3KO2

I-MsoI re-designed for altered DNA cleavage specificity (-7C)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs.

Ashworth, J.Taylor, G.K.Havranek, J.J.Quadri, S.A.Stoddard, B.L.Baker, D.

(2010) Nucleic Acids Res. 38: 5601-5608

  • DOI: 10.1093/nar/gkq283
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Site-specific homing endonucleases are capable of inducing gene conversion via homologous recombination. Reprogramming their cleavage specificities allows the targeting of specific biological sites for gene correction or conversion. We used computati ...

    Site-specific homing endonucleases are capable of inducing gene conversion via homologous recombination. Reprogramming their cleavage specificities allows the targeting of specific biological sites for gene correction or conversion. We used computational protein design to alter the cleavage specificity of I-MsoI for three contiguous base pair substitutions, resulting in an endonuclease whose activity and specificity for its new site rival that of wild-type I-MsoI for the original site. Concerted design for all simultaneous substitutions was more successful than a modular approach against individual substitutions, highlighting the importance of context-dependent redesign and optimization of protein-DNA interactions. We then used computational design based on the crystal structure of the designed complex, which revealed significant unanticipated shifts in DNA conformation, to create an endonuclease that specifically cleaves a site with four contiguous base pair substitutions. Our results demonstrate that specificity switches for multiple concerted base pair substitutions can be computationally designed, and that iteration between design and structure determination provides a route to large scale reprogramming of specificity.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. ashwortj@u.washington.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Site-specific DNA endonuclease I-MsoI
A, B, F, G
170Monomastix sp. (strain OKE-1)Mutation(s): 4 
Gene Names: orf170
Find proteins for C0JWR6 (Monomastix sp. (strain OKE-1))
Go to UniProtKB:  C0JWR6
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*CP*AP*GP*AP*CP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3'C,H24N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*GP*TP*CP*TP*GP*C)-3'D,I24N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, C, F, H
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.248 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 49.031α = 81.66
b = 70.006β = 70.00
c = 72.258γ = 89.48
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
CrystalCleardata collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance