8UX2

Chromobacterium violaceum mono-ADP-ribosyltransferase CteC in complex with NAD+

  • Classification: TRANSFERASE
  • Organism(s): Chromobacterium violaceum
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2023-11-08 Released: 2024-01-17 
  • Deposition Author(s): Zhang, Z., Rondon, H., Das, C.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of bacterial ubiquitin ADP-ribosyltransferase CteC reveals a substrate-recruiting insertion.

Zhang, Z.Rondon-Cordero, H.M.Das, C.

(2023) J Biol Chem 300: 105604-105604

  • DOI: https://doi.org/10.1016/j.jbc.2023.105604
  • Primary Citation of Related Structures:  
    8UX2

  • PubMed Abstract: 

    ADP-ribosylation is a post-translational modification involved in regulation of diverse cellular pathways. Interestingly, many pathogens have been identified to utilize ADP-ribosylation as a way for host manipulation. A recent study found that CteC, an effector from the bacterial pathogen Chromobacterium violaceum, hinders host ubiquitin (Ub) signaling pathways via installing mono-ADP-ribosylation on threonine 66 of Ub. However, the molecular basis of substrate recognition by CteC is not well understood. In this article, we probed the substrate specificity of this effector at protein and residue levels. We also determined the crystal structure of CteC in complex with NAD + , which revealed a canonical mono-ADP-ribosyltransferase fold with an additional insertion domain. The AlphaFold-predicted model differed significantly from the experimentally determined structure, even in regions not used in crystal packing. Biochemical and biophysical studies indicated unique features of the NAD + binding pocket, while showing selectivity distinction between Ub and structurally close Ub-like modifiers and the role of the insertion domain in substrate recognition. Together, this study provides insights into the enzymatic specificities and the key structural features of a novel bacterial ADP-ribosyltransferase involved in host-pathogen interaction.


  • Organizational Affiliation

    Department of Chemistry, Purdue University, West Lafayette, Indiana, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(+)--protein-threonine ADP-ribosyltransferase
A, B, C
246Chromobacterium violaceumMutation(s): 0 
Gene Names: cteC
UniProt
Find proteins for Q7NY09 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757))
Explore Q7NY09 
Go to UniProtKB:  Q7NY09
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7NY09
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.656α = 90
b = 82.937β = 90
c = 151.212γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
AutoSolphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM126296
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21AI171709
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesT32AI148103

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Database references