› 1evw

X-ray diffraction
3.1Å resolution

L116A MUTANT OF THE HOMING ENDONUCLEASE I-PPOI COMPLEXED TO HOMING SITE DNA.

Released:
DOI: 10.2210/pdb1evw/pdb
PDB entry 1evw coloured by chain, front view.
PDB entry 1evw coloured by chain, side view.
PDB entry 1evw coloured by chain, top view.
Source organism: Physarum polycephalum
Primary publication:
Conformational changes and cleavage by the homing endonuclease I-PpoI: a critical role for a leucine residue in the active site.
Galburt EA, Chadsey MS, Jurica MS, Chevalier BS, Erho D, Tang W, Monnat RJ, Stoddard BL
J Mol Biol 300 877-87 (2000)
PMID: 10891275

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113772 (preferred)
Entry contents:
1 distinct polypeptide molecule
4 distinct DNA molecules
Macromolecules (5 distinct):
Intron-encoded endonuclease I-PpoI Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 163 amino acids
Theoretical weight: 17.77 KDa
Source organism: Physarum polycephalum
Expression system: Escherichia coli
UniProt:
  • Canonical: Q94702 (Residues: 1-163; Coverage: 100%)
Sequence domains: Zinc-binding loop region of homing endonuclease
Structure domains: Homing Intron 3 (I-ppo) Encoded Endonuclease; Chain A
DNA (5'-D(*TP*GP*GP*CP*TP*AP*CP*CP*TP*TP*AP*A)-3') Chains: E, G
Molecule details ›
Chains: E, G
Length: 12 nucleotides
Theoretical weight: 3.64 KDa
Source organism: Physarum polycephalum
Expression system: Not provided
DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3') Chains: M, N
Molecule details ›
Chains: M, N
Length: 8 nucleotides
Theoretical weight: 2.48 KDa
Source organism: Physarum polycephalum
Expression system: Not provided
DNA (5'-D(*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3') Chains: F, H
Molecule details ›
Chains: F, H
Length: 12 nucleotides
Theoretical weight: 3.61 KDa
Source organism: Physarum polycephalum
Expression system: Not provided
DNA (5'-D(P*GP*GP*TP*AP*GP*CP*CP*A)-3') Chains: O, P
Molecule details ›
Chains: O, P
Length: 8 nucleotides
Theoretical weight: 2.45 KDa
Source organism: Physarum polycephalum
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 4 x MG
Ligand ZN 8 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: C2
Unit cell:
a: 182Å b: 73.1Å c: 92.7Å
α: 90° β: 95.4° γ: 90°
R-values:
R R work R free
0.273 0.273 0.32
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility.
Chevalier et al. (2001)
1 more