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| - | | + | #REDIRECT [[7oyz]] This PDB entry is obsolete and replaced by 7oyz |
| - | ==Crystal structure of a PotF mutant complexed with spermidine==
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| - | <StructureSection load='4jdf' size='340' side='right'caption='[[4jdf]], [[Resolution|resolution]] 1.69Å' scene=''>
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| - | == Structural highlights ==
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| - | <table><tr><td colspan='2'>[[4jdf]] is a 1 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=4JDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JDF FirstGlance]. <br>
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| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SPD:SPERMIDINE'>SPD</scene></td></tr>
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| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4jdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jdf OCA], [https://pdbe.org/4jdf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jdf RCSB], [https://www.ebi.ac.uk/pdbsum/4jdf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jdf ProSAT]</span></td></tr>
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| - | </table>
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| - | == Function ==
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| - | [https://www.uniprot.org/uniprot/POTF_ECOLI POTF_ECOLI] Required for the activity of the bacterial periplasmic transport system of putrescine. Polyamine binding protein.
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| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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| - | Recognition and discrimination of small molecules are crucial for biological processes in living systems. Understanding the mechanisms that underlie binding specificity is of particular interest to synthetic biology, e.g. the engineering of biosensors with de novo ligand affinities. Promising scaffolds for such biosensors are the periplasmic binding proteins (PBPs) due to their ligand-mediated structural change that can be translated into a physically measurable signal. In this study we focused on the two homologous polyamine binding proteins PotF and PotD. Despite their structural similarity, PotF and PotD have different binding specificities for the polyamines putrescine and spermidine. To elucidate how specificity is determined, we grafted the binding site of PotD onto PotF. The introduction of 7 mutations in the first shell of the binding pocket leads to a swap in the binding profile as confirmed by isothermal titration calorimetry. Furthermore, the 1.7A crystal structure of the new variant complexed with spermidine reveals the interactions of the specificity determining residues including a defined water network. Altogether our study shows that specificity is encoded in the first shell residues of the PotF binding pocket and that transplantation of these residues allows the swap of the binding specificity.
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| - | Change in protein-ligand specificity through binding pocket grafting.,Scheib U, Shanmugaratnam S, Farias-Rico JA, Hocker B J Struct Biol. 2013 Jun 17. pii: S1047-8477(13)00157-3. doi:, 10.1016/j.jsb.2013.06.002. PMID:23792166<ref>PMID:23792166</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 4jdf" style="background-color:#fffaf0;"></div>
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| - | == References ==
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| - | <references/>
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| - | __TOC__
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| - | </StructureSection>
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| - | [[Category: Escherichia coli K-12]]
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| - | [[Category: Large Structures]]
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| - | [[Category: Farias-Rico JA]]
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| - | [[Category: Hocker B]]
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| - | [[Category: Scheib U]]
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| - | [[Category: Shanmugaratnam S]]
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