7oyz

From Proteopedia

E.coli's putrescine receptor variant PotF/D in complex with spermidine

PDB ID 7oyz

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Structural highlights

7oyz is a 1 chain structure with sequence from Escherichia coli K-12. This structure supersedes the now removed PDB entry 4jdf. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.49Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

POTF_ECOLI Required for the activity of the bacterial periplasmic transport system of putrescine. Polyamine binding protein.

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