5ZQ5

SidE-Ubi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.487 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Insights into Non-canonical Ubiquitination Catalyzed by SidE.

Wang, Y.Shi, M.Feng, H.Zhu, Y.Liu, S.Gao, A.Gao, P.

(2018) Cell 173: 1231-1243.e16

  • DOI: 10.1016/j.cell.2018.04.023
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ubiquitination constitutes one of the most important signaling mechanisms in eukaryotes. Conventional ubiquitination is catalyzed by the universally conserved E1-E2-E3 three-enzyme cascade in an ATP-dependent manner. The newly identified SidE family ...

    Ubiquitination constitutes one of the most important signaling mechanisms in eukaryotes. Conventional ubiquitination is catalyzed by the universally conserved E1-E2-E3 three-enzyme cascade in an ATP-dependent manner. The newly identified SidE family effectors of the pathogen Legionella pneumophila ubiquitinate several human proteins by a different mechanism without engaging any of the conventional ubiquitination machinery. We now report the crystal structures of SidE alone and in complex with ubiquitin, NAD, and ADP-ribose, thereby capturing different conformations of SidE before and after ubiquitin and ligand binding. The structures of ubiquitin bound to both mART and PDE domains reveal several unique features of the two reaction steps catalyzed by SidE. Further, the structural and biochemical results demonstrate that SidE family members do not recognize specific structural folds of the substrate proteins. Our studies provide both structural explanations for the functional observations and new insights into the molecular mechanisms of this non-canonical ubiquitination machinery.


    Organizational Affiliation

    CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: gaopu@ibp.ac.cn.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA. Electronic address: ang.gao@nyumc.org.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SidE
A, C
845Legionella pneumophilaMutation(s): 0 
Gene Names: laiD
Find proteins for Q6BBR6 (Legionella pneumophila)
Go to UniProtKB:  Q6BBR6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
B, D
79Homo sapiensMutation(s): 1 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.487 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 92.672α = 90.00
b = 129.084β = 90.00
c = 191.507γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHENIXphasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
China91753133
China31670903
China31700687
ChinaXDB08020204

Revision History 

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2018-05-30
    Type: Data collection, Database references