8db7: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[8db7]] 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=8DB7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DB7 FirstGlance]. <br>
<table><tr><td colspan='2'>[[8db7]] 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=8DB7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DB7 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=R2O:N-(4-fluorophenyl)-4,5-dihydro-1H-imidazol-2-amine'>R2O</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]] 2.33&#8491;</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=R2O:N-(4-fluorophenyl)-4,5-dihydro-1H-imidazol-2-amine'>R2O</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=8db7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8db7 OCA], [https://pdbe.org/8db7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8db7 RCSB], [https://www.ebi.ac.uk/pdbsum/8db7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8db7 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=8db7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8db7 OCA], [https://pdbe.org/8db7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8db7 RCSB], [https://www.ebi.ac.uk/pdbsum/8db7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8db7 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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8db7" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>

Latest revision as of 10:25, 3 April 2024

Adenosine/guanosine nucleoside hydrolase bound to a fragment inhibitorAdenosine/guanosine nucleoside hydrolase bound to a fragment inhibitor

Structural highlights

8db7 is a 4 chain structure with sequence from Trichomonas vaginalis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.33Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A2EYV3_TRIVA

8db7, resolution 2.33Å

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