3UVF

Expanding LAGALIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.378 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.285 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Expanding LAGLIDADG endonuclease scaffold diversity by rapidly surveying evolutionary sequence space.

Jacoby, K.Metzger, M.Shen, B.W.Certo, M.T.Jarjour, J.Stoddard, B.L.Scharenberg, A.M.

(2012) Nucleic Acids Res 40: 4954-4964

  • DOI: https://doi.org/10.1093/nar/gkr1303
  • Primary Citation of Related Structures:  
    3UVF

  • PubMed Abstract: 

    LAGLIDADG homing endonucleases (LHEs) are a family of highly specific DNA endonucleases capable of recognizing target sequences ≈ 20 bp in length, thus drawing intense interest for their potential academic, biotechnological and clinical applications. Methods for rational design of LHEs to cleave desired target sites are presently limited by a small number of high-quality native LHEs to serve as scaffolds for protein engineering-many are unsatisfactory for gene targeting applications. One strategy to address such limitations is to identify close homologs of existing LHEs possessing superior biophysical or catalytic properties. To test this concept, we searched public sequence databases to identify putative LHE open reading frames homologous to the LHE I-AniI and used a DNA binding and cleavage assay using yeast surface display to rapidly survey a subset of the predicted proteins. These proteins exhibited a range of capacities for surface expression and also displayed locally altered binding and cleavage specificities with a range of in vivo cleavage activities. Of these enzymes, I-HjeMI demonstrated the greatest activity in vivo and was readily crystallizable, allowing a comparative structural analysis. Taken together, our results suggest that even highly homologous LHEs offer a readily accessible resource of related scaffolds that display diverse biochemical properties for biotechnological applications.


  • Organizational Affiliation

    Program in Molecular and Cellular Biology, University of Washington, Box 357275, Seattle, WA 98195, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Intron-encoded DNA endonuclease I-HjeMIA,
D [auth B]
255Trichoderma reeseiMutation(s): 0 
Gene Names: I-AniI
EC: 3.1
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
synthetic oligoB [auth C],
E
28N/A
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
synthetic oligoC [auth D],
F
28N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
J [auth A],
L [auth B],
Q [auth E],
R [auth F]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
M [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
K [auth B]
O [auth E]
G [auth A],
H [auth A],
I [auth A],
K [auth B],
O [auth E],
P [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
N [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.378 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.285 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.591α = 90
b = 73.592β = 90
c = 82.031γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-29
    Type: Initial release
  • Version 1.1: 2012-06-20
    Changes: Database references
  • Version 1.2: 2012-07-18
    Changes: Structure summary
  • Version 1.3: 2012-08-01
    Changes: Structure summary
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description