PDBsum entry 1lvm

Viral protein

PDB id: 1lvm

Contents

Protein chains

229 a.a. *

Ligands

ACE-GLU-ASN-LEU-TYR-PHE-GLN ×2

GLU-ALA-THR-GLN-LEU-MET-ASN

Waters ×574

* Residue conservation analysis

PDB id:

1lvm

Name:

Viral protein

Title:

Catalytically active tobacco etch virus protease complexed with product

Structure:

Catalytic domain of the nuclear inclusion protein a (nia). Chain: a, b. Fragment: residues 1-221. Engineered: yes. Mutation: yes. Oligopeptide substrate for the protease. Chain: c, d. Fragment: residues 302-310. Engineered: yes.

Source:

Tobacco etch virus. Organism_taxid: 12227. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.171 R-free: 0.230

Authors:

J.Phan,A.Zdanov,A.G.Evdokimov,J.E.Tropea,H.K.Peters Iii,R.B.Kapust, M.Li,A.Wlodawer,D.S.Waugh

Key ref:

J.Phan et al. (2002). Structural basis for the substrate specificity of tobacco etch virus protease. J Biol Chem, 277, 50564-50572. PubMed id: 12377789 DOI: 10.1074/jbc.M207224200

Date:

28-May-02 Release date: 27-Nov-02

Protein chains

P04517  (POLG_TEV) -  Genome polyprotein from Tobacco etch virus

Seq: 3054 a.a.

Struc: 229 a.a.*

* PDB and UniProt seqs differ at 9 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 3: E.C.3.4.21.- - ?????
• Enzyme class 4: E.C.3.4.22.44 - nuclear-inclusion-a endopeptidase.
• Reaction: Hydrolyzes glutaminyl bonds, and activity is further restricted by preferences for the amino acids in P6 - P1' that vary with the species of potyvirus, e.g. Glu-Xaa-Xaa-Tyr-Xaa-Gln+(Ser or Gly) for the enzyme from tobacco etch virus. The natural substrate is the viral polyprotein, but other proteins and oligopeptides containing the appropriate consensus sequence are also cleaved.
• Enzyme class 5: E.C.3.4.22.45 - helper-component proteinase.
• Reaction: Hydrolyzes a Gly-|-Gly bond at its own C-terminus, commonly in the sequence -Tyr-Xaa-Val-Gly-|-Gly, in the processing of the potyviral polyprotein.
• Enzyme class 6: E.C.3.6.4.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1074/jbc.M207224200

J Biol Chem 277:50564-50572 (2002)

PubMed id: 12377789

Structural basis for the substrate specificity of tobacco etch virus protease.

J.Phan, A.Zdanov, A.G.Evdokimov, J.E.Tropea, H.K.Peters, R.B.Kapust, M.Li, A.Wlodawer, D.S.Waugh.

ABSTRACT

Because of its stringent sequence specificity, the 3C-type protease from tobacco etch virus (TEV) is frequently used to remove affinity tags from recombinant proteins. It is unclear, however, exactly how TEV protease recognizes its substrates with such high selectivity. The crystal structures of two TEV protease mutants, inactive C151A and autolysis-resistant S219D, have now been solved at 2.2- and 1.8-A resolution as complexes with a substrate and product peptide, respectively. The enzyme does not appear to have been perturbed by the mutations in either structure, and the modes of binding of the product and substrate are virtually identical. Analysis of the protein-ligand interactions helps to delineate the structural determinants of substrate specificity and provides guidance for reengineering the enzyme to further improve its utility for biotechnological applications.

Selected figure(s)

Figure 1.
Fig. 1. Ribbon models of the TEV (C151A) and TEV(S219D) protease structures. A, stereo diagram of the S219D monomer (molecule A). The residues that compose the catalytic triad and the N-terminal His tag are depicted as ball-and-stick models (carbon, violet; nitrogen, blue; oxygen, red; and sulfur, yellow). The peptide product is also colored blue to distinguish it from the protein. B, the C151A dimer. C, the S219D dimer. Molecule B (red) is shown in the same orientation in B and C to illustrate the difference between the two dimers. The peptides are colored blue. Residue 151, which is Ala in the C151A protease and Cys in the S219D protease, is depicted as a ball-and-stick model. Residues 230-236, which are visible only in molecule A of the S219D protease, are colored yellow.

Figure 4.
Fig. 4. Stereo diagram of the peptide substrate bound to TEV (C151A) protease. A ribbon model of the enzyme active-site cleft and a ball-and-stick model of the peptide substrate are overlaid on difference electron density contoured at 1.5 from an omit map. The carbon atoms in the substrate and the catalytic triad residues in the protease are colored yellow and green, respectively.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 50564-50572) copyright 2002.

Figures were selected by an automated process.