7p1f - Revision history

OCA at 11:04, 15 November 2023

2023-11-15T11:04:22Z

←Older revision		Revision as of 11:04, 15 November 2023
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	<StructureSection load='7p1f' size='340' side='right'caption='[[7p1f]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='7p1f' size='340' side='right'caption='[[7p1f]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7p1f]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P1F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P1F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7p1f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_terreus_NIH2624 Aspergillus terreus NIH2624]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P1F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P1F FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=KFN:(4S,5R,6R)-4,5-DIHYDROXY-6-[(1R,2R)-1,2,3-TRIHYDROXYPROPYL]-5,6-DIHYDRO-4H-PYRAN-2-CARBOXYLIC+ACID'>KFN</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]] 1.45Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=SNN:L-3-AMINOSUCCINIMIDE'>SNN</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=KFN:(4S,5R,6R)-4,5-DIHYDROXY-6-[(1R,2R)-1,2,3-TRIHYDROXYPROPYL]-5,6-DIHYDRO-4H-PYRAN-2-CARBOXYLIC+ACID'>KFN</scene>, <scene name='pdbligand=SNN:L-3-AMINOSUCCINIMIDE'>SNN</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=7p1f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p1f OCA], [https://pdbe.org/7p1f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p1f RCSB], [https://www.ebi.ac.uk/pdbsum/7p1f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p1f 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=7p1f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p1f OCA], [https://pdbe.org/7p1f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p1f RCSB], [https://www.ebi.ac.uk/pdbsum/7p1f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p1f ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q0CMX0_ASPTN Q0CMX0_ASPTN]
	<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: Aspergillus terreus NIH2624]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gloster~~, T M~~]]	+	[[Category: Gloster TM]]
-	[[Category: McMahon~~, S A]]~~	+	[[Category: McMahon SA]]
-	~~[[Category: Carbohydrate]]~~	+
-	~~[[Category: Carbohydrate metabolism]]~~	+
-	~~[[Category: Enzyme structure]]~~	+
-	~~[[Category: Kdn]]~~	+
-	~~[[Category: Kdnase]]~~	+
-	~~[[Category: Protein structure]]~~	+
-	~~[[Category: Sialic acid]]~~	+
-	~~[[Category: Sialidase~~]]	+

OCA at 13:06, 4 May 2022

2022-05-04T13:06:05Z

←Older revision		Revision as of 13:06, 4 May 2022
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	==Structure of KDNase from Aspergillus terrerus in complex with 2,3-didehydro-2,3-dideoxy-D-glycero-D-galacto-nonulosonic acid.==		==Structure of KDNase from Aspergillus terrerus in complex with 2,3-didehydro-2,3-dideoxy-D-glycero-D-galacto-nonulosonic acid.==
-	<StructureSection load='7p1f' size='340' side='right'caption='[[7p1f]]' scene=''>	+	<StructureSection load='7p1f' size='340' side='right'caption='[[7p1f]], [[Resolution\|resolution]] 1.45Å' 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=7P1F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P1F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7p1f]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P1F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P1F 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=7p1f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p1f OCA], [https://pdbe.org/7p1f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p1f RCSB], [https://www.ebi.ac.uk/pdbsum/7p1f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p1f 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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=KFN:(4S,5R,6R)-4,5-DIHYDROXY-6-[(1R,2R)-1,2,3-TRIHYDROXYPROPYL]-5,6-DIHYDRO-4H-PYRAN-2-CARBOXYLIC+ACID'>KFN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SNN:L-3-AMINOSUCCINIMIDE'>SNN</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=7p1f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p1f OCA], [https://pdbe.org/7p1f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p1f RCSB], [https://www.ebi.ac.uk/pdbsum/7p1f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p1f ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Sialidases catalyze the release of sialic acid from the terminus of glycan chains. We previously characterized the sialidase from the opportunistic fungal pathogen, Aspergillus fumigatus, and showed that it is a Kdnase. That is, this enzyme prefers 3-deoxy-d-glycero-d-galacto-non-2-ulosonates (Kdn glycosides) as the substrate compared to N-acetylneuraminides (Neu5Ac). Here, we report characterization and crystal structures of putative sialidases from two other ascomycete fungal pathogens, Aspergillus terreus (AtS) and Trichophyton rubrum (TrS). Unlike A. fumigatus Kdnase (AfS), hydrolysis with the Neu5Ac substrates was negligible for TrS and AtS; thus, TrS and AtS are selective Kdnases. The second-order rate constant for hydrolysis of aryl Kdn glycosides by AtS is similar to that by AfS but 30-fold higher by TrS. The structures of these glycoside hydrolase family 33 (GH33) enzymes in complex with a range of ligands for both AtS and TrS show subtle changes in ring conformation that mimic the Michaelis complex, transition state, and covalent intermediate formed during catalysis. In addition, they can aid identification of important residues for distinguishing between Kdn and Neu5Ac substrates. When A. fumigatus, A. terreus, and T. rubrum were grown in chemically defined media, Kdn was detected in mycelial extracts, but Neu5Ac was only observed in A. terreus or T. rubrum extracts. The C8 monosaccharide 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) was also identified in A. fumigatus and T. rubrum samples. A fluorescent Kdn probe was synthesized and revealed the localization of AfS in vesicles at the cell surface.
		+
		+	Kinetic and Structural Characterization of Sialidases (Kdnases) from Ascomycete Fungal Pathogens.,Nejatie A, Steves E, Gauthier N, Baker J, Nesbitt J, McMahon SA, Oehler V, Thornton NJ, Noyovitz B, Khazaei K, Byers BW, Zandberg WF, Gloster TM, Moore MM, Bennet AJ ACS Chem Biol. 2021 Nov 19;16(11):2632-2640. doi: 10.1021/acschembio.1c00666., Epub 2021 Nov 1. PMID:34724608<ref>PMID:34724608</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7p1f" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gloster TM]]	+	[[Category: Gloster, T M]]
-	[[Category: McMahon SA]]	+	[[Category: McMahon, S A]]
		+	[[Category: Carbohydrate]]
		+	[[Category: Carbohydrate metabolism]]
		+	[[Category: Enzyme structure]]
		+	[[Category: Kdn]]
		+	[[Category: Kdnase]]
		+	[[Category: Protein structure]]
		+	[[Category: Sialic acid]]
		+	[[Category: Sialidase]]

