6YE6

E.coli's Putrescine receptor PotF complexed with Agmatine

Summary for 6YE6

• Entry DOI: 10.2210/pdb6ye6/pdb
• Related: 6YE0
• Descriptor: Putrescine-binding periplasmic protein, (2~{S})-1-(2-methoxyethoxy)propan-2-amine, (2R)-1-methoxypropan-2-amine, ... (8 entities in total)
• Functional Keywords: periplasmic binding protein, e.coli, agmatine, transport protein
• Biological source: Escherichia coli (strain K12)
• Total number of polymer chains: 2
• Total formula weight: 81624.02

Authors

Shanmugaratnam, S.,Kroeger, P.,Hocker, B. (deposition date: 2020-03-24, release date: 2021-01-20, Last modification date: 2024-10-23)

Primary citation

Kroger, P.,Shanmugaratnam, S.,Ferruz, N.,Schweimer, K.,Hocker, B.
A comprehensive binding study illustrates ligand recognition in the periplasmic binding protein PotF.
Structure, 29:433-, 2021

PubMed Abstract: 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 H-N HSQC NMR spectroscopy. This combined analysis provides a robust framework for understanding ligand binding for future developments in drug design and protein engineering.

PubMed: 33406388
DOI: 10.1016/j.str.2020.12.005

Experimental method

X-RAY DIFFRACTION (1.56 Å)