1urp: Difference between revisions

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-[[Image:1urp.gif|left|200px]]
- {{Structure
+==D-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI==
-|PDB= 1urp |SIZE=350|CAPTION= <scene name='initialview01'>1urp</scene>, resolution 2.3&Aring;
+<StructureSection load='1urp' size='340' side='right'caption='[[1urp]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND=
+<table><tr><td colspan='2'>[[1urp]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1URP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1URP FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-|GENE=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1urp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1urp OCA], [https://pdbe.org/1urp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1urp RCSB], [https://www.ebi.ac.uk/pdbsum/1urp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1urp ProSAT]</span></td></tr>
-}}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RBSB_ECOLI RBSB_ECOLI] Involved in the high-affinity D-ribose membrane transport system and also serves as the primary chemoreceptor for chemotaxis.
+== 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/ur/1urp_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=1urp ConSurf].
+<div style="clear:both"></div>
-'''D-RIBOSE-BINDING PROTEIN FROM ESCHERICHIA COLI'''
+==See Also==
+*[[Ribose-binding protein|Ribose-binding protein]]
+__TOC__
-==Overview==
+</StructureSection>
-Conformational changes are necessary for the function of bacterial periplasmic receptors in chemotaxis and transport. Such changes allow entry and exit of ligand, and enable the correct interaction of the ligand-bound proteins with the membrane components of each system. Three open, ligand-free forms of the Escherichia coli ribose-binding protein were observed here by X-ray crystallographic studies. They are opened by 43 degrees, 50 degrees and 64 degrees with respect to the ligand-bound protein reported previously. The three open forms are not distinct, but show a clear relationship to each other. All are the product of a similar opening motion, and are stabilized by a new, almost identical packing interface between the domains. The changes are generated by similar bond rotations, although some differences in the three hinge segments are needed to accommodate the various structural scenarios. Some local repacking also occurs as interdomain contacts are lost. The least open (43 degrees) form is probably the dominant one in solution under normal conditions, although a mixture of species seems likely. The open and closed forms have distinct surfaces in the regions known to be important in chemotaxis and transport, which will differentiate their interactions with the membrane components. It seems certain that the conformational path that links the forms described here is that followed during ligand retrieval, and in ligand release into the membrane-bound permease system.
+[[Category: Escherichia coli K-12]]
+[[Category: Large Structures]]
-==About this Structure==
+[[Category: Bjorkman AJ]]
-URP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1URP OCA].
+[[Category: Mowbray SL]]
-==Reference==
-Multiple open forms of ribose-binding protein trace the path of its conformational change., Bjorkman AJ, Mowbray SL, J Mol Biol. 1998 Jun 12;279(3):651-64. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9641984 9641984]
-[[Category: Escherichia coli]]
-[[Category: Single protein]]
-[[Category: Bjorkman, A J.]]
-[[Category: Mowbray, S L.]]
-[[Category: chemotaxis]]
-[[Category: periplasm]]
-[[Category: transport]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:35:48 2008''