1POY

SPERMIDINE/PUTRESCINE-BINDING PROTEIN COMPLEXED WITH SPERMIDINE (DIMER FORM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of PotD, the primary receptor of the polyamine transport system in Escherichia coli.

Sugiyama, S.Vassylyev, D.G.Matsushima, M.Kashiwagi, K.Igarashi, K.Morikawa, K.

(1996) J Biol Chem 271: 9519-9525

  • DOI: https://doi.org/10.1074/jbc.271.16.9519
  • Primary Citation of Related Structures:  
    1POY

  • PubMed Abstract: 

    PotD protein is a periplasmic binding protein and the primary receptor of the polyamine transport system, which regulates the polyamine content in Escherichia coli. The crystal structure of PotD in complex with spermidine has been solved at 2.5-A resolution. The PotD protein consists of two domains with an alternating beta-alpha-beta topology. The polyamine binding site is in a central cleft lying in the interface between the domains. In the cleft, four acidic residues recognize the three positively charged nitrogen atoms of spermidine, while five aromatic side chains anchor the methylene backbone by van der Waals interactions. The overall fold of PotD is similar to that of other periplasmic binding proteins, and in particular to the maltodextrin-binding protein from E. coli, despite the fact that sequence identity is as low as 20%. The comparison of the PotD structure with the two maltodextrin-binding protein structures, determined in the presence and absence of the substrate, suggests that spermidine binding rearranges the relative orientation of the PotD domains to create a more compact structure.


  • Organizational Affiliation

    Protein Engineering Research Institute, Suita, Osaka, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SPERMIDINE/PUTRESCINE-BINDING PROTEINA [auth 1],
B [auth 2],
C [auth 3],
D [auth 4]
323Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AFK9 (Escherichia coli (strain K12))
Explore P0AFK9 
Go to UniProtKB:  P0AFK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFK9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.3α = 90
b = 69.1β = 107.6
c = 72.5γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
WELMSdata reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-07-11
    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: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Other