Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 27.04 kDa 
• Atom Count: 2007 
• Residue Count: 217 
• Unique protein chains: 1

4Y1W

Vis toxin, an ADP-ribosyltransferase from Vibrio Splendidus

• DOI: 10.2210/pdb4Y1W/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio splendidus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-02-09 Released: 2015-11-04 
• Deposition Author(s): Ravulapalli, R., Tempel, W., Merrrill, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.185 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 

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

• PubMed: 26352925 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
NAD(+)--arginine ADP-ribosyltransferase Vis	A	239	Vibrio splendidus	Mutation(s): 0  Gene Names: V12B01_18061 EC: 2.4.2.31
Find proteins for A3UNN4 (Vibrio splendidus (strain 12B01)) Go to UniProtKB:  A3UNN4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.185 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.5	α = 90
b = 51.8	β = 90
c = 102.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-02-09 
• Released Date: 2015-11-04 
Deposition Author(s): Ravulapalli, R., Tempel, W., Merrrill, A.R.

Revision History 

• Version 1.0: 2015-11-04
  Type: Initial release