1i9h: Difference between revisions

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-{{Seed}}
-[[Image:1i9h.png|left|200px]]
-<!--
+==CORE STREPTAVIDIN-BNA COMPLEX==
-The line below this paragraph, containing "STRUCTURE_1i9h", creates the "Structure Box" on the page.
+<StructureSection load='1i9h' size='340' side='right'caption='[[1i9h]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1i9h]] 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=1I9H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1I9H FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#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>
-{{STRUCTURE_1i9h|  PDB=1i9h  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1i9h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i9h OCA], [https://pdbe.org/1i9h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1i9h RCSB], [https://www.ebi.ac.uk/pdbsum/1i9h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1i9h 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/i9/1i9h_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=1i9h ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Avidin and its bacterial analogue streptavidin exhibit similarly high affinities toward the vitamin biotin. The extremely high affinity of these two proteins has been utilized as a powerful tool in many biotechnological applications. Although avidin and streptavidin have similar tertiary and quaternary structures, they differ in many of their properties. Here we show that avidin enhances the alkaline hydrolysis of biotinyl p-nitrophenyl ester, whereas streptavidin protects this reaction even under extreme alkaline conditions (pH &gt; 12). Unlike normal enzymatic catalysis, the hydrolysis reaction proceeds as a single cycle with no turnover because of the extremely high affinity of the protein for one of the reaction products (i.e. free biotin). The three-dimensional crystal structures of avidin (2 A) and streptavidin (2.4 A) complexed with the amide analogue, biotinyl p-nitroanilide, as a model for the p-nitrophenyl ester, revealed structural insights into the factors that enhance or protect the hydrolysis reaction. The data demonstrate that several molecular features of avidin are responsible for the enhanced hydrolysis of biotinyl p-nitrophenyl ester. These include the nature of a decisive flexible loop, the presence of an obtrusive arginine 114, and a newly formed critical interaction between lysine 111 and the nitro group of the substrate. The open conformation of the loop serves to expose the substrate to the solvent, and the arginine shifts the p-nitroanilide moiety toward the interacting lysine, which increases the electron withdrawing characteristics and consequent electrophilicity of the carbonyl group of the substrate. Streptavidin lacked such molecular properties, and analogous interactions with the substrate were consequently absent. The information derived from these structures may provide insight into the action of artificial protein catalysts and the evolution of catalytic sites in general.
-===CORE STREPTAVIDIN-BNA COMPLEX===
+Chicken avidin exhibits pseudo-catalytic properties. Biochemical, structural, and electrostatic consequences.,Huberman T, Eisenberg-Domovich Y, Gitlin G, Kulik T, Bayer EA, Wilchek M, Livnah O J Biol Chem. 2001 Aug 24;276(34):32031-9. Epub 2001 Jun 6. PMID:11395489<ref>PMID:11395489</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1i9h" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11395489}}, adds the Publication Abstract to the page
+*[[Avidin 3D structures|Avidin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 11395489 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11395489}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-I9H is a [[Single protein]] structure of 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=1I9H OCA].
-==Reference==
-Chicken avidin exhibits pseudo-catalytic properties. Biochemical, structural, and electrostatic consequences., Huberman T, Eisenberg-Domovich Y, Gitlin G, Kulik T, Bayer EA, Wilchek M, Livnah O, J Biol Chem. 2001 Aug 24;276(34):32031-9. Epub 2001 Jun 6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11395489 11395489]
-[[Category: Single protein]]
 [[Category: Streptomyces avidinii]]
-[[Category: Bayer, E A.]]
+[[Category: Bayer EA]]
-[[Category: Eisenberg-Domovich, Y.]]
+[[Category: Eisenberg-Domovich Y]]
-[[Category: Huberman, T.]]
+[[Category: Huberman T]]
-[[Category: Livnah, O.]]
+[[Category: Livnah O]]
-[[Category: Wilchek, M.]]
+[[Category: Wilchek M]]
-[[Category: Classical beta barrel]]
-[[Category: Protein-ligand complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 10:37:30 2008''