8pms - Revision history

OCA at 09:03, 6 December 2023

OCA — Wed, 06 Dec 2023 09:03:14 GMT

←Older revision		Revision as of 09:03, 6 December 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8pms is ~~ON HOLD until Paper~~ Publication	+	==NADase from Aspergillus fumigatus with replaced C-terminus from Neurospora crassa==
		+	<StructureSection load='8pms' size='340' side='right'caption='[[8pms]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8pms]] is a 4 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=8PMS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8PMS FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.4Å</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=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=8pms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8pms OCA], [https://pdbe.org/8pms PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8pms RCSB], [https://www.ebi.ac.uk/pdbsum/8pms PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8pms ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nicotinamide adenine dinucleotide (NAD) is an essential molecule in all kingdoms of life, mediating energy metabolism and cellular signaling. Recently, a new class of highly active fungal surface NADases was discovered. The enzyme from the opportunistic human pathogen Aspergillus fumigatus was thoroughly characterized. It harbors a catalytic domain that resembles that of the tuberculosis necrotizing toxin from Mycobacterium tuberculosis, which efficiently cleaves NAD(+) to nicotinamide and ADP-ribose, thereby depleting the dinucleotide pool. Of note, the A. fumigatus NADase has an additional Ca(2+)-binding motif at the C-terminus of the protein. Despite the presence of NADases in several fungal divisions, the Ca(2+)-binding motif is uniquely found in the Eurotiales order, which contains species that have immense health and economic impacts on humans. To identify the potential roles of the metal ion-binding site in catalysis or protein stability, we generated and characterized A. fumigatus NADase variants lacking the ability to bind calcium. X-ray crystallographic analyses revealed that the mutation causes a drastic and dynamic structural rearrangement of the homodimer, resulting in decreased thermal stability. Even though the calcium-binding site is at a long distance from the catalytic center, the structural reorganization upon the loss of calcium binding allosterically alters the active site, thereby negatively affecting NAD-glycohydrolase activity. Together, these findings reveal that this unique calcium-binding site affects the protein fold, stabilizing the dimeric structure, but also mediates long-range effects resulting in an increased catalytic rate.

-	~~Authors~~:	+	Novel Calcium-Binding Motif Stabilizes and Increases the Activity of Aspergillus fumigatus Ecto-NADase.,Ferrario E, Kallio JP, Stromland O, Ziegler M Biochemistry. 2023 Nov 7. doi: 10.1021/acs.biochem.3c00360. PMID:37934975<ref>PMID:37934975</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8pms" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Aspergillus fumigatus Af293]]
		+	[[Category: Large Structures]]
		+	[[Category: Ferrario E]]
		+	[[Category: Kallio JP]]
		+	[[Category: Stromland O]]
		+	[[Category: Ziegler M]]

OCA: Replacing page with ''''Unreleased structure''' The entry 8pms is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures'

OCA — Wed, 22 Nov 2023 05:38:17 GMT

Replacing page with ''''Unreleased structure''' The entry 8pms is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures'

←Older revision		Revision as of 05:38, 22 November 2023
Line 1:		Line 1:
		+	'''Unreleased structure'''

-	~~==NADase from Aspergillus fumigatus with replaced C-terminus from Neurospora crassa==~~	+	The entry 8pms is ON HOLD until Paper Publication
-	~~<StructureSection load='~~8pms~~' size='340' side='right'caption='[[8pms]], [[Resolution\|resolution]] 2.40Å' scene=''>~~	+
-	~~== Structural highlights ==~~	+
-	~~<table><tr><td colspan='2'>[[8pms]]~~ is a 4 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=8PMS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8PMS FirstGlance]. <br>	+
-	~~</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.4Å</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=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=8pms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8pms OCA], [https://pdbe.org/8pms PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8pms RCSB], [https://www.ebi.ac.uk/pdbsum/8pms PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8pms ProSAT]</span></td></tr>	+
-	~~</table>~~	+
-	~~== Function ==~~	+
-	[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>	+
-	~~<div style="background-color:#fffaf0;">~~	+
-	== Publication ~~Abstract from PubMed ==~~	+
-	Nicotinamide adenine dinucleotide (NAD) is an essential molecule in all kingdoms of life, mediating energy metabolism and cellular signaling. Recently, a new class of highly active fungal surface NADases was discovered. The enzyme from the opportunistic human pathogen Aspergillus fumigatus was thoroughly characterized. It harbors a catalytic domain that resembles that of the tuberculosis necrotizing toxin from Mycobacterium tuberculosis, which efficiently cleaves NAD(+) to nicotinamide and ADP-ribose, thereby depleting the dinucleotide pool. Of note, the A. fumigatus NADase has an additional Ca(2+)-binding motif at the C-terminus of the protein. Despite the presence of NADases in several fungal divisions, the Ca(2+)-binding motif is uniquely found in the Eurotiales order, which contains species that have immense health and economic impacts on humans. To identify the potential roles of the metal ion-binding site in catalysis or protein stability, we generated and characterized A. fumigatus NADase variants lacking the ability to bind calcium. X-ray crystallographic analyses revealed that the mutation causes a drastic and dynamic structural rearrangement of the homodimer, resulting in decreased thermal stability. Even though the calcium-binding site is at a long distance from the catalytic center, the structural reorganization upon the loss of calcium binding allosterically alters the active site, thereby negatively affecting NAD-glycohydrolase activity. Together, these findings reveal that this unique calcium-binding site affects the protein fold, stabilizing the dimeric structure, but also mediates long-range effects resulting in an increased catalytic rate.	+

