› 1jva

X-ray diffraction
2.1Å resolution

CRYSTAL STRUCTURE OF THE VMA1-DERIVED ENDONUCLEASE BEARING THE N AND C EXTEIN PROPEPTIDES

Released:
DOI: 10.2210/pdb1jva/pdb
PDB entry 1jva coloured by chain, front view.
PDB entry 1jva coloured by chain, side view.
PDB entry 1jva coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Protein-splicing reaction via a thiazolidine intermediate: crystal structure of the VMA1-derived endonuclease bearing the N and C-terminal propeptides.
Mizutani R, Nogami S, Kawasaki M, Ohya Y, Anraku Y, Satow Y
J Mol Biol 316 919-29 (2002)
PMID: 11884132

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-147903 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Endonuclease PI-SceI Chains: A, B
Molecule details ›
Chains: A, B
Length: 475 amino acids
Theoretical weight: 53.15 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P17255 (Residues: 273-747; Coverage: 44%)
Gene names: CLS8, D1286, TFP1, VMA1, YDL185W
Sequence domains:
Structure domains:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL40B2
Spacegroup: P1
Unit cell:
a: 66.178Å b: 68.846Å c: 58.524Å
α: 103.1° β: 98.79° γ: 78.98°
R-values:
R R work R free
0.2 0.198 0.24
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Protein splicing in cis and in trans.
Saleh et al. (2006)
4 more

6 mentions without citation

Reflections on protein splicing: structures, functions and mechanisms.
Anraku et al. (2009)
5 more