1A99

PUTRESCINE RECEPTOR (POTF) FROM E. COLI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure and mutational analysis of the Escherichia coli putrescine receptor. Structural basis for substrate specificity.

Vassylyev, D.G.Tomitori, H.Kashiwagi, K.Morikawa, K.Igarashi, K.

(1998) J Biol Chem 273: 17604-17609

  • DOI: 10.1074/jbc.273.28.17604
  • Primary Citation of Related Structures:  
    1A99

  • PubMed Abstract: 
  • PotF protein is a periplasmic substrate-binding protein of the putrescine transport system in Escherichia coli. We have determined the crystal structure of PotF protein in complex with the substrate at 2.3-A resolution. The PotF molecule has dimensio ...

    PotF protein is a periplasmic substrate-binding protein of the putrescine transport system in Escherichia coli. We have determined the crystal structure of PotF protein in complex with the substrate at 2.3-A resolution. The PotF molecule has dimensions of 54 x 42 x 30 A and consists of two similar globular domains. The PotF structure is reminiscent of other periplasmic receptors with a highest structural homology to another polyamine-binding protein, PotD. Putrescine is tightly bound in the deep cleft between the two domains of PotF through 12 hydrogen bonds and 36 van der Waals interactions. The comparison of the PotF structure with that of PotD provides the insight into the differences in the specificity between the two proteins. The PotF structure, in combination with the mutational analysis, revealed the residues crucial for putrescine binding (Trp-37, Ser-85, Glu-185, Trp-244, Asp-247, and Asp-278) and the importance of water molecules for putrescine recognition.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Analysis of the Periplasmic Receptor (Potf) of the Putrescine Transport System in Escherichia Coli
      Vassylyev, D.G., Kashiwagi, T., Tomitori, H., Kashiwagi, K., Igarashi, K., Morikawa, K.
      (1998) Acta Crystallogr D Biol Crystallogr 54: 132
    • Characteristics of the Operon for a Putrescine Transport System that Maps at 19 Minutes on the Escherichia Coli Chromosome
      Pistocchi, R., Kashiwagi, K., Miyamoto, S., Nukui, E., Sadakata, Y., Kobayashi, H., Igarashi, K.
      (1993) J Biol Chem 268: 146

    Organizational Affiliation

    Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka, 565-0874, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PUTRESCINE-BINDING PROTEINABCD344Escherichia coliMutation(s): 0 
Gene Names: PUCPOTF
Find proteins for P31133 (Escherichia coli (strain K12))
Explore P31133 
Go to UniProtKB:  P31133
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PUT
Query on PUT

Download CCD File 
A, B, C, D
1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PUTKd :  2000   nM  PDBBind
PUTKd:  2000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 269.4α = 90
b = 82.33β = 90
c = 93.74γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-21
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-04-01
    Changes: Advisory, Derived calculations, Other