Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report

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

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

Macromolecule Content

• Total Structure Weight: 18.27 kDa 
• Atom Count: 1484 
• Modelled Residue Count: 160 
• Deposited Residue Count: 169 
• Unique protein chains: 1

4DT4

Crystal structure of the PPIase-chaperone SlpA with the chaperone binding site occupied by the linker of the purification tag

• DOI: 10.2210/pdb4DT4/pdb

• Classification: ISOMERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-02-20 Released: 2012-07-04 
• Deposition Author(s): Quistgaard, E.M., Nordlund, P., Loew, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.201 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 

Literature

High-resolution insights into binding of unfolded polypeptides by the PPIase chaperone SlpA.

Quistgaard, E.M., Nordlund, P., Low, C.

(2012) FASEB J 26: 4003-4013

• PubMed: 22735173 
• DOI: 10.1096/fj.12-208397
• Primary Citation of Related Structures:  
  4DT4


• PubMed Abstract: 
  

SlpA is a 2-domain protein consisting of an FK506-binding protein (FKBP) domain that harbors the peptidyl-prolyl cis/trans-isomerase (PPIase) active site and a small insert-in-flap (IF) domain that endows the protein with chaperone activity. We have determined the structure of SlpA from Escherichia coli at 1.35-Å resolution. The overall structure is similar to other known structures of the FKBP-IF subfamily. However, by serendipity, the linker region of the purification tag binds in the chaperone binding groove of the IF domain, making this the first structure of an FKBP-IF protein in complex with a mimic of an unfolded chaperone substrate. The linker binds by β-sheet augmentation, thus completing the incomplete β barrel of the IF domain and shielding a considerable hydrophobic surface area from the solvent. Interestingly, a proline residue in trans configuration appears to be specifically recognized in a small pocket within the binding groove. Hence, the IF domain can preselect and prealign substrates with proline residues, which may explain how it enhances the catalytic efficiency and modulates the specificity of the FKBP domain in addition to its chaperone function. Based on pulldown results, we suggest that SlpA is likely to be involved in ribosome assembly.

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Organizational Affiliation: 

Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, SE-171 77 Stockholm, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FKBP-type 16 kDa peptidyl-prolyl cis-trans isomerase	A	169	Escherichia coli K-12	Mutation(s): 0  Gene Names: fkpB, slpA, yaaD, b0028, JW0026 EC: 5.2.1.8
UniProt
Find proteins for P0AEM0 (Escherichia coli (strain K12)) Explore P0AEM0  Go to UniProtKB:  P0AEM0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.201 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.12	α = 90
b = 29.23	β = 93.2
c = 60.69	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-02-20 
• Released Date: 2012-07-04 
Deposition Author(s): Quistgaard, E.M., Nordlund, P., Loew, C.

Revision History  

• Version 1.0: 2012-07-04
  Type: Initial release
  
• Version 1.1: 2012-12-19
  Changes: Database references