6BCF

I-LtrI G183A bound to cognate substrate (pre-cleavage complex)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.242 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Active site residue identity regulates cleavage preference of LAGLIDADG homing endonucleases.

McMurrough, T.A.Brown, C.M.Zhang, K.Hausner, G.Junop, M.S.Gloor, G.B.Edgell, D.R.

(2018) Nucleic Acids Res 46: 11990-12007

  • DOI: https://doi.org/10.1093/nar/gky976
  • Primary Citation of Related Structures:  
    6BCE, 6BCF, 6BCG, 6BCI, 6BCN, 6BCT

  • PubMed Abstract: 

    LAGLIDADG homing endonucleases (meganucleases) are site-specific mobile endonucleases that can be adapted for genome-editing applications. However, one problem when reprogramming meganucleases on non-native substrates is indirect readout of DNA shape and flexibility at the central 4 bases where cleavage occurs. To understand how the meganuclease active site regulates DNA cleavage, we used functional selections and deep sequencing to profile the fitness landscape of 1600 I-LtrI and I-OnuI active site variants individually challenged with 67 substrates with central 4 base substitutions. The wild-type active site was not optimal for cleavage on many substrates, including the native I-LtrI and I-OnuI targets. Novel combinations of active site residues not observed in known meganucleases supported activity on substrates poorly cleaved by the wild-type enzymes. Strikingly, combinations of E or D substitutions in the two metal-binding residues greatly influenced cleavage activity, and E184D variants had a broadened cleavage profile. Analyses of I-LtrI E184D and the wild-type proteins co-crystallized with the non-cognate AACC central 4 sequence revealed structural differences that correlated with kinetic constants for cleavage of individual DNA strands. Optimizing meganuclease active sites to enhance cleavage of non-native central 4 target sites is a straightforward addition to engineering workflows that will expand genome-editing applications.


  • Organizational Affiliation

    Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein 3/homing endonuclease-like fusion proteinA [auth D],
D [auth A],
G,
J
315Leptographium truncatumMutation(s): 1 
Gene Names: HEG fusionrps3
UniProt
Find proteins for C7SWF3 (Leptographium truncatum)
Explore C7SWF3 
Go to UniProtKB:  C7SWF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7SWF3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (26-MER)B [auth E],
E [auth B],
H,
K
26Leptographium truncatum
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (26-MER)C [auth F],
F [auth C],
I,
L
26Leptographium truncatum
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
M [auth D]
N [auth D]
O [auth D]
P [auth A]
Q [auth A]
M [auth D],
N [auth D],
O [auth D],
P [auth A],
Q [auth A],
R [auth B],
S [auth G],
T [auth G],
U [auth H],
V [auth J],
W [auth J],
X [auth L]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.242 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.956α = 90.12
b = 66.77β = 90.08
c = 169.414γ = 90.06
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2018-11-07
    Changes: Data collection, Database references
  • Version 1.2: 2018-12-26
    Changes: Data collection, Database references
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description