6yed

From Proteopedia

(Difference between revisions)

Current revision

E.coli's Putrescine receptor PotF in its open apo state

Structural highlights

Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.18Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

Periplasmic binding proteins (PBPs) are ubiquitous receptors in gram-negative bacteria. They sense solutes and play key roles in nutrient uptake. Escherichia coli's putrescine receptor PotF has been reported to bind putrescine and spermidine. We reveal that several similar biogenic polyamines are recognized by PotF. Using isothermal titration calorimetry paired with X-ray crystallography of the different complexes, we unveil PotF's binding modes in detail. The binding site for PBPs is located between two lobes that undergo a large conformational change upon ligand recognition. Hence, analyzing the influence of ligands on complex formation is crucial. Therefore, we solved crystal structures of an open and closed apo state and used them as a basis for molecular dynamics simulations. In addition, we accessed structural behavior in solution for all complexes by (1)H-(15)N HSQC NMR spectroscopy. This combined analysis provides a robust framework for understanding ligand binding for future developments in drug design and protein engineering.

A comprehensive binding study illustrates ligand recognition in the periplasmic binding protein PotF.,Kroger P, Shanmugaratnam S, Ferruz N, Schweimer K, Hocker B Structure. 2020 Dec 30. pii: S0969-2126(20)30472-X. doi:, 10.1016/j.str.2020.12.005. PMID:33406388^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kroger P, Shanmugaratnam S, Ferruz N, Schweimer K, Hocker B. A comprehensive binding study illustrates ligand recognition in the periplasmic binding protein PotF. Structure. 2020 Dec 30. pii: S0969-2126(20)30472-X. doi:, 10.1016/j.str.2020.12.005. PMID:33406388 doi:http://dx.doi.org/10.1016/j.str.2020.12.005

1 Structural highlights
2 Publication Abstract from PubMed
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6yed"

Categories: Large Structures | Hocker B | Kroeger P | Shanmugaratnam S

@@ Line 3: / Line 3: @@
 <StructureSection load='6yed' size='340' side='right'caption='[[6yed]], [[Resolution|resolution]] 2.18&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6yed]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YED FirstGlance]. <br>
+<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YED FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.18&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6ye0|6ye0]], [[6ye6|6ye6]], [[6ye7|6ye7]], [[6ye8|6ye8]], [[6yec|6yec]], [[6yeb|6yeb]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">potF, b0854, JW0838 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=6yed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yed OCA], [https://pdbe.org/6yed PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yed RCSB], [https://www.ebi.ac.uk/pdbsum/6yed PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yed ProSAT]</span></td></tr>
 </table>
-== Function ==
-[[https://www.uniprot.org/uniprot/POTF_ECOLI POTF_ECOLI]] Required for the activity of the bacterial periplasmic transport system of putrescine. Polyamine binding protein.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 21: @@
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
 [[Category: Large Structures]]
-[[Category: Hocker, B]]
+[[Category: Hocker B]]
-[[Category: Kroeger, P]]
+[[Category: Kroeger P]]
-[[Category: Shanmugaratnam, S]]
+[[Category: Shanmugaratnam S]]
-[[Category: E coli]]
-[[Category: Open apo]]
-[[Category: Periplasmic binding protein]]
-[[Category: Transport protein]]

6yed

From Proteopedia

Current revision

E.coli's Putrescine receptor PotF in its open apo state

Structural highlights

Publication Abstract from PubMed

References

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