1rxj: Difference between revisions

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 ==Crystal structure of streptavidin mutant (M2) where the L3,4 loop was replace by that of avidin==
-<StructureSection load='1rxj' size='340' side='right' caption='[[1rxj]], [[Resolution|resolution]] 1.14&Aring;' scene=''>
+<StructureSection load='1rxj' size='340' side='right'caption='[[1rxj]], [[Resolution|resolution]] 1.14&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1rxj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_avidinii Streptomyces avidinii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RXJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RXJ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1rxj]] is a 4 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=1RXJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RXJ FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BNI:5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC+ACID+(4-NITRO-PHENYL)-AMIDE'>BNI</scene><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]] 1.14&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ij8|1ij8]], [[1i9h|1i9h]], [[1rxh|1rxh]], [[1rxk|1rxk]]</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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rxj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rxj RCSB], [http://www.ebi.ac.uk/pdbsum/1rxj PDBsum]</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=1rxj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rxj OCA], [https://pdbe.org/1rxj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rxj RCSB], [https://www.ebi.ac.uk/pdbsum/1rxj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rxj ProSAT]</span></td></tr>
-<table>
+</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/1rxj_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rx/1rxj_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1rxj ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-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.
-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:15079055<ref>PMID:15079055</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Avidin|Avidin]]
+*[[Avidin 3D structures|Avidin 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[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: Avidin]]
-[[Category: Pseudo enzymatic activity]]
-[[Category: Streptavidin]]
-[[Category: Unknown function]]