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1avd

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(New page: 200px<br /><applet load="1avd" size="450" color="white" frame="true" align="right" spinBox="true" caption="1avd, resolution 2.7&Aring;" /> '''THREE-DIMENSIONAL STR...)
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[[Image:1avd.jpg|left|200px]]<br /><applet load="1avd" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1avd, resolution 2.7&Aring;" />
 
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'''THREE-DIMENSIONAL STRUCTURE OF THE TETRAGONAL CRYSTAL FORM OF EGG-WHITE AVIDIN IN ITS FUNCTIONAL COMPLEX WITH BIOTIN AT 2.7 ANGSTROMS RESOLUTION'''<br />
 
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==Overview==
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==THREE-DIMENSIONAL STRUCTURE OF THE TETRAGONAL CRYSTAL FORM OF EGG-WHITE AVIDIN IN ITS FUNCTIONAL COMPLEX WITH BIOTIN AT 2.7 ANGSTROMS RESOLUTION==
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The three-dimensional structure of hen egg-white avidin, crystallized in a, tetragonal crystal form, has been solved at 2.7 A resolution by molecular, replacement methods. After refinement the crystallographic R-factor is, 16.8%, for the 7255 reflections in the 10.0 to 2.7 A resolution range. The, asymmetric unit contains two avidin polypeptide chains (M(r) 2 x 15,600), which build up the functional tetramer through a crystallographic 2-fold, axis parallel to the c unit cell direction. The avidin tetramer has almost, exact 222 molecular symmetry; the three possible dimers display quite, distinct packing interfaces. Each protomer is organized in an, eight-stranded antiparallel orthogonal beta-barrel, with extended loop, regions. The avidin binding site within each promoter is located in a deep, pocket, at the center of the barrel, displaying both hydrophobic and polar, residues for recognition of the tightly bound vitamin. Two Trp residues, Trp70 and Trp97, and Phe79 are in close contact with biotin. Moreover, the, binding pocket is partly closed in its outer rim by residue Trp110 of a, neighboring subunit. Once bound, biotin is almost completely buried in the, protein core, with the exception of the valeryl side-chain carboxylate, group which is exposed to solvent, hydrogen bonds to residues Ala39, Thr40, and Ser75, and triggers the formation of a network of hydrogen bonded, water molecules. Modeling of synthetic biotin analogues allows us to, rationalize functional data available for the binding of these compounds, and to analyze them in terms of biotin recognition mechanism. Hen, egg-white avidin shows clear structural homology to streptavidin, from, Streptomyces avidinii, but significant deviations can be observed in some, regions.
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<StructureSection load='1avd' size='340' side='right'caption='[[1avd]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1avd]] 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=1AVD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AVD 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]] 2.7&#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=BTN:BIOTIN'>BTN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
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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=1avd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1avd OCA], [https://pdbe.org/1avd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1avd RCSB], [https://www.ebi.ac.uk/pdbsum/1avd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1avd ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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).
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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/av/1avd_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=1avd ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1AVD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] with NAG and BTN as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1AVD OCA].
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*[[Avidin 3D structures|Avidin 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Three-dimensional structure of the tetragonal crystal form of egg-white avidin in its functional complex with biotin at 2.7 A resolution., Pugliese L, Coda A, Malcovati M, Bolognesi M, J Mol Biol. 1993 Jun 5;231(3):698-710. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8515446 8515446]
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[[Category: Gallus gallus]]
[[Category: Gallus gallus]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Bolognesi, M.]]
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[[Category: Bolognesi M]]
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[[Category: Coda, A.]]
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[[Category: Coda A]]
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[[Category: Malcovati, M.]]
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[[Category: Malcovati M]]
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[[Category: Pugliese, L.]]
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[[Category: Pugliese L]]
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[[Category: BTN]]
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[[Category: NAG]]
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[[Category: biotin-binding protein]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 11:09:24 2007''
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Current revision

THREE-DIMENSIONAL STRUCTURE OF THE TETRAGONAL CRYSTAL FORM OF EGG-WHITE AVIDIN IN ITS FUNCTIONAL COMPLEX WITH BIOTIN AT 2.7 ANGSTROMS RESOLUTION

PDB ID 1avd

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