6VVF image
Entry Detail
PDB ID:
6VVF
Keywords:
Title:
Scabin (Y129H) toxin from Streptomyces scabies
Biological Source:
PDB Version:
Deposition Date:
2020-02-17
Release Date:
2021-01-20
Method Details:
Experimental Method:
Resolution:
1.75 Å
R-Value Free:
0.20
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Scabin
Mutations:Y129H
Chain IDs:A
Chain Length:195
Number of Molecules:1
Biological Source:Streptomyces scabiei (strain 87.22)
Primary Citation
Mapping the DNA-Binding Motif of Scabin Toxin, a Guanine Modifying Enzyme from Streptomyces scabies .
Toxins 13 ? ? (2021)
PMID: 33450958 DOI: 10.3390/toxins13010055

Abstact

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 Rβ1-RLa-NLc-STTβ2-WPN-WARTT-(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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Primary Citation of related structures