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PDBsum entry 1z56

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protein ligands Protein-protein interface(s) links
Ligase PDB id
1z56
Jmol
Contents
Protein chains
77 a.a. *
237 a.a. *
45 a.a. *
37 a.a. *
30 a.a. *
20 a.a. *
13 a.a. *
Ligands
UNK-UNK-UNK-UNK-
UNK-UNK-UNK-UNK
UNK-UNK-UNK-UNK-
UNK-UNK-UNK
×2
* Residue conservation analysis
PDB id:
1z56
Name: Ligase
Title: Co-crystal structure of lif1p-lig4p
Structure: Ligase interacting factor 1. Chain: a, b. Engineered: yes. DNA ligase iv. Chain: c. Synonym: polydeoxyribonucleotide synthase [atp], DNA ligase iv homolog. Engineered: yes. Ligase interacting factor 1.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: lif1. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Gene: dnl4, lig4. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
3.92Å     R-factor:   0.403     R-free:   0.467
Authors: A.S.Dore,N.Furnham,O.R.Davies,B.L.Sibanda,D.Y.Chirgadze, S.P.Jackson,L.Pellegrini,T.L.Blundell
Key ref: A.S.Doré et al. (2006). Structure of an Xrcc4-DNA ligase IV yeast ortholog complex reveals a novel BRCT interaction mode. DNA Repair (Amst), 5, 362-368. PubMed id: 16388993 DOI: 10.1016/j.dnarep.2005.11.004
Date:
17-Mar-05     Release date:   31-Jan-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P53150  (LIF1_YEAST) -  Ligase-interacting factor 1
Seq:
Struc:
421 a.a.
77 a.a.
Protein chain
Pfam   ArchSchema ?
Q08387  (DNLI4_YEAST) -  DNA ligase 4
Seq:
Struc:
 
Seq:
Struc:
944 a.a.
237 a.a.
Protein chain
No UniProt id for this chain
Struc: 45 a.a.
Protein chain
No UniProt id for this chain
Struc: 37 a.a.
Protein chain
No UniProt id for this chain
Struc: 30 a.a.
Protein chain
No UniProt id for this chain
Struc: 20 a.a.
Protein chain
No UniProt id for this chain
Struc: 13 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain C: 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!
  Cellular component     nucleus   1 term 
  Biological process     DNA repair   4 terms 
  Biochemical function     DNA binding     3 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.dnarep.2005.11.004 DNA Repair (Amst) 5:362-368 (2006)
PubMed id: 16388993  
 
 
Structure of an Xrcc4-DNA ligase IV yeast ortholog complex reveals a novel BRCT interaction mode.
A.S.Doré, N.Furnham, O.R.Davies, B.L.Sibanda, D.Y.Chirgadze, S.P.Jackson, L.Pellegrini, T.L.Blundell.
 
