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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 21.82 kDa 
• Atom Count: 1379 
• Modelled Residue Count: 161 
• Deposited Residue Count: 195 
• Unique protein chains: 1

6VV4

Scabin (V109G) toxin from Streptomyces scabies

• DOI: 10.2210/pdb6VV4/pdb

• Classification: TOXIN
• Organism(s): Streptomyces scabiei 87.22
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-02-16 Released: 2021-01-20 
• Deposition Author(s): Heney, K., Lyons, B., Merrill, A.R.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.209 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Literature

Mapping the DNA-Binding Motif of Scabin Toxin, a Guanine Modifying Enzyme from Streptomyces scabies .

Vatta, M., Lyons, B., Heney, K.A., Lidster, T., Merrill, A.R.

(2021) Toxins (Basel) 13

• PubMed: 33450958 
• DOI: 10.3390/toxins13010055
• Primary Citation of Related Structures:  
  6VPA, 6VV4, 6VVF, 6VUV


• PubMed Abstract: 
  

Scabin is a mono-ADP-ribosyltransferase toxin/enzyme and possible virulence factor produced by the agriculture pathogen, Streptomyces scabies . Recently, molecular dynamic approaches and MD simulations revealed its interaction with both NAD ⁺ and DNA substrates. An Essential Dynamics Analysis identified a crab-claw-like mechanism, including coupled changes in the exposed motifs, and the R _β1 -R _La -N _Lc -STT _β2 -W _PN -W _ARTT -(QxE) _ARTT sequence motif was proposed as a catalytic signature of the Pierisin family of DNA-acting toxins. A new fluorescence assay was devised to measure the kinetics for both RNA and DNA substrates. Several protein variants were prepared to probe the Scabin-NAD-DNA molecular model and to reveal the reaction mechanism for the transfer of ADP-ribose to the guanine base in the DNA substrate. The results revealed that there are several lysine and arginine residues in Scabin that are important for binding the DNA substrate; also, key residues such as Asn110 in the mechanism of ADP-ribose transfer to the guanine base were identified. The DNA-binding residues are shared with ScARP from Streptomyces coelicolor but are not conserved with Pierisin-1, suggesting that the modification of guanine bases by ADP-ribosyltransferases is divergent even in the Pierisin family.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Scabin	A	195	Streptomyces scabiei 87.22	Mutation(s): 1  Gene Names: SCAB_27771
Find proteins for C9Z6T8 (Streptomyces scabiei (strain 87.22)) Explore C9Z6T8  Go to UniProtKB:  C9Z6T8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.209 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.91	α = 90
b = 61.07	β = 99.92
c = 37.97	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-02-16 
• Released Date: 2021-01-20 
Deposition Author(s): Heney, K., Lyons, B., Merrill, A.R.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History  

• Version 1.0: 2021-01-20
  Type: Initial release
  
• Version 1.1: 2021-01-27
  Changes: Database references