3WRY

Crystal structure of helicase complex 2

Summary for 3WRY

• Entry DOI: 10.2210/pdb3wry/pdb
• Related: 3VKW 3WRV 3WRW 3WRX
• Descriptor: Tm-1 protein, Replicase large subunit, PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER, ... (6 entities in total)
• Functional Keywords: alpha/beta domain, helicase, transferase
• Biological source: Solanum lycopersicum (Tomato); More
• Total number of polymer chains: 4
• Total formula weight: 195518.52

Authors

Matsumura, H.,Katoh, E. (deposition date: 2014-02-27, release date: 2014-08-13, Last modification date: 2024-03-20)

Primary citation

Ishibashi, K.,Kezuka, Y.,Kobayashi, C.,Kato, M.,Inoue, T.,Nonaka, T.,Ishikawa, M.,Matsumura, H.,Katoh, E.
Structural basis for the recognition-evasion arms race between Tomato mosaic virus and the resistance gene Tm-1
Proc.Natl.Acad.Sci.USA, 111:E3486-E3495, 2014

PubMed Abstract: The tomato mosaic virus (ToMV) resistance gene Tm-1 encodes a protein that shows no sequence homology to functionally characterized proteins. Tm-1 binds ToMV replication proteins and thereby inhibits replication complex formation. ToMV mutants that overcome this resistance have amino acid substitutions in the helicase domain of the replication proteins (ToMV-Hel). A small region of Tm-1 in the genome of the wild tomato Solanum habrochaites has been under positive selection during its antagonistic coevolution with ToMV. Here we report crystal structures for the N-terminal inhibitory domains of Tm-1 and a natural Tm-1 variant with an I91-to-T substitution that has a greater ability to inhibit ToMV RNA replication and their complexes with ToMV-Hel. Each complex contains a Tm-1 dimer and two ToMV-Hel monomers with the interfaces between Tm-1 and ToMV-Hel bridged by ATP. Residues in ToMV-Hel and Tm-1 involved in antagonistic coevolution are found at the interface. The structural differences between ToMV-Hel in its free form and in complex with Tm-1 suggest that Tm-1 affects nucleoside triphosphatase activity of ToMV-Hel, and this effect was confirmed experimentally. Molecular dynamics simulations of complexes formed by Tm-1 with ToMV-Hel variants showed how the amino acid changes in ToMV-Hel impair the interaction with Tm-1 to overcome the resistance. With these findings, together with the biochemical properties of the interactions between ToMV-Hel and Tm-1 variants and effects of the mutations in the polymorphic residues of Tm-1, an atomic view of a step-by-step coevolutionary arms race between a plant resistance protein and a viral protein emerges.

PubMed: 25092327
DOI: 10.1073/pnas.1407888111

Experimental method

X-RAY DIFFRACTION (2.3 Å)