6ACI

Crystal structure of EPEC effector NleB in complex with FADD death domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.164 

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
T3SS secreted effector NleB homolog
A
306Escherichia coli O127:H6 (strain E2348/69 / EPEC)Mutation(s): 1 
Find proteins for B7UI21 (Escherichia coli O127:H6 (strain E2348/69 / EPEC))
Go to UniProtKB:  B7UI21
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FAS-associated death domain protein
H
92Homo sapiensMutation(s): 0 
Gene Names: FADD (MORT1)
Find proteins for Q13158 (Homo sapiens)
Go to Gene View: FADD
Go to UniProtKB:  Q13158
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
UDP
Query on UDP

Download SDF File 
Download CCD File 
A
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.164 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 84.590α = 90.00
b = 84.590β = 90.00
c = 145.881γ = 120.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
PHENIXrefinement
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-07-26 
  • 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