tr><td colspan='2'>[[7t5c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Neurospora_crassa Neurospora crassa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7T5C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7T5C FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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]] 1.5Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=7t5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7t5c OCA], [https://pdbe.org/7t5c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7t5c RCSB], [https://www.ebi.ac.uk/pdbsum/7t5c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7t5c 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=7t5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7t5c OCA], [https://pdbe.org/7t5c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7t5c RCSB], [https://www.ebi.ac.uk/pdbsum/7t5c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7t5c ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:52, 28 December 2022

OCA — Wed, 28 Dec 2022 08:52:12 GMT

←Older revision		Revision as of 08:52, 28 December 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7t5c is ~~ON HOLD until Paper~~ Publication	+	==X-ray structure of Neurospora crassa Polysaccharide Monooxygenase 9D (NcLPMO9D) at low pH==
		+	<StructureSection load='7t5c' size='340' side='right'caption='[[7t5c]], [[Resolution\|resolution]] 1.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7t5c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Neurospora_crassa Neurospora crassa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7T5C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7T5C FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=7t5c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7t5c OCA], [https://pdbe.org/7t5c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7t5c RCSB], [https://www.ebi.ac.uk/pdbsum/7t5c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7t5c ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8WZQ2_NEUCS Q8WZQ2_NEUCS]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Metalloproteins perform a diverse array of redox-related reactions facilitated by the increased chemical functionality afforded by their metallocofactors. Lytic polysaccharide monooxygenases (LPMOs) are a class of copper-dependent enzymes that are responsible for the breakdown of recalcitrant polysaccharides via oxidative cleavage at the glycosidic bond. The activated copper-oxygen intermediates and their mechanism of formation remains to be established. Neutron protein crystallography which permits direct visualization of protonation states was used to investigate the initial steps of oxygen activation directly following active site copper reduction in Neurospora crassa LPMO9D. Herein, we cryo-trap an activated dioxygen intermediate in a mixture of superoxo and hydroperoxo states, and we identify the conserved second coordination shell residue His157 as the proton donor. Density functional theory calculations indicate that both superoxo and hydroperoxo active site states are stable. The hydroperoxo formed is potentially an early LPMO catalytic reaction intermediate or the first step in the mechanism of hydrogen peroxide formation in the absence of substrate. We observe that the N-terminal amino group of the copper coordinating His1 remains doubly protonated directly following molecular oxygen reduction by copper. Aided by molecular dynamics and mining minima free energy calculations we establish that the conserved second-shell His161 in MtPMO3* displays conformational flexibility in solution and that this flexibility is also observed, though to a lesser extent, in His157 of NcLPMO9D. The imidazolate form of His157 observed in our structure following oxygen intermediate protonation can be attributed to abolished His157 flexibility due steric hindrance in the crystal as well as the solvent-occluded active site environment due to crystal packing. A neutron crystal structure of NcLPMO9D at low pH further supports occlusion of the active site since His157 remains singly protonated even at acidic conditions.

-	~~Authors:~~ Schroder, ~~G.C.~~, ~~Meilleur~~, F.	+	Capture of activated dioxygen intermediates at the copper-active site of a lytic polysaccharide monooxygenase.,Schroder GC, O'Dell WB, Webb SP, Agarwal PK, Meilleur F Chem Sci. 2022 Nov 2;13(45):13303-13320. doi: 10.1039/d2sc05031e. eCollection , 2022 Nov 23. PMID:36507176<ref>PMID:36507176</ref>

-	~~Description: X-ray structure~~ of ~~Neurospora crassa Polysaccharide Monooxygenase 9D (NcLPMO9D) at low pH~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Meilleur, F]]	+	<div class="pdbe-citations 7t5c" style="background-color:#fffaf0;"></div>
-	[[Category: Schroder~~, G.C~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Neurospora crassa]]
		+	[[Category: Meilleur F]]
		+	[[Category: Schroder GC]]

OCA at 05:26, 27 January 2022

OCA — Thu, 27 Jan 2022 05:26:17 GMT

←Older revision		Revision as of 05:26, 27 January 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7t5c is ON HOLD	+	The entry 7t5c is ON HOLD until Paper Publication

	Authors: Schroder, G.C., Meilleur, F.		Authors: Schroder, G.C., Meilleur, F.

OCA: Protected "7t5c" [edit=sysop:move=sysop]

OCA — Wed, 22 Dec 2021 14:04:53 GMT

Protected "7t5c" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:04, 22 December 2021

OCA: New page: '''Unreleased structure''' The entry 7t5c is ON HOLD Authors: Schroder, G.C., Meilleur, F. Description: X-ray structure of Neurospora crassa Polysaccharide Monooxygenase 9D (NcLPMO9D) ...

OCA — Wed, 22 Dec 2021 14:04:52 GMT

New page: '''Unreleased structure''' The entry 7t5c is ON HOLD Authors: Schroder, G.C., Meilleur, F. Description: X-ray structure of Neurospora crassa Polysaccharide Monooxygenase 9D (NcLPMO9D) ...

New page

'''Unreleased structure'''

The entry 7t5c is ON HOLD

Authors: Schroder, G.C., Meilleur, F.

Description: X-ray structure of Neurospora crassa Polysaccharide Monooxygenase 9D (NcLPMO9D) at low pH
[[Category: Unreleased Structures]]
[[Category: Meilleur, F]]
[[Category: Schroder, G.C]]