3EH8

Crystal structure of Y2 I-AniI variant (F13Y/S111Y)/DNA complex with calcium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Optimization of in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation.

Takeuchi, R.Certo, M.Caprara, M.G.Scharenberg, A.M.Stoddard, B.L.

(2009) Nucleic Acids Res. 37: 877-890

  • DOI: 10.1093/nar/gkn1007

  • PubMed Abstract: 
  • The LAGLIDADG homing endonuclease (LHE) I-AniI has adopted an extremely efficient secondary RNA splicing activity that is beneficial to its host, balanced against inefficient DNA cleavage. A selection experiment identified point mutations in the enzy ...

    The LAGLIDADG homing endonuclease (LHE) I-AniI has adopted an extremely efficient secondary RNA splicing activity that is beneficial to its host, balanced against inefficient DNA cleavage. A selection experiment identified point mutations in the enzyme that act synergistically to improve endonuclease activity. The amino-acid substitutions increase target affinity, alter the thermal cleavage profile and significantly increase targeted recombination in transfected cells. The RNA splicing activity is not affected by these mutations. The improvement in DNA cleavage activity is largely focused on one of the enzyme's two active sites, corresponding to a rearrangement of a lysine residue hypothesized to act as a general base. Most of the constructs isolated in the screen contain one or more mutations that revert an amino-acid identity to a residue found in one or more close homologues of I-AniI. This implies that mutations that have previously reduced the endonuclease activity of I-AniI are identified and reversed, sometimes in combination with additional 'artificial' mutations, to optimize its in vivo activity.


    Organizational Affiliation

    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Intron-encoded DNA endonuclease I-AniI
A, D, G
254Emericella nidulansMutation(s): 4 
Gene Names: I-AniI
Find proteins for P03880 (Emericella nidulans)
Go to UniProtKB:  P03880
Entity ID: 2
MoleculeChainsLengthOrganism
31-MERB,E,H31N/A
Entity ID: 3
MoleculeChainsLengthOrganism
31-MERC,F,I31N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, D, G
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.198 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 107.555α = 90.00
b = 192.603β = 90.00
c = 161.800γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-01-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2013-06-26
    Type: Database references