8db8 - Revision history

OCA at 07:25, 3 April 2024

OCA — Wed, 03 Apr 2024 07:25:33 GMT

←Older revision		Revision as of 07:25, 3 April 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8db8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichomonas_vaginalis Trichomonas vaginalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8DB8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DB8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[8db8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichomonas_vaginalis Trichomonas vaginalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8DB8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DB8 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=IMH:1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL'>IMH</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]] 2.21Å</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=IMH:1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL'>IMH</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=8db8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8db8 OCA], [https://pdbe.org/8db8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8db8 RCSB], [https://www.ebi.ac.uk/pdbsum/8db8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8db8 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=8db8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8db8 OCA], [https://pdbe.org/8db8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8db8 RCSB], [https://www.ebi.ac.uk/pdbsum/8db8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8db8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/A2EYV3_TRIVA A2EYV3_TRIVA]]	+	[https://www.uniprot.org/uniprot/A2EYV3_TRIVA A2EYV3_TRIVA]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Trichomonas vaginalis is the causative parasitic protozoan of the disease trichomoniasis, the most prevalent, nonviral sexually transmitted disease in the world. T. vaginalis is a parasite that scavenges nucleosides from the host organism via catalysis by nucleoside hydrolase (NH) enzymes to yield purine and pyrimidine bases. One of the four NH enzymes identified within the genome of T. vaginalis displays unique specificity toward purine nucleosides, adenosine and guanosine, but not inosine, and atypically shares greater sequence similarity to the pyrimidine hydrolases. Bioinformatic analysis of this enzyme, adenosine/guanosine-preferring nucleoside ribohydrolase (AGNH), was incapable of identifying the residues responsible for this uncommon specificity, highlighting the need for structural information. Here, we report the X-ray crystal structures of holo, unliganded AGNH and three additional structures of the enzyme bound to fragment and small-molecule inhibitors. Taken together, these structures facilitated the identification of residue Asp231, which engages in substrate interactions in the absence of those residues that typically support the canonical purine-specific tryptophan-stacking specificity motif. An altered substrate-binding pose is mirrored by repositioning within the protein scaffold of the His80 general acid/base catalyst. The newly defined structure-determined sequence markers allowed the assignment of additional NH orthologs, which are proposed to exhibit the same specificity for adenosine and guanosine alone and further delineate specificity classes for these enzymes.	+
-		+
-	Structure-Guided Insight into the Specificity and Mechanism of a Parasitic Nucleoside Hydrolase.,Muellers SN, Nyitray MM, Reynarowych N, Saljanin E, Benzie AL, Schoenfeld AR, Stockman BJ, Allen KN Biochemistry. 2022 Sep 6;61(17):1853-1861. doi: 10.1021/acs.biochem.2c00361. Epub, 2022 Aug 22. PMID:35994320<ref>PMID:35994320</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 8db8" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 18:47, 7 September 2022

OCA — Wed, 07 Sep 2022 18:47:47 GMT

←Older revision		Revision as of 18:47, 7 September 2022
Line 9:		Line 9:
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/A2EYV3_TRIVA A2EYV3_TRIVA]]		[[https://www.uniprot.org/uniprot/A2EYV3_TRIVA A2EYV3_TRIVA]]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Trichomonas vaginalis is the causative parasitic protozoan of the disease trichomoniasis, the most prevalent, nonviral sexually transmitted disease in the world. T. vaginalis is a parasite that scavenges nucleosides from the host organism via catalysis by nucleoside hydrolase (NH) enzymes to yield purine and pyrimidine bases. One of the four NH enzymes identified within the genome of T. vaginalis displays unique specificity toward purine nucleosides, adenosine and guanosine, but not inosine, and atypically shares greater sequence similarity to the pyrimidine hydrolases. Bioinformatic analysis of this enzyme, adenosine/guanosine-preferring nucleoside ribohydrolase (AGNH), was incapable of identifying the residues responsible for this uncommon specificity, highlighting the need for structural information. Here, we report the X-ray crystal structures of holo, unliganded AGNH and three additional structures of the enzyme bound to fragment and small-molecule inhibitors. Taken together, these structures facilitated the identification of residue Asp231, which engages in substrate interactions in the absence of those residues that typically support the canonical purine-specific tryptophan-stacking specificity motif. An altered substrate-binding pose is mirrored by repositioning within the protein scaffold of the His80 general acid/base catalyst. The newly defined structure-determined sequence markers allowed the assignment of additional NH orthologs, which are proposed to exhibit the same specificity for adenosine and guanosine alone and further delineate specificity classes for these enzymes.
		+
		+	Structure-Guided Insight into the Specificity and Mechanism of a Parasitic Nucleoside Hydrolase.,Muellers SN, Nyitray MM, Reynarowych N, Saljanin E, Benzie AL, Schoenfeld AR, Stockman BJ, Allen KN Biochemistry. 2022 Sep 6;61(17):1853-1861. doi: 10.1021/acs.biochem.2c00361. Epub, 2022 Aug 22. PMID:35994320<ref>PMID:35994320</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 8db8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:42, 7 September 2022

OCA — Wed, 07 Sep 2022 16:42:03 GMT

←Older revision		Revision as of 16:42, 7 September 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 8db8 is ~~ON HOLD until Paper Publication~~	+	==Adenosine/guanosine nucleoside hydrolase bound to ImH==
-		+	<StructureSection load='8db8' size='340' side='right'caption='[[8db8]], [[Resolution\|resolution]] 2.21Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[8db8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichomonas_vaginalis Trichomonas vaginalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8DB8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DB8 FirstGlance]. <br>
-	~~Description~~:	+	</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=IMH:1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL'>IMH</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8db8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8db8 OCA], [https://pdbe.org/8db8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8db8 RCSB], [https://www.ebi.ac.uk/pdbsum/8db8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8db8 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/A2EYV3_TRIVA A2EYV3_TRIVA]]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Trichomonas vaginalis]]
		+	[[Category: Allen KN]]
		+	[[Category: Muellers SN]]
		+	[[Category: Stockman BJ]]

OCA at 04:24, 20 July 2022

OCA — Wed, 20 Jul 2022 04:24:14 GMT

←Older revision		Revision as of 04:24, 20 July 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8db8 is ON HOLD	+	The entry 8db8 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "8db8" [edit=sysop:move=sysop]

OCA — Wed, 22 Jun 2022 07:29:13 GMT

Protected "8db8" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:29, 22 June 2022

OCA: New page: '''Unreleased structure''' The entry 8db8 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 22 Jun 2022 07:29:12 GMT

New page: '''Unreleased structure''' The entry 8db8 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8db8 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]