4HTP

Crystal structure of the DBD domain of human DNA ligase IV bound to Artemis peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2502 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  

  • 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, B
240Homo sapiensMutation(s): 0 
Gene Names: LIG4
EC: 6.5.1.1
Find proteins for P49917 (Homo sapiens)
Go to Gene View: LIG4
Go to UniProtKB:  P49917
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein artemis
C, E
11Homo sapiensMutation(s): 0 
Gene Names: DCLRE1C (ARTEMIS, ASCID, SCIDA, SNM1C)
EC: 3.1.-.-
Find proteins for Q96SD1 (Homo sapiens)
Go to Gene View: DCLRE1C
Go to UniProtKB:  Q96SD1
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2502 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 61.210α = 90.00
b = 72.830β = 90.00
c = 158.050γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
HKL-2000data collection
PHASERphasing

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