6UW0

Engineered variant of I-OnuI meganuclease with improved thermostability and fully altered specificity targeting cholera toxin A subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.228 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

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This is version 1.3 of the entry. See complete history


Literature

Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition.

Lambert, A.R.Hallinan, J.P.Werther, R.Glow, D.Stoddard, B.L.

(2020) Structure 28: 760-775.e8

  • DOI: https://doi.org/10.1016/j.str.2020.04.009
  • Primary Citation of Related Structures:  
    6UVW, 6UW0, 6UWG, 6UWH, 6UWJ, 6UWK

  • PubMed Abstract: 

    The redesign of a macromolecular binding interface and corresponding alteration of recognition specificity is a challenging endeavor that remains recalcitrant to computational approaches. This is particularly true for the redesign of DNA binding specificity, which is highly dependent upon bending, hydrogen bonds, electrostatic contacts, and the presence of solvent and counterions throughout the molecular interface. Thus, redesign of protein-DNA binding specificity generally requires iterative rounds of amino acid randomization coupled to selections. Here, we describe the importance of scaffold thermostability for protein engineering, coupled with a strategy that exploits the protein's specificity profile, to redesign the specificity of a pair of meganucleases toward three separate genomic targets. We determine and describe a series of changes in protein sequence, stability, structure, and activity that accumulate during the engineering process, culminating in fully retargeted endonucleases.


  • Organizational Affiliation

    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., Seattle, WA 98109, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
I-OnuI-e-Therm-bCtxA
A, B
296synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (27-MER)
C, E
27synthetic construct
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (27-MER)
D, F
27synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.246α = 90
b = 79.679β = 90
c = 168.941γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM105691

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2020-05-13
    Changes: Database references
  • Version 1.2: 2020-07-22
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description