5DWA: Crystal Structure Of Pre-specific Restriction Endonuclease Agei-dna Complex

Although all Type II restriction endonucleases catalyze phosphodiester bond hydrolysis within or close to their DNA target sites, they form different oligomeric assemblies ranging from monomers, dimers, tetramers to higher order oligomers to generate a double strand break in DNA. Type IIP restriction endonuclease AgeI recognizes a palindromic sequence 5-A/CCGGT-3 and cuts it ('/' denotes the cleavage site) producing staggered DNA ends. Here, we present crystal structures of AgeI in apo and DNA-bound forms. The structure of AgeI is similar to the restriction enzymes that share in their target sites a conserved CCGG tetranucleotide and a cleavage pattern. Structure analysis and biochemical data indicate, that AgeI is a monomer in the apo-form both in the crystal and in solution, however, it binds and cleaves the palindromic target site as a dimer. DNA cleavage mechanism of AgeI is novel among Type IIP restriction endonucleases.
PDB ID: 5DWADownload
MMDB ID: 143682
PDB Deposition Date: 2015/9/22
Updated in MMDB: 2016/10
Experimental Method:
x-ray diffraction
Resolution: 1.5  Å
Source Organism:
Thalassobius gelatinovorus
Similar Structures:
Biological Unit for 5DWA: tetrameric; determined by author and by software (PISA)
Molecular Components in 5DWA
Label Count Molecule
Proteins (2 molecules)
Type-2 Restriction Enzyme Agei
Molecule annotation
Nucleotide(1 molecule)
DNA (5'-d(*tp*cp*gp*ap*cp*cp*gp*gp*tp*cp*g*)-3')
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB