6ygg - Revision history

OCA at 07:40, 1 May 2024

OCA — Wed, 01 May 2024 07:40:03 GMT

←Older revision		Revision as of 07:40, 1 May 2024
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	<StructureSection load='6ygg' size='340' side='right'caption='[[6ygg]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='6ygg' size='340' side='right'caption='[[6ygg]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ygg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Aspfu Aspfu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YGG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YGG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ygg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_fumigatus_Af293 Aspergillus fumigatus Af293]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YGG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YGG 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=DQV:[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl+[(2R,3S,4R,5S)-5-(3-carbamoylphenyl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl+dihydrogen+diphosphate+(non-preferred+name)'>DQV</scene>, <scene name='pdbligand=NA:~~SODIUM+ION~~'>NA</scene>, <scene name='pdbligand=~~NAG~~:~~N-ACETYL-D-GLUCOSAMINE~~'>~~NAG~~</scene>, <scene name='pdbligand=~~FUC~~:~~ALPHA~~-L-~~FUCOSE~~'>~~FUC~~</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6yge\|6yge]]</div></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=DQV:[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl+[(2R,3S,4R,5S)-5-(3-carbamoylphenyl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl+dihydrogen+diphosphate+(non-preferred+name)'>DQV</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AFUA_6G14470 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=330879 ASPFU])~~</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=6ygg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ygg OCA], [https://pdbe.org/6ygg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ygg RCSB], [https://www.ebi.ac.uk/pdbsum/6ygg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ygg 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=6ygg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ygg OCA], [https://pdbe.org/6ygg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ygg RCSB], [https://www.ebi.ac.uk/pdbsum/6ygg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ygg ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/NADA_ASPFU NADA_ASPFU] Conidial surface nicotinamide adenine dinucleotide glycohydrolase that cleave NAD(+) and NADP(+) but not their reduced counterparts, NADH and NADPH (PubMed:33712585). Lacks both ADP-ribosyl cyclase and base exchange activity and does not mediate synthesis of calcium messengers cADPR or NAADP (PubMed:33712585). Plays a role in pathogenicity by depleting the host's NAD(+) pool (PubMed:33712585).<ref>PMID:33712585</ref>
-	~~Nicotinamide~~ adenine dinucleotide (~~NAD~~) ~~is a key molecule in cellular bioenergetics~~ and ~~signalling. Various bacterial pathogens release NADase enzymes into the host cell that deplete the host's NAD~~(+) ~~pool~~, ~~thereby causing rapid cell death. Here, we report the identification of NADases on the surface of fungi such as the pathogen Aspergillus fumigatus~~ and ~~the saprophyte Neurospora crassa. The enzymes harbour a tuberculosis necrotizing toxin~~ (~~TNT~~) ~~domain and are predominately present in pathogenic species~~. ~~The 1.6 A X~~-~~ray structure of the homodimeric A. fumigatus protein reveals unique properties including N-linked glycosylation~~ and ~~a Ca~~(2+)~~-binding site whose occupancy regulates activity~~. ~~The structure~~ in complex with a substrate analogue suggests a catalytic mechanism that is distinct from those of known NADases, ADP-ribosyl cyclases and transferases. We propose that fungal NADases may convey advantages during interaction with the host ~~or competing microorganisms.~~	+
-		+
-	Discovery of fungal surface NADases predominantly present in pathogenic species.,Stromland O, Kallio JP, Pschibul A, Skoge RH, Harethardottir HM, Sverkeli LJ, Heinekamp T, Kniemeyer O, Migaud M, Makarov MV, Gossmann TI, Brakhage AA, Ziegler M Nat Commun. 2021 Mar 12;12(1):~~1631~~. ~~doi: 10.1038/s41467-021-21307-z. PMID:33712585~~<ref>PMID:33712585</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6ygg" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aspfu~~]]	+	[[Category: Aspergillus fumigatus Af293]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kallio~~, J P~~]]	+	[[Category: Kallio JP]]
-	[[Category: Stromland, O]]	+	[[Category: Stromland O]]
-	[[Category: Ziegler, M]]	+	[[Category: Ziegler M]]
-	~~[[Category: Benzamide adenine dinucleotide]]~~	+
-	~~[[Category: Ca-binding]]~~	+
-	~~[[Category: Glycoprotein]]~~	+
-	~~[[Category: Homodimer]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nad]]~~	+
-	~~[[Category: Nad+ glycohydrolase~~]]	+

