3uk0: Difference between revisions

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-[[Image:3uk0.jpg|left|200px]]
-<!--
+==RPD_1889 protein, an extracellular ligand-binding receptor from Rhodopseudomonas palustris.==
-The line below this paragraph, containing "STRUCTURE_3uk0", creates the "Structure Box" on the page.
+<StructureSection load='3uk0' size='340' side='right'caption='[[3uk0]], [[Resolution|resolution]] 1.49&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'>[[3uk0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhops Rhops]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3snr 3snr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UK0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UK0 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ENO:3-(4-HYDROXY-PHENYL)PYRUVIC+ACID'>ENO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
--->
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_3uk0|  PDB=3uk0  |  SCENE=  }}
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RPD_1889 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316057 RHOPS])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3uk0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uk0 OCA], [https://pdbe.org/3uk0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3uk0 RCSB], [https://www.ebi.ac.uk/pdbsum/3uk0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3uk0 ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Lignin comprises 15-25% of plant biomass and represents a major environmental carbon source for utilization by soil microorganisms. Access to this energy resource requires the action of fungal and bacterial enzymes to break down the lignin polymer into a complex assortment of aromatic compounds that can be transported into the cells. To improve our understanding of the utilization of lignin by microorganisms, we characterized the molecular properties of solute binding proteins of ATP-binding cassette transporter proteins that interact with these compounds. A combination of functional screens and structural studies characterized the binding specificity of the solute binding proteins for aromatic compounds derived from lignin such as p-coumarate, 3-phenylpropionic acid and compounds with more complex ring substitutions. A ligand screen based on thermal stabilization identified several binding protein clusters that exhibit preferences based on the size or number of aromatic ring substituents. Multiple X-ray crystal structures of protein-ligand complexes for these clusters identified the molecular basis of the binding specificity for the lignin-derived aromatic compounds. The screens and structural data provide new functional assignments for these solute-binding proteins which can be used to infer their transport specificity. This knowledge of the functional roles and molecular binding specificity of these proteins will support the identification of the specific enzymes and regulatory proteins of peripheral pathways that funnel these compounds to central metabolic pathways and will improve the predictive power of sequence-based functional annotation methods for this family of proteins. (c) Proteins 2013;. (c) 2013 Wiley Periodicals, Inc.
-===RPD_1889 protein, an extracellular ligand-binding receptor from Rhodopseudomonas palustris.===
+Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-coumaric acid and related aromatic acids.,Tan K, Chang C, Cuff M, Osipiuk J, Landorf E, Mack JC, Zerbs S, Joachimiak A, Collart FR Proteins. 2013 Apr 22. doi: 10.1002/prot.24305. PMID:23606130<ref>PMID:23606130</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-==About this Structure==
+</div>
-[[3uk0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodopseudomonas_palustris Rhodopseudomonas palustris]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3snr 3snr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UK0 OCA].
+<div class="pdbe-citations 3uk0" style="background-color:#fffaf0;"></div>
-[[Category: Rhodopseudomonas palustris]]
+== References ==
-[[Category: Collart, F.]]
+<references/>
-[[Category: Joachimiak, A.]]
+__TOC__
-[[Category: MCSG, Midwest Center for Structural Genomics.]]
+</StructureSection>
-[[Category: Mack, J.]]
+[[Category: Large Structures]]
-[[Category: Osipiuk, J.]]
+[[Category: Rhops]]
-[[Category: Zerbs, S.]]
+[[Category: Collart, F]]
+[[Category: Joachimiak, A]]
+[[Category: Structural genomic]]
+[[Category: Mack, J]]
+[[Category: Osipiuk, J]]
+[[Category: Zerbs, S]]
 [[Category: Amino-acid transport]]
 [[Category: Extracellular receptor]]
 [[Category: Mcsg]]
-[[Category: Midwest center for structural genomic]]
 [[Category: Psi-biology]]
-[[Category: Structural genomic]]
 [[Category: Transport protein]]