5t7j - Revision history

OCA at 15:37, 6 March 2024

OCA — Wed, 06 Mar 2024 15:37:39 GMT

←Older revision		Revision as of 15:37, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='5t7j' size='340' side='right'caption='[[5t7j]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='5t7j' size='340' side='right'caption='[[5t7j]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5t7j]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Aspor Aspor~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T7J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5T7J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5t7j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_oryzae_RIB40 Aspergillus oryzae RIB40]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T7J FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NAG:N~~-~~ACETYL-D-GLUCOSAMINE'>NAG</scene>~~, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.65Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=HIC:4-METHYL-HISTIDINE'>HIC</scene><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HIC:4-METHYL-HISTIDINE'>HIC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">AO090701000246 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=510516 ASPOR])~~</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=5t7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t7j OCA], [https://pdbe.org/5t7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t7j RCSB], [https://www.ebi.ac.uk/pdbsum/5t7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t7j ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5t7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t7j OCA], [~~http~~://pdbe.org/5t7j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5t7j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5t7j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5t7j ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/AA13_ASPOR AA13_ASPOR] Lytic polysaccharide monooxygenase-related protein that has no activity towards starch.<ref>PMID:25608804</ref>
-	Lytic polysaccharide ~~monooxygenases (LPMOs) are a class of copper~~-~~dependent enzymes discovered within the last ten years. They oxidatively cleave polysaccharides (chitin, lignocellulose, hemicellulose and~~ starch-derived), presumably making recalcitrant substrates accessible to glycoside hydrolases. Recently, the first crystal structure of an LPMO-substrate complex was reported, giving insights into the interaction of LPMOs with beta-linked substrates (Frandsen et al., 2016). The LPMOs acting on alpha-linked glycosidic bonds (family AA13) display binding surfaces that are quite different from those of LPMOs that act on beta-linked glycosidic bonds (families AA9-AA11), as revealed from the first determined structure (Lo Leggio et al., 2015), and thus presumably the AA13s interact with their substrate in a distinct fashion. Here, several new structures of the same AA13 enzyme, Aspergillus oryzae AA13, are presented. Crystals obtained in the presence of high zinc-ion concentrations were used, as they can be obtained more reproducibly than those used to refine the deposited copper-containing structure. One structure with an ordered zinc-bound active site was solved at 1.65 A resolution, and three structures from crystals soaked with maltooligosaccharides in solutions devoid of zinc ions were solved at resolutions of up to 1.10 A. Despite similar unit-cell parameters, small rearrangements in the crystal packing occur when the crystals are depleted of zinc ions, resulting in a more occluded substrate-binding surface. In two of the three structures maltooligosaccharide ligands are bound, but not at the active site. Two of the structures presented show a His-ligand conformation that is incompatible with metal-ion binding. In one of these structures this conformation is the principal one (80% occupancy), giving a rare atomic resolution view of a substantially misfolded enzyme that is presumably rendered inactive.	+

-	Learning from oligosaccharide soaks of crystals of an AA13 lytic polysaccharide monooxygenase: crystal packing, ligand binding and active-site disorder.,Frandsen KE, Poulsen JC, Tovborg M, Johansen KS, Lo Leggio L Acta Crystallogr D Struct Biol. 2017 Jan 1;73(Pt 1):64-76. doi:, 10.1107/S2059798316019641. Epub 2017 Jan 1. PMID:28045386<ref>PMID:28045386</ref>	+	==See Also==
-		+	*[[Monooxygenase 3D structures\|Monooxygenase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 5t7j" style~~=~~"background-color:#fffaf0;"></div>~~	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aspor~~]]	+	[[Category: Aspergillus oryzae RIB40]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Frandsen~~, K E.H~~]]	+	[[Category: Frandsen KEH]]
-	[[Category: Johansen~~, K S~~]]	+	[[Category: Johansen KS]]
-	[[Category: Leggio, L Lo]]	+	[[Category: Lo Leggio L]]
-	[[Category: Poulsen, J ~~C.N~~]]	+	[[Category: Poulsen J-CN]]
-	[[Category: Tovborg, M]]	+	[[Category: Tovborg M]]
-	~~[[Category: Aspergillus oryzae aa13 lpmo]]~~	+
-	~~[[Category: Enzyme]]~~	+
-	~~[[Category: Metal binding protein~~]]	+

OCA at 11:25, 16 September 2020

OCA — Wed, 16 Sep 2020 11:25:07 GMT

←Older revision		Revision as of 11:25, 16 September 2020
Line 1:		Line 1:

	==X-ray crystal structure of AA13 LPMO==		==X-ray crystal structure of AA13 LPMO==
-	<StructureSection load='5t7j' size='340' side='right' caption='[[5t7j]], [[Resolution\|resolution]] 1.65Å' scene=''>	+	<StructureSection load='5t7j' size='340' side='right'caption='[[5t7j]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5t7j]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T7J OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5T7J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5t7j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspor Aspor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T7J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5T7J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=HIC:4-METHYL-HISTIDINE'>HIC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=HIC:4-METHYL-HISTIDINE'>HIC</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=5t7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t7j OCA], [http://pdbe.org/5t7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t7j RCSB], [http://www.ebi.ac.uk/pdbsum/5t7j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t7j ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AO090701000246 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=510516 ASPOR])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5t7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t7j OCA], [http://pdbe.org/5t7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t7j RCSB], [http://www.ebi.ac.uk/pdbsum/5t7j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t7j ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aspor]]
		+	[[Category: Large Structures]]
	[[Category: Frandsen, K E.H]]		[[Category: Frandsen, K E.H]]
	[[Category: Johansen, K S]]		[[Category: Johansen, K S]]

