6AC0

Crystal structure of TRADD death domain GlcNAcylated by EPEC effector NleB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.449 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Functional Insights into Host Death Domains Inactivation by the Bacterial Arginine GlcNAcyltransferase Effector.

Ding, J.Pan, X.Du, L.Yao, Q.Xue, J.Yao, H.Wang, D.C.Li, S.Shao, F.

(2019) Mol.Cell 74: 922

  • DOI: 10.1016/j.molcel.2019.03.028
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Enteropathogenic E. coli NleB and related type III effectors catalyze arginine GlcNAcylation of death domain (DD) proteins to block host defense, but the underlying mechanism is unknown. Here we solve crystal structures of NleB alone and in complex w ...

    Enteropathogenic E. coli NleB and related type III effectors catalyze arginine GlcNAcylation of death domain (DD) proteins to block host defense, but the underlying mechanism is unknown. Here we solve crystal structures of NleB alone and in complex with FADD-DD, UDP, and Mn 2+ as well as NleB-GlcNAcylated DDs of TRADD and RIPK1. NleB adopts a GT-A fold with a unique helix-pair insertion to hold FADD-DD; the interface contacts explain the selectivity of NleB for certain DDs. The acceptor arginine is fixed into a cleft, in which Glu253 serves as a base to activate the guanidinium. Analyses of the enzyme-substrate complex and the product structures reveal an inverting sugar-transfer reaction and a detailed catalytic mechanism. These structural insights are validated by mutagenesis analyses of NleB-mediated GlcNAcylation in vitro and its function in mouse infection. Our study builds a structural framework for understanding of NleB-catalyzed arginine GlcNAcylation of host death domain.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,Bio-Medical Center, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China.,Bio-Medical Center, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China. Electronic address: lishan@mail.hzau.edu.cn.,National Institute of Biological Sciences, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China. Electronic address: shaofeng@nibs.ac.cn.,National Institute of Biological Sciences, Beijing 102206, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; National Institute of Biological Sciences, Beijing 102206, China. Electronic address: jding@ibp.ac.cn.,College of Chemistry and Chemical Engineering, High-Field Nuclear Magnetic Resonance Center, Xiamen University, Xiamen, Fujian 361005, China.,Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor receptor type 1-associated DEATH domain protein
A
118Homo sapiensMutation(s): 0 
Gene Names: TRADD
Find proteins for Q15628 (Homo sapiens)
Go to Gene View: TRADD
Go to UniProtKB:  Q15628
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.449 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.184 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 28.600α = 90.00
b = 28.600β = 90.00
c = 264.720γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PHASERphasing
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-07-24 
  • Released Date: 2019-05-01 
  • Deposition Author(s): Ding, J., Shao, F.

Revision History 

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-06-26
    Type: Data collection, Database references