PDBsum entry 5dwc

Hydrolase

PDB id: 5dwc

Contents

Protein chain

274 a.a.

Waters ×19

PDB id:

5dwc

Name:

Hydrolase

Title:

Crystal structure of restriction endonuclease agei

Structure:

Type-2 restriction enzyme agei. Chain: a. Synonym: r.Agei,endonuclease agei,type ii restriction enzyme agei. Engineered: yes

Source:

Thalassobius gelatinovorus. Organism_taxid: 53501. Gene: ageir. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.50Å R-factor: 0.219 R-free: 0.256

Authors:

G.Tamulaitiene,I.Ramonaite,S.Grazulis,V.Siksnys

Key ref:

G.Tamulaitiene et al. (2017). Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA. Nucleic Acids Res, 45, 3547-3558. PubMed id: 28039325

Date:

22-Sep-15 Release date: 28-Sep-16

Protein chain

Q9KHV6  (T2A1_THAGE) -  Type II restriction enzyme AgeI from Thalassovita gelatinovora

Seq: 278 a.a.

Struc: 274 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.1.21.4 - type Ii site-specific deoxyribonuclease.
• Reaction: Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.
• Cofactor: Mg(2+)

Nucleic Acids Res 45:3547-3558 (2017)

PubMed id: 28039325

Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA.

G.Tamulaitiene, V.Jovaisaite, G.Tamulaitis, I.Songailiene, E.Manakova, M.Zaremba, S.Grazulis, S.Y.Xu, V.Siksnys.

ABSTRACT

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.