PDBsum entry 3ii6

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protein metals Protein-protein interface(s) links
Ligase/DNA binding protein PDB id
Protein chains
201 a.a. *
256 a.a. *
_CL ×2
Waters ×281
* Residue conservation analysis
PDB id:
Name: Ligase/DNA binding protein
Title: Structure of human xrcc4 in complex with the tandem brct domains of DNA ligaseiv.
Structure: DNA repair protein xrcc4. Chain: a, b, c, d. Fragment: residues 1-203. Synonym: x-ray repair cross-complementing protein 4. Engineered: yes. Mutation: yes. DNA ligase 4. Chain: x, y. Fragment: c-terminal tandem brct domains, residues 654-911.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: xrcc4. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: lig4.
2.40Å     R-factor:   0.240     R-free:   0.280
Authors: S.Meesala,M.Junop
Key ref: P.Y.Wu et al. (2009). Structural and functional interaction between the human DNA repair proteins DNA ligase IV and XRCC4. Mol Cell Biol, 29, 3163-3172. PubMed id: 19332554
31-Jul-09     Release date:   11-Aug-09    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q13426  (XRCC4_HUMAN) -  DNA repair protein XRCC4
336 a.a.
201 a.a.*
Protein chains
Pfam   ArchSchema ?
P49917  (DNLI4_HUMAN) -  DNA ligase 4
911 a.a.
256 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains X, Y: E.C.  - Dna ligase (ATP).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m)
+ (deoxyribonucleotide)(n)
+ (deoxyribonucleotide)(m)
+ diphosphate
+ (deoxyribonucleotide)(n+m)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     DNA repair   4 terms 
  Biochemical function     DNA binding     3 terms  


Mol Cell Biol 29:3163-3172 (2009)
PubMed id: 19332554  
Structural and functional interaction between the human DNA repair proteins DNA ligase IV and XRCC4.
P.Y.Wu, P.Frit, S.Meesala, S.Dauvillier, M.Modesti, S.N.Andres, Y.Huang, J.Sekiguchi, P.Calsou, B.Salles, M.S.Junop.
Nonhomologous end-joining represents the major pathway used by human cells to repair DNA double-strand breaks. It relies on the XRCC4/DNA ligase IV complex to reseal DNA strands. Here we report the high-resolution crystal structure of human XRCC4 bound to the carboxy-terminal tandem BRCT repeat of DNA ligase IV. The structure differs from the homologous Saccharomyces cerevisiae complex and reveals an extensive DNA ligase IV binding interface formed by a helix-loop-helix structure within the inter-BRCT linker region, as well as significant interactions involving the second BRCT domain, which induces a kink in the tail region of XRCC4. We further demonstrate that interaction with the second BRCT domain of DNA ligase IV is necessary for stable binding to XRCC4 in cells, as well as to achieve efficient dominant-negative effects resulting in radiosensitization after ectopic overexpression of DNA ligase IV fragments in human fibroblasts. Together our findings provide unanticipated insight for understanding the physical and functional architecture of the nonhomologous end-joining ligation complex.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21070942 M.Hammel, Y.Yu, S.Fang, S.P.Lees-Miller, and J.A.Tainer (2010).
XLF regulates filament architecture of the XRCC4·ligase IV complex.
  Structure, 18, 1431-1442.  
  20862368 T.Ochi, B.L.Sibanda, Q.Wu, D.Y.Chirgadze, V.M.Bolanos-Garcia, and T.L.Blundell (2010).
Structural biology of DNA repair: spatial organisation of the multicomponent complexes of nonhomologous end joining.
  J Nucleic Acids, 2010, 0.  
19542097 M.W.Killen, D.M.Stults, N.Adachi, L.Hanakahi, and A.J.Pierce (2009).
Loss of Bloom syndrome protein destabilizes human gene cluster architecture.
  Hum Mol Genet, 18, 3417-3428.  
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