6ZTH

Phospholipase PlaB from Legionella pneumophila


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.413 
  • R-Value Work: 0.364 
  • R-Value Observed: 0.366 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

NAD(H)-mediated tetramerization controls the activity of Legionella pneumophila phospholipase PlaB.

Diwo, M.Michel, W.Aurass, P.Kuhle-Keindorf, K.Pippel, J.Krausze, J.Wamp, S.Lang, C.Blankenfeldt, W.Flieger, A.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: 10.1073/pnas.2017046118
  • Primary Citation of Related Structures:  
    6ZTH, 6ZTI

  • PubMed Abstract: 
  • The virulence factor PlaB promotes lung colonization, tissue destruction, and intracellular replication of Legionella pneumophila , the causative agent of Legionnaires' disease. It is a highly active phospholipase exposed at the bacterial surface and shows an extraordinary activation mechanism by tetramer deoligomerization ...

    The virulence factor PlaB promotes lung colonization, tissue destruction, and intracellular replication of Legionella pneumophila , the causative agent of Legionnaires' disease. It is a highly active phospholipase exposed at the bacterial surface and shows an extraordinary activation mechanism by tetramer deoligomerization. To unravel the molecular basis for enzyme activation and localization, we determined the crystal structure of PlaB in its tetrameric form. We found that the tetramer is a dimer of identical dimers, and a monomer consists of an N-terminal α/β-hydrolase domain expanded by two noncanonical two-stranded β-sheets, β-6/β-7 and β-9/β-10. The C-terminal domain reveals a fold displaying a bilobed β-sandwich with a hook structure required for dimer formation and structural complementation of the enzymatic domain in the neighboring monomer. This highlights the dimer as the active form. Δβ-9/β-10 mutants showed a decrease in the tetrameric fraction and altered activity profiles. The variant also revealed restricted binding to membranes resulting in mislocalization and bacterial lysis. Unexpectedly, we observed eight NAD(H) molecules at the dimer/dimer interface, suggesting that these molecules stabilize the tetramer and hence lead to enzyme inactivation. Indeed, addition of NAD(H) increased the fraction of the tetramer and concomitantly reduced activity. Together, these data reveal structural elements and an unprecedented NAD(H)-mediated tetramerization mechanism required for spatial and enzymatic control of a phospholipase virulence factor. The allosteric regulatory process identified here is suited to fine tune PlaB in a way that protects Legionella pneumophila from self-inflicted lysis while ensuring its activity at the pathogen-host interface.


    Related Citations: 
    • NAD(H)-mediated tetramerization controls the activity of Legionella pneumophila phospholipase PlaB
      Diwo, M., Michel, W., Aurass, P., Kuhle-Keindorf, K., Pippel, J., Krausze, J., Lang, C., Blankenfeldt, W., Flieger, A.
      (2020) Biorxiv --: --

    Organizational Affiliation

    Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, 38855 Wernigerode, Germany; wulf.blankenfeldt@helmholtz-hzi.de fliegera@rki.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PlaB phospholipaseA, B, C, D489Legionella pneumophilaMutation(s): 0 
Gene Names: plaBNCTC12000_01733
UniProt
Find proteins for A0A378K488 (Legionella pneumophila)
Explore A0A378K488 
Go to UniProtKB:  A0A378K488
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A378K488
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.413 
  • R-Value Work: 0.364 
  • R-Value Observed: 0.366 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.806α = 90
b = 170.578β = 92.86
c = 93.485γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyFL359/4-2/3
German Research Foundation (DFG)Germany281361126/GRK2223

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-02
    Type: Initial release
  • Version 1.1: 2021-06-16
    Changes: Database references