4YC0

Crystal structure of ADP-ribosyltransferase Vis in complex with M6 Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Characterization of Vis Toxin, a Novel ADP-Ribosyltransferase from Vibrio splendidus.

Ravulapalli, R.Lugo, M.R.Pfoh, R.Visschedyk, D.Poole, A.Fieldhouse, R.J.Pai, E.F.Merrill, A.R.

(2015) Biochemistry 54: 5920-5936

  • DOI: 10.1021/acs.biochem.5b00921
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Vis toxin was identified by a bioinformatics strategy as a putative virulence factor produced by Vibrio splendidus with mono-ADP-ribosyltransferase activity. Vis was purified to homogeneity as a 28 kDa single-domain enzyme and was shown to possess NA ...

    Vis toxin was identified by a bioinformatics strategy as a putative virulence factor produced by Vibrio splendidus with mono-ADP-ribosyltransferase activity. Vis was purified to homogeneity as a 28 kDa single-domain enzyme and was shown to possess NAD(+)-glycohydrolase [KM(NAD(+)) = 276 ± 12 μM] activity and with an R-S-E-X-E motif; it targets arginine-related compounds [KM(agmatine) = 272 ± 18 mM]. Mass spectrometry analysis revealed that Vis labels l-arginine with ADP-ribose from the NAD(+) substrate at the amino nitrogen of the guanidinium side chain. Vis is toxic to yeast when expressed in the cytoplasm under control of the CUP1 promotor, and catalytic variants lost the ability to kill the yeast host, indicating that the toxin exerts its lethality through its enzyme activity. Several small molecule inhibitors were identified from a virtual screen, and the most potent compounds were found to inhibit the transferase activity of the enzyme with Ki values ranging from 25 to 134 μM. Inhibitor compound M6 bears the necessary attributes of a solid candidate as a lead compound for therapeutic development. Vis toxin was crystallized, and the structures of the apoenzyme (1.4 Å) and the enzyme bound with NAD(+) (1.8 Å) and with the M6 inhibitor (1.5 Å) were determined. The structures revealed that Vis represents a new subgroup within the mono-ADP-ribosyltransferase toxin family.


    Organizational Affiliation

    Department of Molecular and Cellular Biology, University of Guelph , Guelph, Ontario, Canada N1G 2W1.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative NAD(+)--arginine ADP-ribosyltransferase VisA239Vibrio splendidusMutation(s): 0 
Gene Names: V12B01_18061
EC: 2.4.2.31
Find proteins for A3UNN4 (Vibrio splendidus (strain 12B01))
Explore A3UNN4 
Go to UniProtKB:  A3UNN4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5OF
Query on 5OF

Download CCD File 
A
2-(4-oxidanylidene-3~{H}-phthalazin-1-yl)ethanoic acid
C10 H8 N2 O3
ZEDQLIHBPGNGEC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5OFKi:  74000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.23α = 90
b = 52.16β = 90
c = 101.6γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Derived calculations, Structure summary