Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1074/jbc.273.28.17604
  • Primary Citation of Related Structures:  

  • 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 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
344Escherichia coliMutation(s): 0 
Gene Names: PUCPOTF
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
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
PUT PDBBind:  1A99 Kd: 2000 (nM) from 1 assay(s)
Binding MOAD:  1A99 Kd: 2000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • 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

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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