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PDBsum entry 4hto

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protein ligands links
Ligase, DNA binding protein PDB id
4hto
Jmol
Contents
Protein chain
214 a.a.
Ligands
PO4 ×2
Waters ×23
PDB id:
4hto
Name: Ligase, DNA binding protein
Title: Crystal structure of the dbd domain of human DNA ligase iv a
Structure: DNA ligase 4. Chain: a. Fragment: DNA binding domain. Synonym: DNA ligase iv, polydeoxyribonucleotide synthase [a engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: lig4. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.81Å     R-factor:   0.210     R-free:   0.259
Authors: P.E.De Ioannes,A.K.Aggarwal
Key ref: P.De Ioannes et al. (2012). Structural basis of DNA ligase IV-Artemis interaction in nonhomologous end-joining. Cell Rep, 2, 1505-1512. PubMed id: 23219551
Date:
01-Nov-12     Release date:   26-Dec-12    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P49917  (DNLI4_HUMAN) -  DNA ligase 4
Seq:
Struc:
 
Seq:
Struc:
911 a.a.
214 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.5.1.1  - Dna ligase (ATP).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m)
ATP
+ (deoxyribonucleotide)(n)
+ (deoxyribonucleotide)(m)
= AMP
+
diphosphate
Bound ligand (Het Group name = PO4)
matches with 55.56% similarity
+ (deoxyribonucleotide)(n+m)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA repair   2 terms 
  Biochemical function     DNA binding     2 terms  

 

 
    reference    
 
 
Cell Rep 2:1505-1512 (2012)
PubMed id: 23219551  
 
 
Structural basis of DNA ligase IV-Artemis interaction in nonhomologous end-joining.
P.De Ioannes, S.Malu, P.Cortes, A.K.Aggarwal.
 
  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 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.