6VPA

Scabin (N110A) toxin from Streptomyces scabies

Summary for 6VPA

• Entry DOI: 10.2210/pdb6vpa/pdb
• Descriptor: Scabin (2 entities in total)
• Functional Keywords: transferase, toxin
• Biological source: Streptomyces scabiei (strain 87.22)
• Total number of polymer chains: 1
• Total formula weight: 21814.15

Authors

Lyons, B.,Lidster, T.,Merrill, A.R. (deposition date: 2020-02-02, release date: 2021-01-13, Last modification date: 2024-10-30)

Primary citation

Vatta, M.,Lyons, B.,Heney, K.A.,Lidster, T.,Merrill, A.R.
Mapping the DNA-Binding Motif of Scabin Toxin, a Guanine Modifying Enzyme from Streptomyces scabies .
Toxins, 13:-, 2021

PubMed Abstract: 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.

PubMed: 33450958
DOI: 10.3390/toxins13010055

Experimental method

X-RAY DIFFRACTION (1.5 Å)