OCA at 10:09, 7 July 2021

OCA — Wed, 07 Jul 2021 10:09:01 GMT

←Older revision		Revision as of 10:09, 7 July 2021
Line 1:		Line 1:

	==NADase from Aspergillus fumigatus complexed with a substrate anologue==		==NADase from Aspergillus fumigatus complexed with a substrate anologue==
-	<StructureSection load='6ygg' size='340' side='right'caption='[[6ygg]]' scene=''>	+	<StructureSection load='6ygg' size='340' side='right'caption='[[6ygg]], [[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=6YGG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6YGG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ygg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspfu Aspfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YGG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YGG FirstGlance]. <br>
-	</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=6ygg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ygg OCA], [~~http~~://pdbe.org/6ygg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ygg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ygg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ygg 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=DQV:[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl+[(2R,3S,4R,5S)-5-(3-carbamoylphenyl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl+dihydrogen+diphosphate+(non-preferred+name)'>DQV</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6yge\|6yge]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AFUA_6G14470 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=330879 ASPFU])</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=6ygg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ygg OCA], [https://pdbe.org/6ygg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ygg RCSB], [https://www.ebi.ac.uk/pdbsum/6ygg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ygg ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nicotinamide adenine dinucleotide (NAD) is a key molecule in cellular bioenergetics and signalling. Various bacterial pathogens release NADase enzymes into the host cell that deplete the host's NAD(+) pool, thereby causing rapid cell death. Here, we report the identification of NADases on the surface of fungi such as the pathogen Aspergillus fumigatus and the saprophyte Neurospora crassa. The enzymes harbour a tuberculosis necrotizing toxin (TNT) domain and are predominately present in pathogenic species. The 1.6 A X-ray structure of the homodimeric A. fumigatus protein reveals unique properties including N-linked glycosylation and a Ca(2+)-binding site whose occupancy regulates activity. The structure in complex with a substrate analogue suggests a catalytic mechanism that is distinct from those of known NADases, ADP-ribosyl cyclases and transferases. We propose that fungal NADases may convey advantages during interaction with the host or competing microorganisms.
		+
		+	Discovery of fungal surface NADases predominantly present in pathogenic species.,Stromland O, Kallio JP, Pschibul A, Skoge RH, Harethardottir HM, Sverkeli LJ, Heinekamp T, Kniemeyer O, Migaud M, Makarov MV, Gossmann TI, Brakhage AA, Ziegler M Nat Commun. 2021 Mar 12;12(1):1631. doi: 10.1038/s41467-021-21307-z. PMID:33712585<ref>PMID:33712585</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ygg" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aspfu]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kallio JP]]	+	[[Category: Kallio, J P]]
-	[[Category: Stromland O]]	+	[[Category: Stromland, O]]
-	[[Category: Ziegler M]]	+	[[Category: Ziegler, M]]
		+	[[Category: Benzamide adenine dinucleotide]]
		+	[[Category: Ca-binding]]
		+	[[Category: Glycoprotein]]
		+	[[Category: Homodimer]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nad]]
		+	[[Category: Nad+ glycohydrolase]]

OCA at 10:33, 24 December 2020

OCA — Thu, 24 Dec 2020 10:33:30 GMT

←Older revision		Revision as of 10:33, 24 December 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ygg is ~~ON HOLD until Paper Publication~~	+	==NADase from Aspergillus fumigatus complexed with a substrate anologue==
-		+	<StructureSection load='6ygg' size='340' side='right'caption='[[6ygg]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YGG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YGG FirstGlance]. <br>
-	~~Description~~:	+	</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=6ygg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ygg OCA], [http://pdbe.org/6ygg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ygg RCSB], [http://www.ebi.ac.uk/pdbsum/6ygg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ygg ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Kallio JP]]
		+	[[Category: Stromland O]]
		+	[[Category: Ziegler M]]

OCA at 05:31, 15 April 2020

OCA — Wed, 15 Apr 2020 05:31:14 GMT

←Older revision		Revision as of 05:31, 15 April 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ygg is ON HOLD	+	The entry 6ygg is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6ygg" [edit=sysop:move=sysop]

OCA — Wed, 08 Apr 2020 05:42:37 GMT

Protected "6ygg" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:42, 8 April 2020

OCA: New page: '''Unreleased structure''' The entry 6ygg is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 08 Apr 2020 05:42:36 GMT

New page: '''Unreleased structure''' The entry 6ygg is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6ygg is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]