1abf: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-[[Image:1abf.jpg|left|200px]]<br /><applet load="1abf" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1abf, resolution 1.9&Aring;" />
-'''SUBSTRATE SPECIFICITY AND AFFINITY OF A PROTEIN MODULATED BY BOUND WATER MOLECULES'''<br />
-==Overview==
+==SUBSTRATE SPECIFICITY AND AFFINITY OF A PROTEIN MODULATED BY BOUND WATER MOLECULES==
-Water molecules influence molecular interactions in all biological, systems, yet it is extremely difficult to understand their effects in, precise atomic detail. Here we present evidence, based on highly refined, atomic structures of the complexes of the L-arabinose-binding protein with, L-arabinose, D-fucose and D-galactose, that bound water molecules, coupled, with localized conformational changes, can govern substrate specificity, and affinity. The atoms common to the three sugars are identically, positioned in the binding site and the same nine strong hydrogen bonds are, formed in all three complexes. Two hydrogen-bonded water molecules in the, site contribute further to tight binding of L-arabinose but create an, unfavourable interaction with the methyl group of D-fucose. Equally tight, binding of D-galactose is attained by the replacement of one of the, hydrogen-bonded water molecules by its--CH2OH group, coordinated with, localized structural changes which include a shift and redirection of the, hydrogen-bonding interactions of the other water molecule. These, observations illustrate how ordered water molecules can contribute, directly to the properties of proteins by influencing their interaction, with ligands.
+<StructureSection load='1abf' size='340' side='right'caption='[[1abf]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1abf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ABF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ABF FirstGlance]. <br>
-ABF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1ABF OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FCA:ALPHA-D-FUCOSE'>FCA</scene>, <scene name='pdbligand=FCB:BETA-D-FUCOSE'>FCB</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1abf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1abf OCA], [https://pdbe.org/1abf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1abf RCSB], [https://www.ebi.ac.uk/pdbsum/1abf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1abf ProSAT]</span></td></tr>
-Substrate specificity and affinity of a protein modulated by bound water molecules., Quiocho FA, Wilson DK, Vyas NK, Nature. 1989 Aug 3;340(6232):404-7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=2818726 2818726]
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ARAF_ECOLI ARAF_ECOLI] Involved in the high-affinity L-arabinose membrane transport system. Binds with high affinity to arabinose, but can also bind D-galactose (approximately 2-fold reduction) and D-fucose (approximately 40-fold reduction).
+== 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/ab/1abf_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=1abf ConSurf].
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Quiocho, F.A.]]
+[[Category: Quiocho FA]]
-[[Category: Wilson, D.K.]]
+[[Category: Wilson DK]]
-[[Category: binding protein]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 10:44:19 2007''