OCA at 16:31, 20 October 2021

2021-10-20T16:31:41Z

←Older revision		Revision as of 16:31, 20 October 2021
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-	'''Unreleased structure'''

-	~~The entry 7p1f is ON HOLD until Paper Publication~~	+	==Structure of KDNase from Aspergillus terrerus in complex with 2,3-didehydro-2,3-dideoxy-D-glycero-D-galacto-nonulosonic acid.==
-		+	<StructureSection load='7p1f' size='340' side='right'caption='[[7p1f]]' scene=''>
-	~~Authors: Gloster, T.M., McMahon, S.A.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P1F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P1F FirstGlance]. <br>
-	~~Description:~~ Structure of KDNase from Aspergillus terrerus in complex with 2,3-didehydro-2,3-dideoxy-D-glycero-D-galacto-nonulosonic acid.	+	</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=7p1f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p1f OCA], [https://pdbe.org/7p1f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p1f RCSB], [https://www.ebi.ac.uk/pdbsum/7p1f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p1f ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Gloster~~, T.M~~]]	+	__TOC__
-	[[Category: ~~Mcmahon, S.A~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Gloster TM]]
		+	[[Category: McMahon SA]]

OCA at 09:11, 4 August 2021

2021-08-04T09:11:59Z

←Older revision		Revision as of 09:11, 4 August 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7p1f is ON HOLD	+	The entry 7p1f is ON HOLD until Paper Publication

	Authors: Gloster, T.M., McMahon, S.A.		Authors: Gloster, T.M., McMahon, S.A.

OCA: Protected "7p1f" [edit=sysop:move=sysop]

2021-07-07T08:55:58Z

Protected "7p1f" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:55, 7 July 2021

OCA: New page: '''Unreleased structure''' The entry 7p1f is ON HOLD Authors: Gloster, T.M., McMahon, S.A. Description: Structure of KDNase from Aspergillus terrerus in complex with 2,3-didehydro-2,3-...

2021-07-07T08:55:57Z

New page: '''Unreleased structure''' The entry 7p1f is ON HOLD Authors: Gloster, T.M., McMahon, S.A. Description: Structure of KDNase from Aspergillus terrerus in complex with 2,3-didehydro-2,3-...

New page

'''Unreleased structure'''

The entry 7p1f is ON HOLD

Authors: Gloster, T.M., McMahon, S.A.

Description: Structure of KDNase from Aspergillus terrerus in complex with 2,3-didehydro-2,3-dideoxy-D-glycero-D-galacto-nonulosonic acid.
[[Category: Unreleased Structures]]
[[Category: Gloster, T.M]]
[[Category: Mcmahon, S.A]]