5O6G

Structures and dynamics of mesophilic variants from the homing endonuclease I-DmoI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.177 

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Literature

Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI.

Alba, J.Marcaida, M.J.Prieto, J.Montoya, G.Molina, R.D'Abramo, M.

(2017) J. Comput. Aided Mol. Des. 31: 1063-1072

  • DOI: 10.1007/s10822-017-0087-5
  • Primary Citation of Related Structures:  5O6I

  • PubMed Abstract: 
  • I-DmoI, from the hyperthermophilic archaeon Desulfurococcus mobilis, belongs to the LAGLIDADG homing endonuclease protein family. Its members are highly specific enzymes capable of recognizing long DNA target sequences, thus providing potential tools ...

    I-DmoI, from the hyperthermophilic archaeon Desulfurococcus mobilis, belongs to the LAGLIDADG homing endonuclease protein family. Its members are highly specific enzymes capable of recognizing long DNA target sequences, thus providing potential tools for genome manipulation. Working towards this particular application, many efforts have been made to generate mesophilic variants of I-DmoI that function at lower temperatures than the wild-type. Here, we report a structural and computational analysis of two I-DmoI mesophilic mutants. Despite very limited structural variations between the crystal structures of these variants and the wild-type, a different dynamical behaviour near the cleavage sites is observed. In particular, both the dynamics of the water molecules and the protein perturbation effect on the cleavage site correlate well with the changes observed in the experimental enzymatic activity.


    Organizational Affiliation

    Department of Chemistry, Sapienza University of Rome, P.le A. Moro, 5, 00185, Rome, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Homing endonuclease I-DmoI
A, D, G
200Desulfurococcus mobilisEC: 3.1.-.-
Find proteins for P21505 (Desulfurococcus mobilis)
Go to UniProtKB:  P21505
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (25-MER)B,E,H25synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (25-MER)C,F,I25synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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Download CCD File 
A, D, G
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
G
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 107.280α = 90.00
b = 70.500β = 119.89
c = 107.150γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2018-01-03
    Type: Database references