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PDBsum entry 4htp

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protein ligands Protein-protein interface(s) links
Ligase/hydrolase PDB id
4htp
Jmol
Contents
Protein chains
221 a.a.
Ligands
ASP-VAL-PRO-GLN-
TRP-GLU-VAL-PHE-
PHE-LYS
PRO-GLN-TRP-GLU
Waters ×229
PDB id:
4htp
Name: Ligase/hydrolase
Title: Crystal structure of the dbd domain of human DNA ligase iv b artemis peptide
Structure: DNA ligase 4. Chain: a, b. Fragment: DNA binding domain. Synonym: DNA ligase iv, polydeoxyribonucleotide synthase [a engineered: yes. Protein artemis. Chain: c, e. Fragment: c-terminal. Synonym: DNA cross-link repair 1c protein, protein a-scid,
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: lig4. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: this sequence occurs naturally in humans
Resolution:
2.25Å     R-factor:   0.199     R-free:   0.249
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 chains
Pfam   ArchSchema ?
P49917  (DNLI4_HUMAN) -  DNA ligase 4
Seq:
Struc:
 
Seq:
Struc:
911 a.a.
221 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
+ (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   3 terms 
  Biochemical function     DNA binding     3 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.
 

 

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