5DWC

Crystal structure of restriction endonuclease AgeI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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

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

(2017) Nucleic Acids Res. 45: 3547-3558

  • DOI: 10.1093/nar/gkw1310
  • Primary Citation of Related Structures:  

  • PubMed 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 ...

    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.


    Organizational Affiliation

    Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Type-2 restriction enzyme AgeI
A
278Thalassobius gelatinovorusMutation(s): 0 
Gene Names: ageIR
EC: 3.1.21.4
Find proteins for Q9KHV6 (Thalassobius gelatinovorus)
Go to UniProtKB:  Q9KHV6
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.213α = 90.00
b = 59.269β = 90.00
c = 120.915γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
MxCuBEdata collection
SCALAdata scaling
MOSFLMdata reduction
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Council of LithuaniaLithuaniaMIP-41/2013

Revision History 

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2017-01-11
    Type: Database references
  • Version 1.2: 2017-05-03
    Type: Database references
  • Version 1.3: 2018-01-17
    Type: Data collection