1POT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The 1.8-A X-ray structure of the Escherichia coli PotD protein complexed with spermidine and the mechanism of polyamine binding.

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

(1996) Protein Sci. 5: 1984-1990

  • DOI: 10.1002/pro.5560051004

  • PubMed Abstract: 
  • The PotD protein from Escherichia coli is one of the components of the polyamine transport system present in the periplasm. This component specifically binds either spermidine or putrescine. The crystal structure of the E. coli PotD protein complexed ...

    The PotD protein from Escherichia coli is one of the components of the polyamine transport system present in the periplasm. This component specifically binds either spermidine or putrescine. The crystal structure of the E. coli PotD protein complexed with spermidine was solved at 1.8 A resolution and revealed the detailed substrate-binding mechanism. The structure provided the detailed conformation of the bound spermidine. Furthermore, a water molecule was clearly identified in the binding site lying between the amino-terminal domain and carboxyl-terminal domain. Through this water molecule, the bound spermidine molecule forms two hydrogen bonds with Thr 35 and Ser 211. Another periplasmic component of polyamine transport, the PotF protein, exhibits 35% sequence identity with the PotD protein, and it binds only putrescine, not spermidine. To understand these different substrate specificities, model building of the PotF protein was performed on the basis of the PotD crystal structure. The hypothetical structure suggests that the side chain of Lys 349 in PotF inhibits spermidine binding because of the repulsive forces between its positive charge and spermidine. On the other hand, putrescine could be accommodated into the binding site without any steric hindrance because its molecular size is much smaller than that of spermidine, and the positively charged amino group is relatively distant from Lys 349.


    Related Citations: 
    • 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
    • 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


    Organizational Affiliation

    Protein Engineering Research Institute, Osaka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SPERMIDINE/PUTRESCINE-BINDING PROTEIN
A
325Escherichia 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 
A
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
SPDKd: 3200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.198 
  • Space Group: I 41
Unit Cell:
Length (Å)Angle (°)
a = 130.300α = 90.00
b = 130.300β = 90.00
c = 38.700γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement
WELMSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-12-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance