4B20

Structural basis of DNA loop recognition by Endonuclease V


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.227 

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Literature

Structural Basis of DNA Loop Recognition by Endonuclease V.

Rosnes, I.Rowe, A.D.Vik, E.S.Forstrom, R.J.Alseth, I.Bjoras, M.Dalhus, B.

(2013) Structure 21: 257

  • DOI: 10.1016/j.str.2012.12.007

  • PubMed Abstract: 
  • The DNA repair enzyme endonuclease V (EndoV) recognizes and cleaves DNA at deaminated adenine lesions (hypoxanthine). In addition, EndoV cleaves DNA containing various helical distortions such as loops, hairpins, and flaps. To understand the molecula ...

    The DNA repair enzyme endonuclease V (EndoV) recognizes and cleaves DNA at deaminated adenine lesions (hypoxanthine). In addition, EndoV cleaves DNA containing various helical distortions such as loops, hairpins, and flaps. To understand the molecular basis of EndoV's ability to recognize and incise DNA structures with helical distortions, we solved the crystal structure of Thermotoga maritima EndoV in complex with DNA containing a one-nucleotide loop. The structure shows that a strand-separating wedge is crucial for DNA loop recognition, with DNA strands separated precisely at the helical distortion. The additional nucleotide forming the loop rests on the surface of the wedge, while the normal adenine opposite the loop is flipped into a base recognition pocket. Our data show a different principle for DNA loop recognition and cleavage by EndoV, in which a coordinated action of a DNA-intercalating wedge and a base pocket accommodating a flipped normal base facilitate strand incision.


    Organizational Affiliation

    Department of Microbiology, Oslo University Hospital, Rikshospitalet, P.O. Box 4950, Nydalen, N-0424 Oslo, Norway.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDONUCLEASE V
A, B
225Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 0 
Gene Names: nfi
EC: 3.1.21.7
Find proteins for Q9X2H9 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9X2H9
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*CP*GP*AP*CP*AP*GP)-3'C,F7N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*AP*TP*CP*TP*TP*GP*TP*CP*GP*CP)-3'D,G10N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.227 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 55.231α = 90.00
b = 135.370β = 90.00
c = 194.993γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
CNSphasing
MOSFLMdata reduction
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-17
    Type: Initial release