7YCW

Crystal Form 1 of Truncated Antitoxin ParD (2-54,containg RHH domain) from Pseudoalteromonas rubra

Summary for 7YCW

• Entry DOI: 10.2210/pdb7ycw/pdb
• Descriptor: Antitoxin ParD (2 entities in total)
• Functional Keywords: rhh, transcription factor, toxin antitoxin system, antitoxin
• Biological source: Pseudoalteromonas rubra
• Total number of polymer chains: 4
• Total formula weight: 28267.62

Authors

Wang, C.C.,Niu, C.Y.,Niu, L.W. (deposition date: 2022-07-01, release date: 2022-09-21, Last modification date: 2023-11-29)

Primary citation

Wang, C.,Niu, C.,Hidayatullah, K.M.,Xue, L.,Zhu, Z.,Niu, L.
Structural insights into the PrpTA toxin-antitoxin system in Pseudoalteromonas rubra.
Front Microbiol, 13:1053255-1053255, 2022

PubMed Abstract: Bacteria could survive stresses by a poorly understood mechanism that contributes to the emergence of bacterial persisters exhibiting multidrug tolerance (MDT). Recently, module was found to encode a toxin PrpT and corresponding cognate antidote PrpA. In this study, we first reported multiple individual and complex structures of PrpA and PrpT, which uncovered the high-resolution three-dimensional structure of the PrpT:PrpA:PrpT heterotetramer with the aid of size exclusion chromatography-multi-angle light scattering experiments (SEC-MALS). PrpT:PrpA:PrpT is composed of a PrpA homodimer and two PrpT monomers which are relatively isolated from each other and from ParE family. The superposition of antitoxin monomer structures from these structures highlighted the flexible C-terminal domain (CTD). A striking conformational change in the CTDs of PrpA homodimer depolymerized from homotetramer was provoked upon PrpT binding, which accounts for the unique PrpT-PrpA mutual interactions and further neutralizes the toxin PrpT. PrpA-form I and II crystal structures both contain a doughnut-shaped hexadecamer formed by eight homodimers organized in a cogwheel-like form inter-dimer interface dominated by salt bridges and hydrogen bonds. Moreover, PrpA tends to exist in solution as a homodimer other than a homotetramer (SEC-MALS) in the absence of flexible CTD. Multiple multi-dimers, tetramer and hexamer included, of PrpA mediated by the symmetric homodimer interface and the complicated inter-dimer interface could be observed in the solution. SEC-MALS assays highlighted that phosphate buffer (PB) and the increase in the concentration appear to be favorable for the PrpA oligomerization in the solution. Taken together with previous research, a model of PrpA homotetramer in complex with promoter and the improved mechanism underlying how PrpTA controls the plasmid replication were proposed here.

PubMed: 36504814
DOI: 10.3389/fmicb.2022.1053255

Experimental method

X-RAY DIFFRACTION (2.2 Å)