2fn8: Difference between revisions

← Older edit

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

OCA

@@ Line 1: / Line 1: @@
-[[Image:2fn8.png|left|200px]]
-<!--
+==Thermotoga maritima Ribose Binding Protein Ribose Bound Form==
-The line below this paragraph, containing "STRUCTURE_2fn8", creates the "Structure Box" on the page.
+<StructureSection load='2fn8' size='340' side='right'caption='[[2fn8]], [[Resolution|resolution]] 2.15&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'>[[2fn8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FN8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FN8 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]] 2.15&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RIP:RIBOSE(PYRANOSE+FORM)'>RIP</scene></td></tr>
-{{STRUCTURE_2fn8|  PDB=2fn8  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2fn8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fn8 OCA], [https://pdbe.org/2fn8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fn8 RCSB], [https://www.ebi.ac.uk/pdbsum/2fn8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fn8 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9X053_THEMA Q9X053_THEMA]
+== 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/fn/2fn8_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=2fn8 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+BACKGROUND: Members of the periplasmic binding protein (PBP) superfamily are involved in transport and signaling processes in both prokaryotes and eukaryotes. Biological responses are typically mediated by ligand-induced conformational changes in which the binding event is coupled to a hinge-bending motion that brings together two domains in a closed form. In all PBP-mediated biological processes, downstream partners recognize the closed form of the protein. This motion has also been exploited in protein engineering experiments to construct biosensors that transduce ligand binding to a variety of physical signals. Understanding the mechanistic details of PBP conformational changes, both global (hinge bending, twisting, shear movements) and local (rotamer changes, backbone motion), therefore is not only important for understanding their biological function but also for protein engineering experiments. RESULTS: Here we present biochemical characterization and crystal structure determination of the periplasmic ribose-binding protein (RBP) from the hyperthermophile Thermotoga maritima in its ribose-bound and unliganded state. The T. maritima RBP (tmRBP) has 39% sequence identity and is considerably more resistant to thermal denaturation (app Tm value is 108 degrees C) than the mesophilic Escherichia coli homolog (ecRBP) (app Tm value is 56 degrees C). Polar ligand interactions and ligand-induced global conformational changes are conserved among ecRBP and tmRBP; however local structural rearrangements involving side-chain motions in the ligand-binding site are not conserved. CONCLUSION: Although the large-scale ligand-induced changes are mediated through similar regions, and are produced by similar backbone movements in tmRBP and ecRBP, the small-scale ligand-induced structural rearrangements differentiate the mesophile and thermophile. This suggests there are mechanistic differences in the manner by which these two proteins bind their ligands and are an example of how two structurally similar proteins utilize different mechanisms to form a ligand-bound state.
-===Thermotoga maritima Ribose Binding Protein Ribose Bound Form===
+Ligand-induced conformational changes in a thermophilic ribose-binding protein.,Cuneo MJ, Beese LS, Hellinga HW BMC Struct Biol. 2008 Nov 19;8:50. PMID:19019243<ref>PMID:19019243</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_19019243}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2fn8" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 19019243 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_19019243}}
-==About this Structure==
-[[2fn8]] is a 1 chain structure of [[ABC transporter]] with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima_msb8 Thermotoga maritima msb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FN8 OCA].
 ==See Also==
-*[[ABC transporter]]
+*[[ABC transporter 3D structures|ABC transporter 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:19019243</ref><references group="xtra"/>
+__TOC__
-[[Category: Thermotoga maritima msb8]]
+</StructureSection>
-[[Category: Changela, A.]]
+[[Category: Large Structures]]
-[[Category: Cuneo, M J.]]
+[[Category: Thermotoga maritima MSB8]]
-[[Category: Periplasmic binding protein]]
+[[Category: Changela A]]
-[[Category: Rbp]]
+[[Category: Cuneo MJ]]
-[[Category: Ribose binding protein]]
-[[Category: Sugar binding protein]]
-[[Category: Thermophilic protein]]