1POY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 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


  • 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 res ...

    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.


    Related Citations: 
    • Functions of Pota and Potd Proteins in Spermidine-Preferential Uptake System in Escherichia Coli
      Kashiwagi, K.,Miyamoto, S.,Nukui, E.,Kobayashi, H.,Igarashi, K.
      (1993) J.Biol.Chem. 268: 19358
    • Crystallization and Preliminary X-Ray Analysis of the Primary Receptor (Potd) of the Polyamine Transport System in Escherichia Coli
      Sugiyama, S.,Matsushima, M.,Saisho, T.,Kashiwagi, K.,Igarashi, K.,Morikawa, K.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Protein Engineering Research Institute, Suita, Osaka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SPERMIDINE/PUTRESCINE-BINDING PROTEIN
1, 2, 3, 4
323Escherichia coli (strain K12)Gene Names: potD
Find proteins for P0AFK9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AFK9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPD
Query on SPD

Download SDF File 
Download CCD File 
1, 2, 3, 4
SPERMIDINE
N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34)
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SPDKd: 3200 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 145.300α = 90.00
b = 69.100β = 107.60
c = 72.500γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building
WELMSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-07-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance