2ju8: Difference between revisions

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-{{Seed}}
-[[Image:2ju8.png|left|200px]]
-<!--
+==Solution-State Structures of Oleate-Liganded LFABP, Major Form of 1:2 Protein-Ligand Complex==
-The line below this paragraph, containing "STRUCTURE_2ju8", creates the "Structure Box" on the page.
+<StructureSection load='2ju8' size='340' side='right'caption='[[2ju8]]' 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'>[[2ju8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JU8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JU8 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">Solution NMR</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OLA:OLEIC+ACID'>OLA</scene></td></tr>
-{{STRUCTURE_2ju8|  PDB=2ju8  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ju8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ju8 OCA], [https://pdbe.org/2ju8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ju8 RCSB], [https://www.ebi.ac.uk/pdbsum/2ju8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ju8 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/FABPL_RAT FABPL_RAT] Binds free fatty acids and their coenzyme A derivatives, bilirubin, and some other small molecules in the cytoplasm. May be involved in intracellular lipid transport.
+== 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/ju/2ju8_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=2ju8 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Rat liver fatty acid-binding protein (LFABP) is distinctive among intracellular lipid-binding proteins (iLBPs): more than one molecule of long-chain fatty acid and a variety of diverse ligands can be bound within its large cavity, and in vitro lipid transfer to model membranes follows a mechanism that is diffusion-controlled rather than mediated by protein-membrane collisions. Because the apoprotein has proven resistant to crystallization, nuclear magnetic resonance spectroscopy offers a unique route to functionally informative comparisons of molecular structure and dynamics for LFABP in free (apo) and liganded (holo) forms. We report herein the solution-state structures determined for apo-LFABP at pH 6.0 and for holoprotein liganded to two oleates at pH 7.0, as well as the structure of the complex including locations of the ligands. 1H, 13C, and 15N resonance assignments revealed very similar types and locations of secondary structural elements for apo- and holo-LFABP as judged from chemical shift indices. The solution-state tertiary structures of the proteins were derived with the CNS/ARIA computational protocol, using distance and angular restraints based on 1H-1H nuclear Overhauser effects (NOEs), hydrogen-bonding networks, 3J(HNHA) coupling constants, intermolecular NOEs, and residual dipolar (NH) couplings. The holo-LFABP solution-state conformation is in substantial agreement with a previously reported X-ray structure [Thompson, J., Winter, N., Terwey, D., Bratt, J., and Banaszak, L. (1997) The crystal structure of the liver fatty acid-binding protein. A complex with two bound oleates, J. Biol. Chem. 272, 7140-7150], including the typical beta-barrel capped by a helix-turn-helix portal. In the solution state, the internally bound oleate has the expected U-shaped conformation and is tethered electrostatically, but the extended portal ligand can adopt a range of conformations based on the computationally refined structures, in contrast to the single conformation observed in the crystal structure. The apo-LFABP also has a well-defined beta-barrel structural motif typical of other members of the iLBP protein family, but the portal region that is thought to facilitate ligand entry and exit exhibits conformational variability and an unusual "open cap" orientation with respect to the barrel. These structural results allow us to propose a model in which ligand binding to LFABP occurs through conformational fluctuations that adjust the helix-turn-helix motif to open or close the top of the beta-barrel, and solvent accessibility to the protein cavity favors diffusion-controlled ligand transport.
-===Solution-State Structures of Oleate-Liganded LFABP, Major Form of 1:2 Protein-Ligand Complex===
+Solution-state molecular structure of apo and oleate-liganded liver fatty acid-binding protein.,He Y, Yang X, Wang H, Estephan R, Francis F, Kodukula S, Storch J, Stark RE Biochemistry. 2007 Nov 6;46(44):12543-56. Epub 2007 Oct 10. PMID:17927211<ref>PMID:17927211</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2ju8" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17927211}}, adds the Publication Abstract to the page
+*[[Fatty acid-binding protein 3D structures|Fatty acid-binding protein 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17927211 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17927211}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-JU8 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JU8 OCA].
-==Reference==
-Solution-state molecular structure of apo and oleate-liganded liver fatty acid-binding protein., He Y, Yang X, Wang H, Estephan R, Francis F, Kodukula S, Storch J, Stark RE, Biochemistry. 2007 Nov 6;46(44):12543-56. Epub 2007 Oct 10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17927211 17927211]
 [[Category: Rattus norvegicus]]
-[[Category: Single protein]]
+[[Category: Estephan R]]
-[[Category: Estephan, R.]]
+[[Category: Francis F]]
-[[Category: Francis, F.]]
+[[Category: He Y]]
-[[Category: He, Y.]]
+[[Category: Kodukula S]]
-[[Category: Kodukula, S.]]
+[[Category: Stark RE]]
-[[Category: Stark, R E.]]
+[[Category: Storch J]]
-[[Category: Storch, J.]]
+[[Category: Wang H]]
-[[Category: Wang, H.]]
+[[Category: Yang X]]
-[[Category: Yang, X.]]
-[[Category: Acetylation]]
-[[Category: Apo]]
-[[Category: Cytoplasm]]
-[[Category: Fabp]]
-[[Category: Ilbp]]
-[[Category: Lfabp]]
-[[Category: Lipid binding protein]]
-[[Category: Lipid-binding]]
-[[Category: Phosphorylation]]
-[[Category: Protein]]
-[[Category: Transport]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 13:55:30 2008''