1ldo: Difference between revisions

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-[[Image:1ldo.png|left|200px]]
-<!--
+==avidin-norbioitn complex==
-The line below this paragraph, containing "STRUCTURE_1ldo", creates the "Structure Box" on the page.
+<StructureSection load='1ldo' size='340' side='right'caption='[[1ldo]], [[Resolution|resolution]] 2.20&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'>[[1ldo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LDO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LDO 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]] 2.2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SNR:NORBIOTIN'>SNR</scene></td></tr>
-{{STRUCTURE_1ldo|  PDB=1ldo  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ldo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ldo OCA], [https://pdbe.org/1ldo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ldo RCSB], [https://www.ebi.ac.uk/pdbsum/1ldo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ldo ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AVID_CHICK AVID_CHICK] The biological function of avidin is not known. Forms a strong non-covalent specific complex with biotin (one molecule of biotin per subunit of avidin).
+== 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/ld/1ldo_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1ldo ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We have studied the structural elements that affect ligand exchange between the two high affinity biotin-binding proteins, egg white avidin and its bacterial analogue, streptavidin. For this purpose, we have developed a simple assay based on the antipodal behavior of the two proteins toward hydrolysis of biotinyl p-nitrophenyl ester (BNP). The assay provided the experimental basis for these studies. It was found that biotin migrates unidirectionally from streptavidin to avidin. Conversely, the biotin derivative, BNP, is transferred in the opposite direction, from avidin to streptavidin. A previous crystallographic study (Huberman, T., Eisenberg-Domovich, Y., Gitlin, G., Kulik, T., Bayer, E. A., Wilchek, M., and Livnah, O. (2001) J. Biol. Chem. 276, 32031-32039) provided insight into a plausible explanation for these results. These data revealed that the non-hydrolyzable BNP analogue, biotinyl p-nitroanilide, was almost completely sheltered in streptavidin as opposed to avidin in which the disordered conformation of a critical loop resulted in the loss of several hydrogen bonds and concomitant exposure of the analogue to the solvent. In order to determine the minimal modification of the biotin molecule required to cause the disordered loop conformation, the structures of avidin and streptavidin were determined with norbiotin, homobiotin, and a common long-chain biotin derivative, biotinyl epsilon-aminocaproic acid. Six new crystal structures of the avidin and streptavidin complexes with the latter biotin analogues and derivatives were thus elucidated. It was found that extending the biotin side chain by a single CH(2) group (i.e. homobiotin) is sufficient to result in this remarkable conformational change in the loop of avidin. These results bear significant biotechnological importance, suggesting that complexes containing biotinylated probes with streptavidin would be more stable than those with avidin. These findings should be heeded when developing new drugs based on lead compounds because it is difficult to predict the structural and conformational consequences on the resultant protein-ligand interactions.
-===avidin-norbioitn complex===
+Ligand exchange between proteins. Exchange of biotin and biotin derivatives between avidin and streptavidin.,Pazy Y, Kulik T, Bayer EA, Wilchek M, Livnah O J Biol Chem. 2002 Aug 23;277(34):30892-900. Epub 2002 Jun 7. PMID:12055191<ref>PMID:12055191</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_12055191}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1ldo" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 12055191 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_12055191}}
-==About this Structure==
-[[1ldo]] is a 2 chain structure of [[Avidin]] with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LDO OCA].
 ==See Also==
-*[[Avidin]]
+*[[Avidin 3D structures|Avidin 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:12055191</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Gallus gallus]]
-[[Category: Bayer, E A.]]
+[[Category: Large Structures]]
-[[Category: Kulik, T.]]
+[[Category: Bayer EA]]
-[[Category: Livnah, O.]]
+[[Category: Kulik T]]
-[[Category: Pazy, Y.]]
+[[Category: Livnah O]]
-[[Category: Wilchek, M.]]
+[[Category: Pazy Y]]
-[[Category: Avidin]]
+[[Category: Wilchek M]]
-[[Category: Biotin]]
-[[Category: High affinity system]]
-[[Category: Ligand exchange]]
-[[Category: Streptavidin]]
-[[Category: Unknown function]]