Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 77.05 kDa 
• Atom Count: 5656 
• Modelled Residue Count: 682 
• Deposited Residue Count: 692 
• Unique protein chains: 1

3TTM

Crystal structure of SpuD in complex with putrescine

• PDB DOI: 10.2210/pdb3TTM/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-09-15 Released: 2012-03-28 
• Deposition Author(s): Wu, D.H., Lim, S.C., Song, H.W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.255 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 

Literature

Structural Basis of Substrate Binding Specificity Revealed by the Crystal Structures of Polyamine Receptors SpuD and SpuE from Pseudomonas aeruginosa

Wu, D.H., Lim, S.C., Dong, Y.H., Wu, J.E., Tao, F., Zhou, L., Zhang, L.H., Song, H.W.

(2012) J Mol Biol 416: 697-712

• PubMed: 22300763 
• DOI: 10.1016/j.jmb.2012.01.010
• Primary Citation of Related Structures:  
  3TTK, 3TTL, 3TTM, 3TTN


• PubMed Abstract: 
  

The type III secretion system (T3SS) of Pseudomonas aeruginosa is a key virulence determinant whose expression is induced by polyamine signals from mammalian host. SpuD and SpuE were postulated to be spermidine-preferential binding proteins, which regulate the polyamine content in this bacterial pathogen. In this study, we found that SpuD is a putrescine-preferential binding protein, while SpuE binds to spermidine exclusively. We have determined the crystal structures of SpuD in free form and in complex with putrescine and SpuE in free form and in complex with spermidine. Upon ligand binding, SpuD and SpuE undergo an "open-to-closed" conformational switch with the resultant closed ligand-bound forms, SpuD-putrescine and SpuE-spermidine, similar to their Escherichia coli counterparts PotF-putrescine and PotD-spermidine, respectively. Structural comparison suggested that two aromatic residues, Trp271 of SpuE and Phe273 of SpuD in segment II region, are the key structural determinants for putrescine/spermidine recognition specificity. Mutagenesis combined with isothermal titration calorimetry showed that substitution of Trp271 by Phe enabled SpuE to gain substantial binding affinity for putrescine, while replacement of Phe273 by Trp reduced the binding affinity of SpuD toward putrescine by 250-fold. Altogether, these results revealed the molecular mechanism governing polyamine recognition specificity by SpuD and SpuE and provide the basis for further structural and functional studies of polyamine signal importation system in P. aeruginosa.

---

Organizational Affiliation: 

Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyamine transport protein	A, B	346	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: spuD
UniProt
Find proteins for Q9I6J1 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I6J1  Go to UniProtKB:  Q9I6J1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PUT	C [auth A], D [auth B]	1,4-DIAMINOBUTANE C4 H12 N2 KIDHWZJUCRJVML-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PUT	Binding MOAD:  3TTM	Kd: 3 (nM) from 1 assay(s)
	PDBBind:  3TTM	Kd: 3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.255 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.909	α = 90
b = 82.862	β = 90
c = 128.287	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
PHASER	phasing
REFMAC	refinement
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-09-15 
• Released Date: 2012-03-28 
Deposition Author(s): Wu, D.H., Lim, S.C., Song, H.W.

Revision History  

• Version 1.0: 2012-03-28
  Type: Initial release