4U6I

Crystal Structure of the EutL Microcompartment Shell Protein from Clostridium Perfringens Bound to Vitamin B12

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

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Literature

Structure of a bacterial microcompartment shell protein bound to a cobalamin cofactor.

Thompson, M.C., Crowley, C.S., Kopstein, J., Bobik, T.A., Yeates, T.O.

(2014) Acta Crystallogr F Struct Biol Commun 70: 1584-1590

  • DOI: 10.1107/S2053230X1402158X
  • Primary Citation of Related Structures:  
    4U6I

  • PubMed Abstract: 

    • The EutL shell protein is a key component of the ethanolamine-utilization microcompartment, which serves to compartmentalize ethanolamine degradation in diverse bacteria. The apparent function of this shell protein is to facilitate the selective diffusion of large cofactor molecules between the cytoplasm and the lumen of the microcompartment ...

    The EutL shell protein is a key component of the ethanolamine-utilization microcompartment, which serves to compartmentalize ethanolamine degradation in diverse bacteria. The apparent function of this shell protein is to facilitate the selective diffusion of large cofactor molecules between the cytoplasm and the lumen of the microcompartment. While EutL is implicated in molecular-transport phenomena, the details of its function, including the identity of its transport substrate, remain unknown. Here, the 2.1 Å resolution X-ray crystal structure of a EutL shell protein bound to cobalamin (vitamin B12) is presented and the potential relevance of the observed protein-ligand interaction is briefly discussed. This work represents the first structure of a bacterial microcompartment shell protein bound to a potentially relevant cofactor molecule.

    Organizational Affiliation: 

    Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ethanolamine utilization protein EutLA, B, C225Clostridium perfringensMutation(s): 0 
Gene Names: eutL
UniProt
Find proteins for Q8XLZ0 (Clostridium perfringens (strain 13 / Type A))
Explore Q8XLZ0 
Go to UniProtKB:  Q8XLZ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8XLZ0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B12
Query on B12
Download Ideal Coordinates CCD File 
E [auth C]COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.23α = 90
b = 88.23β = 90
c = 252.01γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2014-12-24
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Derived calculations, Other, Refinement description, Source and taxonomy