› 1lvm

X-ray diffraction
1.8Å resolution

CATALYTICALLY ACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH PRODUCT

Released:
DOI: 10.2210/pdb1lvm/pdb
PDB entry 1lvm coloured by chain, front view.
PDB entry 1lvm coloured by chain, side view.
PDB entry 1lvm coloured by chain, top view.
Source organism: Tobacco etch virus
Primary publication:
Structural basis for the substrate specificity of tobacco etch virus protease.
Phan J, Zdanov A, Evdokimov AG, Tropea JE, Peters HK, Kapust RB, Li M, Wlodawer A, Waugh DS
J Biol Chem 277 50564-72 (2002)
PMID: 12377789

Function and Biology Details

Reactions catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
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.
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.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
hetero dimer
hetero pentamer
Assembly name:
PDBe Complex ID:
PDB-CPX-137892 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Nuclear inclusion protein A Chains: A, B
Molecule details ›
Chains: A, B
Length: 229 amino acids
Theoretical weight: 26.15 KDa
Source organism: Tobacco etch virus
Expression system: Escherichia coli
UniProt:
  • Canonical: P04517 (Residues: 2038-2258; Coverage: 7%)
Sequence domains: Peptidase family C4
Structure domains: Trypsin-like serine proteases
Capsid protein Chains: C, D
Molecule details ›
Chains: C, D
Length: 10 amino acids
Theoretical weight: 1.08 KDa
Source organism: Tobacco etch virus
Expression system: Escherichia coli
UniProt:
  • Canonical: P04517 (Residues: 2785-2794; Coverage: 0%)
Nuclear inclusion protein A Chain: E
Molecule details ›
Chain: E
Length: 7 amino acids
Theoretical weight: 806 Da
Source organism: Tobacco etch virus
Expression system: Escherichia coli
UniProt:
  • Canonical: P04517 (Residues: 2267-2273; Coverage: 0%)

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X9B
Spacegroup: P43212
Unit cell:
a: 75.505Å b: 75.505Å c: 183.167Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.171 0.171 0.23
Expression system: Escherichia coli

Quick links

Citations

12 review citations

The protein structures that shape caspase activity, specificity, activation and inhibition.
Fuentes-Prior et al. (2004)
11 more

26 mentions without citation

Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system.
Stynen et al. (2012)
25 more