6DR3

Crystal structure of E. coli LpoA amino terminal domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.181 

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Literature

Crystal structures of the amino-terminal domain of LpoA from Escherichia coli and Haemophilus influenzae.

Kelley, A.Vijayalakshmi, J.Saper, M.A.

(2019) Acta Crystallogr F Struct Biol Commun 75: 368-376

  • DOI: 10.1107/S2053230X19004011
  • Primary Citation of Related Structures:  
    6DCJ, 6DR3

  • PubMed Abstract: 
  • The bacterial periplasmic protein LpoA is an outer membrane lipoprotein and an activator for the cross-linking activity of PBP1A, a bifunctional peptidoglycan synthase. Previous structures of the amino-terminal (N) domain of LpoA showed it to consist entirely of helices and loops, with at least four tetratricopeptide-like repeats ...

    The bacterial periplasmic protein LpoA is an outer membrane lipoprotein and an activator for the cross-linking activity of PBP1A, a bifunctional peptidoglycan synthase. Previous structures of the amino-terminal (N) domain of LpoA showed it to consist entirely of helices and loops, with at least four tetratricopeptide-like repeats. Although the previously determined orthorhombic crystal structure of the N domain of Haemophilus influenzae LpoA showed a typical curved structure with a concave groove, an NMR structure of the same domain from Escherichia coli was relatively flat. Here, a crystal structure of the N domain of E. coli LpoA was determined to a resolution of 2.1 Å and was found to be more similar to the H. influenzae crystal structure than to the E. coli NMR structure. To provide a quantitative description for these comparisons, the various structures were superimposed pairwise by fitting the first half of each structure to its pairwise partner and then calculating the rotation axis that would optimally superimpose the second half. Differences in both the magnitude of the rotation and the direction of the rotation axis were observed between different pairs of structures. A 1.35 Å resolution structure of a monoclinic crystal form of the N domain of H. influenzae LpoA was also determined. In this structure, the subdomains rotate 10° relative to those in the original orthorhombic H. influenzae crystal structure to further narrow the groove between the subdomains. To accommodate this, a bound chloride ion (in place of sulfate) allowed the closer approach of a helix that forms one side of the groove.


    Related Citations: 
    • Structural analyses of the Haemophilus influenzae peptidoglycan synthase activator LpoA suggest multiple conformations in solution.
      Sathiyamoorthy, K., Vijayalakshmi, J., Tirupati, B., Fan, L., Saper, M.A.
      (2017) J Biol Chem 292: 17626
    • Elongated structure of the outer-membrane activator of peptidoglycan synthesis LpoA: implications for PBP1A stimulation.
      Jean, N.L., Bougault, C.M., Lodge, A., Derouaux, A., Callens, G., Egan, A.J., Ayala, I., Lewis, R.J., Vollmer, W., Simorre, J.P.
      (2014) Structure 22: 1047

    Organizational Affiliation

    Department of Biological Chemistry, University of Michigan, 1150 West Medical Center Drive, Ann Arbor, MI 48109-5606, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Penicillin-binding protein activator LpoAA223Escherichia coli K-12Mutation(s): 0 
Gene Names: lpoAyraMb3147JW3116
UniProt
Find proteins for P45464 (Escherichia coli (strain K12))
Explore P45464 
Go to UniProtKB:  P45464
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.181 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.001α = 90
b = 70.001β = 90
c = 97.802γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-05-15
    Changes: Data collection, Database references