5EWY

Scabin toxin from Streptomyces Scabies in complex with inhibitor P6E


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Scabin, a Novel DNA-acting ADP-ribosyltransferase from Streptomyces scabies.

Lyons, B.Ravulapalli, R.Lanoue, J.Lugo, M.R.Dutta, D.Carlin, S.Merrill, A.R.

(2016) J.Biol.Chem. 291: 11198-11215

  • DOI: 10.1074/jbc.M115.707653
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A bioinformatics strategy was used to identify Scabin, a novel DNA-targeting enzyme from the plant pathogen 87.22 strain of Streptomyces scabies Scabin shares nearly 40% sequence identity with the Pierisin family of mono-ADP-ribosyltransferase toxins ...

    A bioinformatics strategy was used to identify Scabin, a novel DNA-targeting enzyme from the plant pathogen 87.22 strain of Streptomyces scabies Scabin shares nearly 40% sequence identity with the Pierisin family of mono-ADP-ribosyltransferase toxins. Scabin was purified to homogeneity as a 22-kDa single-domain enzyme and was shown to possess high NAD(+)-glycohydrolase (Km (NAD) = 68 ± 3 μm; kcat = 94 ± 2 min(-1)) activity with an RSQXE motif; it was also shown to target deoxyguanosine and showed sigmoidal enzyme kinetics (K0.5(deoxyguanosine) = 302 ± 12 μm; kcat = 14 min(-1)). Mass spectrometry analysis revealed that Scabin labels the exocyclic amino group on guanine bases in either single-stranded or double-stranded DNA. Several small molecule inhibitors were identified, and the most potent compounds were found to inhibit the enzyme activity with Ki values ranging from 3 to 24 μm PJ34, a well known inhibitor of poly-ADP-ribosyltransferases, was shown to be the most potent inhibitor of Scabin. Scabin was crystallized, representing the first structure of a DNA-targeting mono-ADP-ribosyltransferase enzyme; the structures of the apo-form (1.45 Å) and with two inhibitors (P6-E, 1.4 Å; PJ34, 1.6 Å) were solved. These x-ray structures are also the first high resolution structures of the Pierisin subgroup of the mono-ADP-ribosyltransferase toxin family. A model of Scabin with its DNA substrate is also proposed.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative ADP-Ribosyltransferase Scabin
A
200Streptomyces scabiei (strain 87.22)Mutation(s): 0 
Find proteins for C9Z6T8 (Streptomyces scabiei (strain 87.22))
Go to UniProtKB:  C9Z6T8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5TQ
Query on 5TQ

Download SDF File 
Download CCD File 
A
4-(8-fluoranyl-6-oxidanylidene-1,3,4,5-tetrahydrobenzo[c][1,6]naphthyridin-2-yl)butanoic acid
C16 H17 F N2 O3
HXURHTYUPWDBOT-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5TQKd: 50000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.153 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 87.170α = 90.00
b = 60.530β = 100.25
c = 37.940γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2016-04-06
    Type: Database references
  • Version 1.2: 2016-06-08
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Advisory, Database references, Derived calculations, Refinement description