4MXP | pdb_00004mxp

Structural Basis for PI(4)P-Specific Membrane Recruitment of the Legionella pneumophila Effector DrrA/SidM

• PDB DOI: https://doi.org/10.2210/pdb4MXP/pdb

• Classification: PI(4)P-BINDING PROTEIN
• Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2013-09-26 Released: 2014-03-19 
• Deposition Author(s): Del Campo, C.M., Mishra, A.K., Wang, Y.H., Roy, C.R., Janmey, P.A., Lambright, D.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.208 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Structural Basis for PI(4)P-Specific Membrane Recruitment of the Legionella pneumophila Effector DrrA/SidM.

Del Campo, C.M., Mishra, A.K., Wang, Y.H., Roy, C.R., Janmey, P.A., Lambright, D.G.

(2014) Structure 22: 397-408

• PubMed: 24530282 
• DOI: https://doi.org/10.1016/j.str.2013.12.018
• Primary Citation Related Structures: 
  4MXP


• PubMed Abstract: 
  

  Recruitment of the Legionella pneumophila effector DrrA to the Legionella-containing vacuole, where it activates and AMPylates Rab1, is mediated by a P4M domain that binds phosphatidylinositol 4-phosphate [PI(4)P] with high affinity and specificity. Despite the importance of PI(4)P in Golgi trafficking and its manipulation by pathogens, the structural bases for PI(4)P-dependent membrane recruitment remain poorly defined. Here, we determined the crystal structure of a DrrA fragment including the P4M domain in complex with dibutyl PI(4)P and investigated the determinants of phosphoinositide recognition and membrane targeting. Headgroup recognition involves an elaborate network of direct and water-mediated interactions with basic and polar residues in the context of a deep, constrictive binding pocket. An adjacent hydrophobic helical element packs against the acyl chains and inserts robustly into PI(4)P-containing monolayers. The structural, biochemical, and biophysical data reported here support a detailed structural mechanism for PI(4)P-dependent membrane targeting by DrrA.

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Organizational Affiliation: 
• Program in Molecular Medicine and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
Institute for Medicine and Engineering and Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
Department of Microbial Pathogenesis, Yale University School of Medicine, Boyer Center for Molecular Medicine, New Haven, CT 06536, USA.
Institute for Medicine and Engineering and Department of Physiology, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA.
Program in Molecular Medicine and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 37.69 kDa 
• Atom Count: 2,696 
• Modeled Residue Count: 310 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Defects in Rab1 recruitment protein A	A	328	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0  Gene Names: drrA, lpg2464, sidM EC: 2.7.7 (PDB Primary Data), 2.7.7.108 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for Q5ZSQ3 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZSQ3  Go to UniProtKB:  Q5ZSQ3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DB4	B [auth A]	(2R)-3-{[(R)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dibutanoate C17 H32 O16 P2 GZEWZLHSHLUSGP-HDIZFQRBSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.208 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.552	α = 90
b = 128.552	β = 90
c = 53.222	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-19 
Deposition Author(s): Del Campo, C.M., Mishra, A.K., Wang, Y.H., Roy, C.R., Janmey, P.A., Lambright, D.G.

Revision History  

• Version 1.0: 2014-03-19
  Type: Initial release
  
• Version 1.1: 2014-03-26
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description