6YE7

E.coli's Putrescine receptor PotF complexed with Cadaverine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.2 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 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P33
Query on P33

Download Ideal Coordinates CCD File 
V [auth B]3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
FA [auth B]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
H [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
TAM
Query on TAM

Download Ideal Coordinates CCD File 
R [auth A]TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
PGE
Query on PGE

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P [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

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K [auth A],
Z [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
N2P (Subject of Investigation/LOI)
Query on N2P

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C [auth A],
CA [auth B]
PENTANE-1,5-DIAMINE
C5 H14 N2
VHRGRCVQAFMJIZ-UHFFFAOYSA-N
MLI
Query on MLI

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X [auth B]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
EDO
Query on EDO

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AA [auth B]
BA [auth B]
D [auth A]
DA [auth B]
E [auth A]
AA [auth B],
BA [auth B],
D [auth A],
DA [auth B],
E [auth A],
EA [auth B],
F [auth A],
G [auth A],
GA [auth B],
HA [auth B],
I [auth A],
IA [auth B],
J [auth A],
JA [auth B],
L [auth A],
LA [auth B],
M [auth A],
N [auth A],
O [auth A],
Q [auth A],
S [auth A],
W [auth B],
Y [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
KA [auth B],
T [auth A],
U [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.869α = 90
b = 70.869β = 90
c = 271.185γ = 120
Software Package:
Software NamePurpose
MxCuBEdata collection
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



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: 2024-01-24
    Changes: Data collection, Database references, Refinement description