OCA at 16:13, 18 January 2017

OCA — Wed, 18 Jan 2017 16:13:39 GMT

←Older revision		Revision as of 16:13, 18 January 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5t7j is ~~ON HOLD until Paper~~ Publication	+	==X-ray crystal structure of AA13 LPMO==
		+	<StructureSection load='5t7j' size='340' side='right' caption='[[5t7j]], [[Resolution\|resolution]] 1.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5t7j]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5T7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5T7J FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=HIC:4-METHYL-HISTIDINE'>HIC</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=5t7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t7j OCA], [http://pdbe.org/5t7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5t7j RCSB], [http://www.ebi.ac.uk/pdbsum/5t7j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5t7j ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Lytic polysaccharide monooxygenases (LPMOs) are a class of copper-dependent enzymes discovered within the last ten years. They oxidatively cleave polysaccharides (chitin, lignocellulose, hemicellulose and starch-derived), presumably making recalcitrant substrates accessible to glycoside hydrolases. Recently, the first crystal structure of an LPMO-substrate complex was reported, giving insights into the interaction of LPMOs with beta-linked substrates (Frandsen et al., 2016). The LPMOs acting on alpha-linked glycosidic bonds (family AA13) display binding surfaces that are quite different from those of LPMOs that act on beta-linked glycosidic bonds (families AA9-AA11), as revealed from the first determined structure (Lo Leggio et al., 2015), and thus presumably the AA13s interact with their substrate in a distinct fashion. Here, several new structures of the same AA13 enzyme, Aspergillus oryzae AA13, are presented. Crystals obtained in the presence of high zinc-ion concentrations were used, as they can be obtained more reproducibly than those used to refine the deposited copper-containing structure. One structure with an ordered zinc-bound active site was solved at 1.65 A resolution, and three structures from crystals soaked with maltooligosaccharides in solutions devoid of zinc ions were solved at resolutions of up to 1.10 A. Despite similar unit-cell parameters, small rearrangements in the crystal packing occur when the crystals are depleted of zinc ions, resulting in a more occluded substrate-binding surface. In two of the three structures maltooligosaccharide ligands are bound, but not at the active site. Two of the structures presented show a His-ligand conformation that is incompatible with metal-ion binding. In one of these structures this conformation is the principal one (80% occupancy), giving a rare atomic resolution view of a substantially misfolded enzyme that is presumably rendered inactive.

-	~~Authors~~: ~~Frandsen~~, ~~K.E.H~~., Poulsen~~, J.-C.N.~~, Tovborg, M., Johansen~~, K.S.~~, Lo Leggio, L.	+	Learning from oligosaccharide soaks of crystals of an AA13 lytic polysaccharide monooxygenase: crystal packing, ligand binding and active-site disorder.,Frandsen KE, Poulsen JC, Tovborg M, Johansen KS, Lo Leggio L Acta Crystallogr D Struct Biol. 2017 Jan 1;73(Pt 1):64-76. doi:, 10.1107/S2059798316019641. Epub 2017 Jan 1. PMID:28045386<ref>PMID:28045386</ref>

-	~~Description: X-ray crystal structure~~ of ~~AA13 LPMO~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Poulsen~~, J.~~-C.N~~]]	+	<div class="pdbe-citations 5t7j" style="background-color:#fffaf0;"></div>
-	[[Category: Johansen, K.S]]	+	== References ==
-	[[Category: ~~Frandsen~~, ~~K.E.H~~]]	+	<references/>
-	[[Category: ~~Lo Leggio~~, L]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Frandsen, K E.H]]
		+	[[Category: Johansen, K S]]
		+	[[Category: Leggio, L Lo]]
		+	[[Category: Poulsen, J C.N]]
	[[Category: Tovborg, M]]		[[Category: Tovborg, M]]
		+	[[Category: Aspergillus oryzae aa13 lpmo]]
		+	[[Category: Enzyme]]
		+	[[Category: Metal binding protein]]

OCA: Protected "5t7j" [edit=sysop:move=sysop]

OCA — Wed, 14 Sep 2016 14:05:50 GMT

Protected "5t7j" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:05, 14 September 2016

OCA: New page: '''Unreleased structure''' The entry 5t7j is ON HOLD until Paper Publication Authors: Frandsen, K.E.H., Poulsen, J.-C.N., Tovborg, M., Johansen, K.S., Lo Leggio, L. Description: X-ray ...

OCA — Wed, 14 Sep 2016 14:05:49 GMT

New page: '''Unreleased structure''' The entry 5t7j is ON HOLD until Paper Publication Authors: Frandsen, K.E.H., Poulsen, J.-C.N., Tovborg, M., Johansen, K.S., Lo Leggio, L. Description: X-ray ...

New page

'''Unreleased structure'''

The entry 5t7j is ON HOLD until Paper Publication

Authors: Frandsen, K.E.H., Poulsen, J.-C.N., Tovborg, M., Johansen, K.S., Lo Leggio, L.

Description: X-ray crystal structure of AA13 LPMO
[[Category: Unreleased Structures]]
[[Category: Poulsen, J.-C.N]]
[[Category: Johansen, K.S]]
[[Category: Frandsen, K.E.H]]
[[Category: Lo Leggio, L]]
[[Category: Tovborg, M]]