5LWA

TURNIP YELLOW MOSAIC VIRUS PROTEASE/DEUBIQUITINASE DOMAIN, I847A MUTANT

DOI: 10.2210/pdb5LWA/pdb

Classification: HYDROLASE
Organism(s): Turnip yellow mosaic virus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-09-15 Released: 2017-10-25
Deposition Author(s): Ayach, M., Bressanelli, S.
Funding Organization(s): French National Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.201
R-Value Work: 0.169
R-Value Observed: 0.172

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

A mobile loop near the active site acts as a switch between the dual activities of a viral protease/deubiquitinase.

Jupin, I., Ayach, M., Jomat, L., Fieulaine, S., Bressanelli, S.

(2017) PLoS Pathog 13: e1006714-e1006714

PubMed: 29117247 Search on PubMedSearch on PubMed Central
DOI: 10.1371/journal.ppat.1006714
Primary Citation of Related Structures:
5LWA, 5LW5

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.

Related Citations:

Crystallization of mutants of Turnip yellow mosaic virus protease/ubiquitin hydrolase designed to prevent protease self-recognition.
Ayach, M., Bressanelli, S.
(2015) Acta Crystallogr F Struct Biol Commun 71: 405

Organizational Affiliation:

Institute for Integrative Biology of the Cell, CEA-CNRS-Univ Paris-Saclay, Gif sur Yvette, France.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA replicase polyprotein	A, B	159	Turnip yellow mosaic virus	Mutation(s): 1 EC: 2.1.1 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.6.4 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
Find proteins for P10358 (Turnip yellow mosaic virus) Explore P10358 Go to UniProtKB: P10358
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Reference Sequence