1rxh: Difference between revisions

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-[[Image:1rxh.gif|left|200px]]<br /><applet load="1rxh" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1rxh, resolution 2.9&Aring;" />
-'''Crystal structure of streptavidin mutant L124R (M1) complexed with biotinyl p-nitroanilide (BNI)'''<br />
-==Overview==
+==Crystal structure of streptavidin mutant L124R (M1) complexed with biotinyl p-nitroanilide (BNI)==
-Avidin enhances the hydrolysis of biotinyl p-nitrophenyl ester (BNP) under, mild alkaline conditions, whereas streptavidin prevents hydrolysis of BNP, up to pH 12. Recently, we imposed hydrolytic activity on streptavidin by, rational mutagenesis, based on the molecular elements responsible for the, hydrolysis by avidin. Three mutants were designed, whereby the desired, features, the distinctive L124R point mutation (M1), the L3,4 loop, replacement (M2), and the combined mutation (M3), were transferred from, avidin to streptavidin. The crystal structures of the mutants, in complex, with biotinyl p-nitroanilide (BNA), the stable amide analogue of BNP, were, determined. The results demonstrate that the point mutation alone has, little effect on hydrolysis, and BNA exhibits a conformation similar to, that of streptavidin. Substitution of a lengthier L3,4 loop (from avidin, to streptavidin), resulted in an open conformation, thus exposing the, ligand to solvent. Moreover, the amide bond of BNA was flipped relative to, that of the streptavidin and M1 complexes, thus deflecting the nitro group, toward Lys-121. Consequently, the leaving group potential of the, nitrophenyl group of BNP is increased, and M2 hydrolyzes BNP at pH values, &gt;8.5. To better emulate the hydrolytic potential of avidin, M3 was, required. The combination of loop replacement and point mutation served to, further increase the leaving group potential by interaction of the nitro, group with Arg-124 and Lys-121. The information derived from this study, may provide insight into the design of enzymes and transfer of desired, properties among homologous proteins.
+<StructureSection load='1rxh' size='340' side='right'caption='[[1rxh]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1rxh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_avidinii Streptomyces avidinii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RXH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RXH 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]] 2.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BNI:5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC+ACID+(4-NITRO-PHENYL)-AMIDE'>BNI</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=1rxh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rxh OCA], [https://pdbe.org/1rxh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rxh RCSB], [https://www.ebi.ac.uk/pdbsum/1rxh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rxh ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SAV_STRAV SAV_STRAV] The biological function of streptavidin is not known. Forms a strong non-covalent specific complex with biotin (one molecule of biotin per subunit of streptavidin).
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rx/1rxh_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1rxh ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-RXH is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_avidinii Streptomyces avidinii] with BNI as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RXH OCA].
+*[[Avidin 3D structures|Avidin 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Structural elements responsible for conversion of streptavidin to a pseudoenzyme., Eisenberg-Domovich Y, Pazy Y, Nir O, Raboy B, Bayer EA, Wilchek M, Livnah O, Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):5916-21. Epub 2004 Apr 12. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15079055 15079055]
+[[Category: Large Structures]]
-[[Category: Single protein]]
 [[Category: Streptomyces avidinii]]
-[[Category: Bayer, E.A.]]
+[[Category: Bayer EA]]
-[[Category: Eisenberg-Domovich, Y.]]
+[[Category: Eisenberg-Domovich Y]]
-[[Category: Livnah, O.]]
+[[Category: Livnah O]]
-[[Category: Nir, O.]]
+[[Category: Nir O]]
-[[Category: Pazy, Y.]]
+[[Category: Pazy Y]]
-[[Category: Raboy, B.]]
+[[Category: Raboy B]]
-[[Category: Wilchek, M.]]
+[[Category: Wilchek M]]
-[[Category: BNI]]
-[[Category: avidin]]
-[[Category: pseudo enzymatic activity]]
-[[Category: streptavidin]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 01:55:53 2007''