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

• Published in: Toxins Vol. 13; no. 1; p. 55
• Main Authors: Vatta, Maritza, Lyons, Bronwyn, Heney, Kayla A, Lidster, Taylor, Merrill, A Rod
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 13.01.2021; MDPI
• Subjects: Adenosine diphosphate; Apoptosis; Arginine; bacterial toxins; Binding; bioinformatics; Crystal structure; crystallography; Deoxyribonucleic acid; DNA; DNA modification; DNA-binding motif; enzyme kinetics; Enzymes; Fluorescence; Guanine; Lysine; Molecular dynamics; NAD; Parasitic diseases; Proteins; Reaction mechanisms; Residues; Ribonucleic acid; Ribose; RNA; Streptomyces scabies; Substrates; Toxins; Virulence; Virulence factors; crystallography; molecular modeling; bioinformatics; DNA modification; bacterial toxins; enzyme kinetics; DNA-binding motif
• ISSN: 2072-6651; 2072-6651
• DOI: 10.3390/toxins13010055

Scabin is a mono-ADP-ribosyltransferase toxin/enzyme and possible virulence factor produced by the agriculture pathogen, . 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 -R -N -STT -W -W -(QxE) 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 but are not conserved with Pierisin-1, suggesting that the modification of guanine bases by ADP-ribosyltransferases is divergent even in the Pierisin family.