6OQQ

Legionella pneumophila SidJ/Saccharomyces cerevisiae calmodulin complex

• PDB DOI: https://doi.org/10.2210/pdb6OQQ/pdb

• Classification: TRANSFERASE
• Organism(s): Legionella pneumophila, Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-04-28 Released: 2019-05-15 
• Deposition Author(s): Tomchick, D.R., Tagliabracci, V.S., Black, M., Osinski, A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), Robert A. Welch Foundation, Other government, Polish National Science Centre

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.234 
• R-Value Work: 0.202 
• R-Value Observed: 0.203 

Literature

Bacterial pseudokinase catalyzes protein polyglutamylation to inhibit the SidE-family ubiquitin ligases.

Black, M.H., Osinski, A., Gradowski, M., Servage, K.A., Pawlowski, K., Tomchick, D.R., Tagliabracci, V.S.

(2019) Science 364: 787-792

• PubMed: 31123136 
• DOI: https://doi.org/10.1126/science.aaw7446
• Primary Citation of Related Structures:  
  6OQQ


• PubMed Abstract: 
  

  Enzymes with a protein kinase fold transfer phosphate from adenosine 5'-triphosphate (ATP) to substrates in a process known as phosphorylation. Here, we show that the Legionella meta-effector SidJ adopts a protein kinase fold, yet unexpectedly catalyzes protein polyglutamylation. SidJ is activated by host-cell calmodulin to polyglutamylate the SidE family of ubiquitin (Ub) ligases. Crystal structures of the SidJ-calmodulin complex reveal a protein kinase fold that catalyzes ATP-dependent isopeptide bond formation between the amino group of free glutamate and the γ-carboxyl group of an active-site glutamate in SidE. We show that SidJ polyglutamylation of SidE, and the consequent inactivation of Ub ligase activity, is required for successful Legionella replication in a viable eukaryotic host cell.

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Organizational Affiliation: 

Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration, isothermal titration calorimetry, immunoprecipitation

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, isothermal titration calorimetry, immunoprecipitation

Macromolecule Content

• Total Structure Weight: 235.38 kDa 
• Atom Count: 15,025 
• Modelled Residue Count: 1,755 
• Deposited Residue Count: 2,040 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Legionella pneumophila SidJ	A, C	873	Legionella pneumophila	Mutation(s): 0  Gene Names: SidJ EC: 6
UniProt
Find proteins for Q5ZTK6 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZTK6  Go to UniProtKB:  Q5ZTK6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin	B, D	147	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: CMD1, YBR109C, YBR0904
UniProt
Find proteins for P06787 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P06787  Go to UniProtKB:  P06787

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	E [auth A], X [auth C]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
POP	F [auth A], Y [auth C], Z [auth C]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
EDO	DA [auth C], EA [auth C], FA [auth C], GA [auth C], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	HA [auth D], IA [auth D], U [auth B], V [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	AA [auth C], BA [auth C], CA [auth C], G [auth A], H [auth A], I [auth A], J [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	K [auth A], W [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.234 
• R-Value Work: 0.202 
• R-Value Observed: 0.203 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.49	α = 90
b = 104.749	β = 103.97
c = 107.77	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
MLPHARE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-05-15 
Deposition Author(s): Tomchick, D.R., Tagliabracci, V.S., Black, M., Osinski, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM008014-34
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	F30HL143859-01
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R00DK099254
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM-7062-44
Robert A. Welch Foundation	United States	I-1911
Other government	United States	RP170674
Polish National Science Centre	Poland	2014/15/B/NZ1/03559

Revision History  

• Version 1.0: 2019-05-15
  Type: Initial release
  
• Version 1.1: 2019-06-12
  Changes: Data collection, Database references
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations