4UN8

THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 1H INCUBATION IN 5MM MN (STATE 2)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Visualizing Phosphodiester-Bond Hydrolysis by an Endonuclease.

Molina, R., Stella, S., Redondo, P., Gomez, H., Marcaida, M.J., Orozco, M., Prieto, J., Montoya, G.

(2015) Nat Struct Mol Biol 22: 65

  • DOI: 10.1038/nsmb.2932
  • Primary Citation of Related Structures:  
    4D6N, 4D6O, 4UN7, 4UN8, 4UN9, 4UNA, 4UNB, 4UNC, 4UT0

  • PubMed Abstract: 

    • The enzymatic hydrolysis of DNA phosphodiester bonds has been widely studied, but the chemical reaction has not yet been observed. Here we follow the generation of a DNA double-strand break (DSB) by the Desulfurococcus mobilis homing endonuclease I-DmoI, trapping sequential stages of a two-metal-ion cleavage mechanism ...

    The enzymatic hydrolysis of DNA phosphodiester bonds has been widely studied, but the chemical reaction has not yet been observed. Here we follow the generation of a DNA double-strand break (DSB) by the Desulfurococcus mobilis homing endonuclease I-DmoI, trapping sequential stages of a two-metal-ion cleavage mechanism. We captured intermediates of the different catalytic steps, and this allowed us to watch the reaction by 'freezing' multiple states. We observed the successive entry of two metals involved in the reaction and the arrival of a third cation in a central position of the active site. This third metal ion has a crucial role, triggering the consecutive hydrolysis of the targeted phosphodiester bonds in the DNA strands and leaving its position once the DSB is generated. The multiple structures show the orchestrated conformational changes in the protein residues, nucleotides and metals during catalysis.

    Organizational Affiliation: 

    1] Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain. [2] Macromolecular Crystallography Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HOMING ENDONUCLEASE I-DMOIA, D199Desulfurococcus mucosusMutation(s): 0 
EC: 3.1
UniProt
Find proteins for P21505 (Desulfurococcus mucosus)
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Go to UniProtKB:  P21505
Entity Groups  
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UniProt GroupP21505
Protein Feature View
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
HOMING ENDONUCLEASE I-DMOIG199Desulfurococcus mucosusMutation(s): 0 
EC: 3.1
UniProt
Find proteins for P21505 (Desulfurococcus mucosus)
Explore P21505 
Go to UniProtKB:  P21505
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21505
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
25MERB, E, H 25synthetic construct
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
25MERC, F, I 25synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN
Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
L [auth D],
M [auth D],
N [auth G],
J [auth A],
K [auth A],
L [auth D],
M [auth D],
N [auth G],
O [auth G]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.186α = 90
b = 70.851β = 119.55
c = 107.232γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-17
    Type: Initial release
  • Version 1.1: 2015-01-21
    Changes: Database references