-	~~Novel Calcium-Binding Motif Stabilizes and Increases the Activity of Aspergillus fumigatus Ecto-NADase.,Ferrario E, Kallio JP, Stromland O, Ziegler M Biochemistry. 2023 Nov 7. doi~~: ~~10.1021/acs.biochem.3c00360. PMID:37934975<ref>PMID:37934975</ref>~~	+	Authors:

-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+	Description:
-	~~</div>~~	+	[[Category: Unreleased Structures]]
-	~~<div class="pdbe-citations 8pms" style="background-color~~:~~#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
-	~~__TOC__~~	+
-	~~</StructureSection>~~	+
-	[[Category: ~~Aspergillus fumigatus Af293]]~~	+
-	~~[[Category: Large~~ Structures]]	+
-	~~[[Category: Ferrario E]]~~	+
-	~~[[Category: Kallio JP]]~~	+
-	~~[[Category: Stromland O]]~~	+
-	~~[[Category: Ziegler M~~]]	+

OCA at 07:40, 15 November 2023

OCA — Wed, 15 Nov 2023 07:40:08 GMT

←Older revision		Revision as of 07:40, 15 November 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8pms is ~~ON HOLD until Paper~~ Publication	+	==NADase from Aspergillus fumigatus with replaced C-terminus from Neurospora crassa==
		+	<StructureSection load='8pms' size='340' side='right'caption='[[8pms]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8pms]] is a 4 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=8PMS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8PMS FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.4Å</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=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=8pms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8pms OCA], [https://pdbe.org/8pms PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8pms RCSB], [https://www.ebi.ac.uk/pdbsum/8pms PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8pms ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nicotinamide adenine dinucleotide (NAD) is an essential molecule in all kingdoms of life, mediating energy metabolism and cellular signaling. Recently, a new class of highly active fungal surface NADases was discovered. The enzyme from the opportunistic human pathogen Aspergillus fumigatus was thoroughly characterized. It harbors a catalytic domain that resembles that of the tuberculosis necrotizing toxin from Mycobacterium tuberculosis, which efficiently cleaves NAD(+) to nicotinamide and ADP-ribose, thereby depleting the dinucleotide pool. Of note, the A. fumigatus NADase has an additional Ca(2+)-binding motif at the C-terminus of the protein. Despite the presence of NADases in several fungal divisions, the Ca(2+)-binding motif is uniquely found in the Eurotiales order, which contains species that have immense health and economic impacts on humans. To identify the potential roles of the metal ion-binding site in catalysis or protein stability, we generated and characterized A. fumigatus NADase variants lacking the ability to bind calcium. X-ray crystallographic analyses revealed that the mutation causes a drastic and dynamic structural rearrangement of the homodimer, resulting in decreased thermal stability. Even though the calcium-binding site is at a long distance from the catalytic center, the structural reorganization upon the loss of calcium binding allosterically alters the active site, thereby negatively affecting NAD-glycohydrolase activity. Together, these findings reveal that this unique calcium-binding site affects the protein fold, stabilizing the dimeric structure, but also mediates long-range effects resulting in an increased catalytic rate.

-	~~Authors~~:	+	Novel Calcium-Binding Motif Stabilizes and Increases the Activity of Aspergillus fumigatus Ecto-NADase.,Ferrario E, Kallio JP, Stromland O, Ziegler M Biochemistry. 2023 Nov 7. doi: 10.1021/acs.biochem.3c00360. PMID:37934975<ref>PMID:37934975</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8pms" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Aspergillus fumigatus Af293]]
		+	[[Category: Large Structures]]
		+	[[Category: Ferrario E]]
		+	[[Category: Kallio JP]]
		+	[[Category: Stromland O]]
		+	[[Category: Ziegler M]]

OCA at 04:02, 9 August 2023

OCA — Wed, 09 Aug 2023 04:02:29 GMT

←Older revision		Revision as of 04:02, 9 August 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8pms is ON HOLD	+	The entry 8pms is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "8pms" [edit=sysop:move=sysop]

OCA — Wed, 05 Jul 2023 04:21:11 GMT

Protected "8pms" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:21, 5 July 2023

OCA: New page: '''Unreleased structure''' The entry 8pms is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 05 Jul 2023 04:21:10 GMT

New page: '''Unreleased structure''' The entry 8pms is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8pms is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]