Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.82 kDa 
• Atom Count: 3056 
• Modelled Residue Count: 341 
• Deposited Residue Count: 353 
• Unique protein chains: 1

4JDF

Crystal structure of a PotF mutant complexed with spermidine

• PDB DOI: 10.2210/pdb4JDF/pdb

• Classification: PROTEIN BINDING
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-02-25 Released: 2013-07-10 
• Deposition Author(s): Scheib, U., Shanmugaratnam, S., Farias-Rico, J.A., Hocker, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.227 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7OYZ

Literature

Change in protein-ligand specificity through binding pocket grafting.

Scheib, U., Shanmugaratnam, S., Farias-Rico, J.A., Hocker, B.

(2014) J Struct Biol 185: 186-192

• PubMed: 23792166 
• DOI: 10.1016/j.jsb.2013.06.002
• Primary Citation of Related Structures:  
  4JDF


• PubMed Abstract: 
  

Recognition and discrimination of small molecules are crucial for biological processes in living systems. Understanding the mechanisms that underlie binding specificity is of particular interest to synthetic biology, e.g. the engineering of biosensors with de novo ligand affinities. Promising scaffolds for such biosensors are the periplasmic binding proteins (PBPs) due to their ligand-mediated structural change that can be translated into a physically measurable signal. In this study we focused on the two homologous polyamine binding proteins PotF and PotD. Despite their structural similarity, PotF and PotD have different binding specificities for the polyamines putrescine and spermidine. To elucidate how specificity is determined, we grafted the binding site of PotD onto PotF. The introduction of 7 mutations in the first shell of the binding pocket leads to a swap in the binding profile as confirmed by isothermal titration calorimetry. Furthermore, the 1.7Å crystal structure of the new variant complexed with spermidine reveals the interactions of the specificity determining residues including a defined water network. Altogether our study shows that specificity is encoded in the first shell residues of the PotF binding pocket and that transplantation of these residues allows the swap of the binding specificity.

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Organizational Affiliation: 

Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076 Tübingen, Germany. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putrescine-binding periplasmic protein	A	353	Escherichia coli K-12	Mutation(s): 7  Gene Names: b0854, JW0838, potF
UniProt
Find proteins for P31133 (Escherichia coli (strain K12)) Explore P31133  Go to UniProtKB:  P31133

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPD	B [auth A]	SPERMIDINE C7 H19 N3 ATHGHQPFGPMSJY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SPD	Binding MOAD:  4JDF	Kd: 6.40e+6 (nM) from 1 assay(s)
	PDBBind:  4JDF	Kd: 6.40e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.227 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.25	α = 90
b = 81.94	β = 90
c = 111.63	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHENIX	model building
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-25 
• Released Date: 2013-07-10 
Deposition Author(s): Scheib, U., Shanmugaratnam, S., Farias-Rico, J.A., Hocker, B.

Revision History  

• Version 1.0: 2013-07-10
  Type: Initial release
  
• Version 1.1: 2014-10-01
  Changes: Database references