6YE6

E.coli's Putrescine receptor PotF complexed with Agmatine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

A comprehensive binding study illustrates ligand recognition in the periplasmic binding protein PotF.

Kroger, P.Shanmugaratnam, S.Ferruz, N.Schweimer, K.Hocker, B.

(2021) Structure 29: 433

  • DOI: https://doi.org/10.1016/j.str.2020.12.005
  • Primary Citation of Related Structures:  
    6YE0, 6YE6, 6YE7, 6YE8, 6YEB, 6YEC, 6YED

  • 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 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.


  • Organizational Affiliation

    Department of Biochemistry, University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany. Electronic address: birte.hoecker@uni-bayreuth.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putrescine-binding periplasmic protein
A, B
352Escherichia coli K-12Mutation(s): 0 
Gene Names: potFb0854JW0838
UniProt
Find proteins for P31133 (Escherichia coli (strain K12))
Explore P31133 
Go to UniProtKB:  P31133
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31133
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ONW
Query on ONW

Download Ideal Coordinates CCD File 
M [auth A](2~{R})-1-[(2~{R})-1-(2-methoxyethoxy)propan-2-yl]oxypropan-2-amine
C9 H21 N O3
JKCPHDAMWZLSSR-RKDXNWHRSA-N
ONT
Query on ONT

Download Ideal Coordinates CCD File 
C [auth A],
H [auth A],
S [auth B],
U [auth B]
(2~{S})-1-(2-methoxyethoxy)propan-2-amine
C6 H15 N O2
CMXIILNXYHCYPP-LURJTMIESA-N
AG2 (Subject of Investigation/LOI)
Query on AG2

Download Ideal Coordinates CCD File 
E [auth A],
T [auth B]
AGMATINE
C5 H14 N4
QYPPJABKJHAVHS-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
DA [auth B],
EA [auth B],
FA [auth B],
N [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
JFN
Query on JFN

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
D [auth A]
F [auth A]
AA [auth B],
BA [auth B],
CA [auth B],
D [auth A],
F [auth A],
G [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
(2R)-1-methoxypropan-2-amine
C4 H11 N O
NXMXETCTWNXSFG-SCSAIBSYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
GA [auth B],
O [auth A],
P [auth A],
Q [auth A],
R [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.161α = 90
b = 71.161β = 90
c = 272.866γ = 120
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
PHENIXrefinement
Cootmodel building
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyHO4022/2-3

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2021-05-19
    Changes: Database references
  • Version 1.2: 2023-03-15
    Changes: Advisory, Database references, Derived calculations
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description