6ZTH | pdb_00006zth

Phospholipase PlaB from Legionella pneumophila


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.413 (Depositor), 0.412 (DCC) 
  • R-Value Work: 
    0.364 (Depositor), 0.363 (DCC) 
  • R-Value Observed: 
    0.366 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1073/pnas.2017046118
  • Primary Citation 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. 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.


  • Organizational Affiliation
    • Structure and Function of Proteins, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany.

Macromolecule Content 

  • Total Structure Weight: 229.48 kDa 
  • Atom Count: 15,842 
  • Modeled Residue Count: 1,881 
  • Deposited Residue Count: 1,956 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PlaB phospholipase
A, B, C, D
489Legionella 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
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D 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 (Depositor), 0.412 (DCC) 
  • R-Value Work:  0.364 (Depositor), 0.363 (DCC) 
  • R-Value Observed: 0.366 (Depositor) 
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

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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
  • Version 1.2: 2024-11-06
    Changes: Advisory, Data collection, Database references, Structure summary