4YIS

Crystal Structure of LAGLIDADG Meganuclease I-CpaMI Bound to Uncleaved DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity.

Lambert, A.R.Hallinan, J.P.Shen, B.W.Chik, J.K.Bolduc, J.M.Kulshina, N.Robins, L.I.Kaiser, B.K.Jarjour, J.Havens, K.Scharenberg, A.M.Stoddard, B.L.

(2016) Structure 24: 862-873

  • DOI: 10.1016/j.str.2016.03.024
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • LAGLIDADG meganucleases are DNA cleaving enzymes used for genome engineering. While their cleavage specificity can be altered using several protein engineering and selection strategies, their overall targetability is limited by highly specific indire ...

    LAGLIDADG meganucleases are DNA cleaving enzymes used for genome engineering. While their cleavage specificity can be altered using several protein engineering and selection strategies, their overall targetability is limited by highly specific indirect recognition of the central four base pairs within their recognition sites. In order to examine the physical basis of indirect sequence recognition and to expand the number of such nucleases available for genome engineering, we have determined the target sites, DNA-bound structures, and central four cleavage fidelities of nine related enzymes. Subsequent crystallographic analyses of a meganuclease bound to two noncleavable target sites, each containing a single inactivating base pair substitution at its center, indicates that a localized slip of the mutated base pair causes a small change in the DNA backbone conformation that results in a loss of metal occupancy at one binding site, eliminating cleavage activity.


    Organizational Affiliation

    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, A3-025, Seattle, WA 98109, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Meganuclease I-CpaMI
A, B
295Cryphonectria parasiticaMutation(s): 0 
Gene Names: mtSrRNA I4 (orf416)
Find proteins for O20960 (Cryphonectria parasitica)
Go to UniProtKB:  O20960
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (28-MER)E,C28synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (28-MER)F,D28synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, D, E, F
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 75.869α = 90.00
b = 91.799β = 90.00
c = 139.636γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM105691

Revision History 

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2016-03-30
    Type: Database references
  • Version 1.2: 2016-05-18
    Type: Database references
  • Version 1.3: 2016-06-15
    Type: Database references
  • Version 1.4: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations