3b9g

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[[Image:3b9g.png|left|200px]]
 
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==Crystal structure of loop deletion mutant of Trypanosoma vivax nucleoside hydrolase (3GTvNH) in complex with ImmH==
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The line below this paragraph, containing "STRUCTURE_3b9g", creates the "Structure Box" on the page.
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<StructureSection load='3b9g' size='340' side='right'caption='[[3b9g]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3b9g]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_vivax Trypanosoma vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B9G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B9G FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4&#8491;</td></tr>
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<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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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{{STRUCTURE_3b9g| PDB=3b9g | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3b9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b9g OCA], [https://pdbe.org/3b9g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b9g RCSB], [https://www.ebi.ac.uk/pdbsum/3b9g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b9g ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q9GPQ4_TRYVI Q9GPQ4_TRYVI]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b9/3b9g_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3b9g ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The nucleoside hydrolase of Trypanosoma vivax hydrolyzes the N-glycosidic bond of purine nucleosides. Structural and kinetic studies on this enzyme have suggested a catalytic role for a flexible loop in the vicinity of the active sites. Here we present the analysis of the role of this flexible loop via the combination of a proline scan of the loop, loop deletion mutagenesis, steady state and pre-steady state analysis, and x-ray crystallography. Our analysis reveals that this loop has an important role in leaving group activation and product release. The catalytic role involves the entire loop and could only be perturbed by deletion of the entire loop and not by single site mutagenesis. We present evidence that the loop closes over the active site during catalysis, thereby ordering a water channel that is involved in leaving group activation. Once chemistry has taken place, the loop dynamics determine the rate of product release.
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===Crystal structure of loop deletion mutant of Trypanosoma vivax nucleoside hydrolase (3GTvNH) in complex with ImmH===
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A flexible loop as a functional element in the catalytic mechanism of nucleoside hydrolase from Trypanosoma vivax.,Vandemeulebroucke A, De Vos S, Van Holsbeke E, Steyaert J, Versees W J Biol Chem. 2008 Aug 8;283(32):22272-82. Epub 2008 Jun 2. PMID:18519562<ref>PMID:18519562</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_18519562}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3b9g" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 18519562 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18519562}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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[[3b9g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Trypanosoma_vivax Trypanosoma vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B9G OCA].
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==Reference==
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<ref group="xtra">PMID:018519562</ref><references group="xtra"/>
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[[Category: Purine nucleosidase]]
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[[Category: Trypanosoma vivax]]
[[Category: Trypanosoma vivax]]
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[[Category: Holsbeke, E Van.]]
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[[Category: De Vos S]]
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[[Category: Steyaert, J.]]
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[[Category: Steyaert J]]
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[[Category: Vandemeulebroucke, A.]]
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[[Category: Van Holsbeke E]]
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[[Category: Versees, W.]]
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[[Category: Vandemeulebroucke A]]
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[[Category: Vos, S De.]]
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[[Category: Versees W]]
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[[Category: Flexible loop deletion]]
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[[Category: Hydrolase]]
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[[Category: Rossmann fold]]
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[[Category: Transition state complex]]
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Current revision

Crystal structure of loop deletion mutant of Trypanosoma vivax nucleoside hydrolase (3GTvNH) in complex with ImmH

PDB ID 3b9g

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