7oyt

From Proteopedia

(Difference between revisions)

Current revision

E.coli's putrescine receptor variant PotF/D (4JDF) with mutations E39D F88L in complex with spermidine

Structural highlights

Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.6Å
Ligands:	, , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

A profound understanding of the molecular interactions between receptors and ligands is important throughout diverse research such as protein design, drug discovery, or neuroscience. What determines specificity and how do proteins discriminate against similar ligands? In this study we analyzed factors that determine binding in two homologs belonging to the well-known superfamily of periplasmic binding proteins (PBPs), PotF and PotD. Building on a previously designed construct modes of polyamine binding were swapped. This change of specificity was approached by analyzing local differences in the binding pocket as well as overall conformational changes in the protein. Throughout the study, protein variants were generated and characterized structurally and thermodynamically, leading to a specificity swap and improvement in affinity. This dataset not only enriches our knowledge applicable to rational protein design, but our results can further lay groundwork for engineering of specific biosensors as well as help to explain the adaptability of pathogenic bacteria.

Fine-tuning spermidine binding modes in the putrescine binding protein PotF.,Kroger P, Shanmugaratnam S, Scheib U, Hocker B J Biol Chem. 2021 Nov 18:101419. doi: 10.1016/j.jbc.2021.101419. PMID:34801550^[1]

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

References

↑ Kroger P, Shanmugaratnam S, Scheib U, Hocker B. Fine-tuning spermidine binding modes in the putrescine binding protein PotF. J Biol Chem. 2021 Nov 18:101419. doi: 10.1016/j.jbc.2021.101419. PMID:34801550 doi:http://dx.doi.org/10.1016/j.jbc.2021.101419

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/7oyt"

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

@@ Line 3: / Line 3: @@
 <StructureSection load='7oyt' size='340' side='right'caption='[[7oyt]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7oyt]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OYT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OYT FirstGlance]. <br>
+<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OYT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OYT FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SPD:SPERMIDINE'>SPD</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]] 1.6&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SPD:SPERMIDINE'>SPD</scene></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=7oyt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7oyt OCA], [https://pdbe.org/7oyt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7oyt RCSB], [https://www.ebi.ac.uk/pdbsum/7oyt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7oyt 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 23: / Line 22: @@
 </StructureSection>
 [[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: Periplasmic binding protein]]
-[[Category: Potf]]
-[[Category: Spermidine]]
-[[Category: Transport protein]]

7oyt

From Proteopedia

Current revision

E.coli's putrescine receptor variant PotF/D (4JDF) with mutations E39D F88L in complex with spermidine

Structural highlights

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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