4ZV4 | pdb_00004zv4

Structure of Tse6 in complex with EF-Tu

• PDB DOI: https://doi.org/10.2210/pdb4ZV4/pdb

• Classification: TRANSLATION
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-05-18 Released: 2015-11-11 
• Deposition Author(s): Whitney, J.C., Sawai, S., Robinson, H., Mougous, J.D.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Defense Threat Reduction Agency (DTRA)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.283 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

An Interbacterial NAD(P)(+) Glycohydrolase Toxin Requires Elongation Factor Tu for Delivery to Target Cells.

Whitney, J.C., Quentin, D., Sawai, S., LeRoux, M., Harding, B.N., Ledvina, H.E., Tran, B.Q., Robinson, H., Goo, Y.A., Goodlett, D.R., Raunser, S., Mougous, J.D.

(2015) Cell 163: 607-619

• PubMed: 26456113 
• DOI: https://doi.org/10.1016/j.cell.2015.09.027
• Primary Citation Related Structures: 
  4ZUY, 4ZV0, 4ZV4


• PubMed Abstract: 
  

  Type VI secretion (T6S) influences the composition of microbial communities by catalyzing the delivery of toxins between adjacent bacterial cells. Here, we demonstrate that a T6S integral membrane toxin from Pseudomonas aeruginosa, Tse6, acts on target cells by degrading the universally essential dinucleotides NAD(+) and NADP(+). Structural analyses of Tse6 show that it resembles mono-ADP-ribosyltransferase proteins, such as diphtheria toxin, with the exception of a unique loop that both excludes proteinaceous ADP-ribose acceptors and contributes to hydrolysis. We find that entry of Tse6 into target cells requires its binding to an essential housekeeping protein, translation elongation factor Tu (EF-Tu). These proteins participate in a larger assembly that additionally directs toxin export and provides chaperone activity. Visualization of this complex by electron microscopy defines the architecture of a toxin-loaded T6S apparatus and provides mechanistic insight into intercellular membrane protein delivery between bacteria.

---

Organizational Affiliation: 
• Department of Microbiology, University of Washington, Seattle, WA 98195, USA.
Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA.
Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.
Department of Microbiology, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 130.17 kDa 
• Atom Count: 8,060 
• Modeled Residue Count: 1,105 
• Deposited Residue Count: 1,170 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation factor Tu	A, D [auth B]	405	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: tufA, PA4265, tufB, PA4277 EC: 3.6.5.3
UniProt
Find proteins for P09591 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P09591  Go to UniProtKB:  P09591

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tse6	B [auth C], C [auth D]	180	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: PA0093 EC: 3.2.2.5
UniProt
Find proteins for Q9I739 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I739  Go to UniProtKB:  Q9I739

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	E [auth A], G [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	F [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.283 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.109	α = 90
b = 176.109	β = 90
c = 86.31	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-11-11 
Deposition Author(s): Whitney, J.C., Sawai, S., Robinson, H., Mougous, J.D.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI080609
Defense Threat Reduction Agency (DTRA)	United States	HDTRA-1-13-014

Revision History  

• Version 1.0: 2015-11-11
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-04-24
  Changes: Author supporting evidence, Data collection
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description