Biological Assembly 1  

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

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 71.17 kDa 
• Atom Count: 5148 
• Modelled Residue Count: 659 
• Deposited Residue Count: 675 
• Unique protein chains: 1

4EDI

Disulfide bonded EutL from Clostridium perfringens

• PDB DOI: 10.2210/pdb4EDI/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Clostridium perfringens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-27 Released: 2013-03-27 
• Deposition Author(s): Thompson, M.C., Cascio, D., Crowley, C.S., Kopstein, J.S., Yeates, T.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.193 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Literature

An allosteric model for control of pore opening by substrate binding in the EutL microcompartment shell protein.

Thompson, M.C., Cascio, D., Leibly, D.J., Yeates, T.O.

(2015) Protein Sci 24: 956-975

• PubMed: 25752492 
• DOI: 10.1002/pro.2672
• Primary Citation of Related Structures:  
  4EDI, 4FDZ, 4TM6, 4TME


• PubMed Abstract: 
  

The ethanolamine utilization (Eut) microcompartment is a protein-based metabolic organelle that is strongly associated with pathogenesis in bacteria that inhabit the human gut. The exterior shell of this elaborate protein complex is composed from a few thousand copies of BMC-domain shell proteins, which form a semi-permeable diffusion barrier that provides the interior enzymes with substrates and cofactors while simultaneously retaining metabolic intermediates. The ability of this protein shell to regulate passage of substrate and cofactor molecules is critical for microcompartment function, but the details of how this diffusion barrier can allow the passage of large cofactors while still retaining small intermediates remain unclear. Previous work has revealed two conformations of the EutL shell protein, providing substantial evidence for a gated pore that might allow the passage of large cofactors. Here we report structural and biophysical evidence to show that ethanolamine, the substrate of the Eut microcompartment, acts as a negative allosteric regulator of EutL pore opening. Specifically, a series of X-ray crystal structures of EutL from Clostridium perfringens, along with equilibrium binding studies, reveal that ethanolamine binds to EutL at a site that exists in the closed-pore conformation and which is incompatible with opening of the large pore for cofactor transport. The allosteric mechanism we propose is consistent with the cofactor requirements of the Eut microcompartment, leading to a new model for EutL function. Furthermore, our results suggest the possibility of redox modulation of the allosteric mechanism, opening potentially new lines of investigation.

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Organizational Affiliation: 

UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California, 90095.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ethanolamine utilization protein	A, B, C	225	Clostridium perfringens	Mutation(s): 0  Gene Names: CPE0900, eutL
UniProt
Find proteins for Q8XLZ0 (Clostridium perfringens (strain 13 / Type A)) Explore Q8XLZ0  Go to UniProtKB:  Q8XLZ0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.193 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.747	α = 90
b = 86.747	β = 90
c = 251.681	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-03-27 
• Released Date: 2013-03-27 
Deposition Author(s): Thompson, M.C., Cascio, D., Crowley, C.S., Kopstein, J.S., Yeates, T.O.

Revision History  

• Version 1.0: 2013-03-27
  Type: Initial release
  
• Version 1.1: 2016-02-10
  Changes: Database references