4HTO

Crystal structure of the DBD domain of human DNA ligase IV Apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8068 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis of DNA Ligase IV-Artemis Interaction in Nonhomologous End-Joining.

De Ioannes, P.Malu, S.Cortes, P.Aggarwal, A.K.

(2012) Cell Rep 2: 1505-1512

  • DOI: 10.1016/j.celrep.2012.11.004
  • Primary Citation of Related Structures:  4HTP

  • PubMed Abstract: 
  • DNA ligase IV (LigIV) and Artemis are central components of the nonhomologous end-joining (NHEJ) machinery that is required for V(D)J recombination and the maintenance of genomic integrity in mammalian cells. We report here crystal structures of the ...

    DNA ligase IV (LigIV) and Artemis are central components of the nonhomologous end-joining (NHEJ) machinery that is required for V(D)J recombination and the maintenance of genomic integrity in mammalian cells. We report here crystal structures of the LigIV DNA binding domain (DBD) in both its apo form and in complex with a peptide derived from the Artemis C-terminal region. We show that LigIV interacts with Artemis through an extended hydrophobic surface. In particular, we find that the helix α2 in LigIV-DBD is longer than in other mammalian ligases and presents residues that specifically interact with the Artemis peptide, which adopts a partially helical conformation on binding. Mutations of key residues on the LigIV-DBD hydrophobic surface abolish the interaction. Together, our results provide structural insights into the specificity of the LigIV-Artemis interaction and how the enzymatic activities of the two proteins may be coordinated during NHEJ.


    Organizational Affiliation

    Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, NY 10029, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA ligase 4
A
240Homo sapiensGene Names: LIG4
EC: 6.5.1.1
Find proteins for P49917 (Homo sapiens)
Go to Gene View: LIG4
Go to UniProtKB:  P49917
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8068 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.207 
  • Space Group: F 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 196.236α = 90.00
b = 196.236β = 90.00
c = 196.236γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-01-16
    Type: Database references
  • Version 1.2: 2017-10-25
    Type: Author supporting evidence