3qk6: Difference between revisions
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==Crystal structure of Escherichia coli PhnD== | ==Crystal structure of Escherichia coli PhnD== | ||
<StructureSection load='3qk6' size='340' side='right' caption='[[3qk6]], [[Resolution|resolution]] 2.40Å' scene=''> | <StructureSection load='3qk6' size='340' side='right'caption='[[3qk6]], [[Resolution|resolution]] 2.40Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3qk6]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3qk6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecout Ecout]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QK6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QK6 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</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> | <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> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3p7i|3p7i]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3p7i|3p7i]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">phnD, UTI89_C4699 ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">phnD, UTI89_C4699 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=364106 ECOUT])</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3qk6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qk6 OCA], [https://pdbe.org/3qk6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qk6 RCSB], [https://www.ebi.ac.uk/pdbsum/3qk6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qk6 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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==See Also== | ==See Also== | ||
*[[ABC transporter|ABC transporter]] | *[[ABC transporter 3D structures|ABC transporter 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Ecout]] | [[Category: Ecout]] | ||
[[Category: Large Structures]] | |||
[[Category: Alicea, I]] | [[Category: Alicea, I]] | ||
[[Category: Schreiter, E R]] | [[Category: Schreiter, E R]] | ||
[[Category: Phosphonate transport protein]] | [[Category: Phosphonate transport protein]] | ||
[[Category: Transport protein]] | [[Category: Transport protein]] | ||
Revision as of 09:12, 8 June 2022
Crystal structure of Escherichia coli PhnDCrystal structure of Escherichia coli PhnD
Structural highlights
Publication Abstract from PubMedThe phnD gene of Escherichia coli encodes the periplasmic binding protein of the phosphonate (Pn) uptake and utilization pathway. We have crystallized and determined structures of E. coli PhnD (EcPhnD) in the absence of ligand and in complex with the environmentally abundant 2-aminoethylphosphonate (2AEP). Similar to other bacterial periplasmic binding proteins, 2AEP binds near the center of mass of EcPhnD in a cleft formed between two lobes. Comparison of the open, unliganded structure with the closed 2AEP-bound structure shows that the two lobes pivot around a hinge by approximately 70 degrees between the two states. Extensive hydrogen bonding and electrostatic interactions stabilize 2AEP, which binds to EcPhnD with low nanomolar affinity. These structures provide insight into Pn uptake by bacteria and facilitated the rational design of high signal-to-noise Pn biosensors based on both coupled small-molecule dyes and autocatalytic fluorescent proteins. Structure of the Escherichia coli Phosphonate Binding Protein PhnD and Rationally Optimized Phosphonate Biosensors.,Alicea I, Marvin JS, Miklos AE, Ellington AD, Looger LL, Schreiter ER J Mol Biol. 2011 Dec 2;414(3):356-69. Epub 2011 Oct 12. PMID:22019591[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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