5DWB

Crystal structure of specific restriction endonuclease AgeI-DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.183 

Starting Model: experimental
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This is version 1.4 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: https://doi.org/10.1093/nar/gkw1310
  • Primary Citation of Related Structures:  
    5DWA, 5DWB, 5DWC

  • 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 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Type-2 restriction enzyme AgeI
A, B
278Thalassovita gelatinovoraMutation(s): 0 
Gene Names: ageIR
EC: 3.1.21.4
UniProt
Find proteins for Q9KHV6 (Thalassovita gelatinovora)
Explore Q9KHV6 
Go to UniProtKB:  Q9KHV6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KHV6
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*TP*CP*GP*AP*CP*CP*GP*GP*TP*CP*GP*A*)-3')
C, D
13synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.587α = 90
b = 87.093β = 99.82
c = 66.521γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Lithuanian Research CouncilLithuaniaMIP-41/2013

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2017-01-11
    Changes: Database references
  • Version 1.2: 2017-05-03
    Changes: Database references
  • Version 1.3: 2019-07-17
    Changes: Data collection, Database references
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Refinement description