5LW5

TURNIP YELLOW MOSAIC VIRUS PROTEASE/DEUBIQUITINASE DOMAIN, DELTAC5 MUTANT

Summary for 5LW5

• Entry DOI: 10.2210/pdb5lw5/pdb
• Related: 4A5U
• Descriptor: RNA replicase polyprotein (2 entities in total)
• Functional Keywords: cysteine protease, deubiquitinase, virus replicase polyprotein, hydrolase
• Biological source: Turnip yellow mosaic virus
• Cellular location: Methyltransferase/Protease: Host chloroplast envelope. Putative helicase: Host chloroplast envelope. RNA-directed RNA polymerase: Host chloroplast envelope: P10358
• Total number of polymer chains: 2
• Total formula weight: 34240.07

Authors

Ayach, M.,Bressanelli, S. (deposition date: 2016-09-15, release date: 2017-10-25, Last modification date: 2024-01-17)

Primary citation

Jupin, I.,Ayach, M.,Jomat, L.,Fieulaine, S.,Bressanelli, S.
A mobile loop near the active site acts as a switch between the dual activities of a viral protease/deubiquitinase.
PLoS Pathog., 13:e1006714-e1006714, 2017

PubMed Abstract: The positive-strand RNA virus Turnip yellow mosaic virus (TYMV) encodes an ovarian tumor (OTU)-like protease/deubiquitinase (PRO/DUB) protein domain involved both in proteolytic processing of the viral polyprotein through its PRO activity, and in removal of ubiquitin chains from ubiquitylated substrates through its DUB activity. Here, the crystal structures of TYMV PRO/DUB mutants and molecular dynamics simulations reveal that an idiosyncratic mobile loop participates in reversibly constricting its unusual catalytic site by adopting "open", "intermediate" or "closed" conformations. The two cis-prolines of the loop form a rigid flap that in the most closed conformation zips up against the other side of the catalytic cleft. The intermediate and closed conformations also correlate with a reordering of the TYMV PRO/DUB catalytic dyad, that then assumes a classical, yet still unusually mobile, OTU DUB alignment. Further structure-based mutants designed to interfere with the loop's mobility were assessed for enzymatic activity in vitro and in vivo, and were shown to display reduced DUB activity while retaining PRO activity. This indicates that control of the switching between the dual PRO/DUB activities resides prominently within this loop next to the active site. Introduction of mutations into the viral genome revealed that the DUB activity contributes to the extent of viral RNA accumulation both in single cells and in whole plants. In addition, the conformation of the mobile flap was also found to influence symptoms severity in planta. Such mutants now provide powerful tools with which to study the specific roles of reversible ubiquitylation in viral infection.

PubMed: 29117247
DOI: 10.1371/journal.ppat.1006714

Experimental method

X-RAY DIFFRACTION (1.649 Å)