5DWB image
Entry Detail
PDB ID:
5DWB
Keywords:
Title:
Crystal structure of specific restriction endonuclease AgeI-DNA complex
Biological Source:
PDB Version:
Deposition Date:
2015-09-22
Release Date:
2016-09-28
Method Details:
Experimental Method:
Resolution:
2.40 Å
R-Value Free:
0.21
R-Value Work:
0.17
R-Value Observed:
0.18
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Type-2 restriction enzyme AgeI
Chain IDs:A, B
Chain Length:278
Number of Molecules:2
Biological Source:Thalassobius gelatinovorus
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*TP*TP*CP*GP*AP*CP*CP*GP*GP*TP*CP*GP*A*)-3')
Chain IDs:C, D
Chain Length:13
Number of Molecules:2
Biological Source:synthetic construct
Primary Citation
Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA.
Nucleic Acids Res. 45 3547 3558 (2017)
PMID: 28039325 DOI: 10.1093/nar/gkw1310

Abstact

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.

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