  ABSTRACT  
 
DNA ligase IV catalyses the final ligation step in the non-homologous end-joining (NHEJ) DNA repair pathway and requires interaction of the ligase with the Xrcc4 'genome-guardian', an essential NHEJ factor. Here we report the 3.9 A crystal structure of the Saccharomyces cerevisiae Xrcc4 ortholog ligase interacting factor 1 (Lif1p) complexed with the C-terminal BRCT domains of DNA ligase IV (Lig4p). The structure reveals a novel mode of protein recognition by a tandem BRCT repeat, and in addition provides a molecular basis for a human LIG4 syndrome clinical condition.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21175772 M.M.Alshahni, T.Yamada, K.Takatori, T.Sawada, and K.Makimura (2011).
Insights into a nonhomologous integration pathway in the dermatophyte Trichophyton mentagrophytes: efficient targeted gene disruption by use of mutants lacking ligase IV.
  Microbiol Immunol, 55, 34-43.  
  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.  
19171966 A.M.Karmali, T.L.Blundell, and N.Furnham (2009).
Model-building strategies for low-resolution X-ray crystallographic data.
  Acta Crystallogr D Biol Crystallogr, 65, 121-127.  
19468735 C.Schorsch, T.Köhler, and E.Boles (2009).
Knockout of the DNA ligase IV homolog gene in the sphingoid base producing yeast Pichia ciferrii significantly increases gene targeting efficiency.
  Curr Genet, 55, 381-389.  
19804756 J.Lloyd, J.R.Chapman, J.A.Clapperton, L.F.Haire, E.Hartsuiker, J.Li, A.M.Carr, S.P.Jackson, and S.J.Smerdon (2009).
A supramodular FHA/BRCT-repeat architecture mediates Nbs1 adaptor function in response to DNA damage.
  Cell, 139, 100-111.
PDB codes: 3i0m 3i0n
19408343 R.C.Tseng, F.J.Hsieh, C.M.Shih, H.S.Hsu, C.Y.Chen, and Y.C.Wang (2009).
Lung cancer susceptibility and prognosis associated with polymorphisms in the nonhomologous end-joining pathway genes: a multiple genotype-phenotype study.
  Cancer, 115, 2939-2948.  
18579587 A.Kumar, W.S.Joo, G.Meinke, S.Moine, E.N.Naumova, and P.A.Bullock (2008).
Evidence for a structural relationship between BRCT domains and the helicase domains of the replication initiators encoded by the Polyomaviridae and Papillomaviridae families of DNA tumor viruses.
  J Virol, 82, 8849-8862.  
18245831 D.Wu, L.M.Topper, and T.E.Wilson (2008).
Recruitment and dissociation of nonhomologous end joining proteins at a DNA double-strand break in Saccharomyces cerevisiae.
  Genetics, 178, 1237-1249.  
18458108 K.Matsuzaki, A.Shinohara, and M.Shinohara (2008).
Forkhead-associated domain of yeast Xrs2, a homolog of human Nbs1, promotes nonhomologous end joining through interaction with a ligase IV partner protein, Lif1.
  Genetics, 179, 213-225.  
18518823 T.Ellenberger, and A.E.Tomkinson (2008).
Eukaryotic DNA ligases: structural and functional insights.
  Annu Rev Biochem, 77, 313-338.  
18768505 V.Margulis, J.Lin, H.Yang, W.Wang, C.G.Wood, and X.Wu (2008).
Genetic susceptibility to renal cell carcinoma: the role of DNA double-strand break repair pathway.
  Cancer Epidemiol Biomarkers Prev, 17, 2366-2373.  
17977804 M.Chovanec, and T.E.Wilson (2007).
Restricting the ligation step of non-homologous end-joining.
  DNA Repair (Amst), 6, 1890-1893.  
17567543 R.A.Deshpande, and T.E.Wilson (2007).
Modes of interaction among yeast Nej1, Lif1 and Dnl4 proteins and comparison to human XLF, XRCC4 and Lig4.
  DNA Repair (Amst), 6, 1507-1516.  
18158905 S.N.Andres, M.Modesti, C.J.Tsai, G.Chu, and M.S.Junop (2007).
Crystal structure of human XLF: a twist in nonhomologous DNA end-joining.
  Mol Cell, 28, 1093-1101.
PDB code: 2r9a
17003123 K.Ishibashi, K.Suzuki, Y.Ando, C.Takakura, and H.Inoue (2006).
Nonhomologous chromosomal integration of foreign DNA is completely dependent on MUS-53 (human Lig4 homolog) in Neurospora.
  Proc Natl Acad Sci U S A, 103, 14871-14876.  
16905105 N.Furnham, A.S.Doré, D.Y.Chirgadze, P.I.de Bakker, M.A.Depristo, and T.L.Blundell (2006).
Knowledge-based real-space explorations for low-resolution structure determination.
  Structure, 14, 1313-1320.  
17038309 P.Hentges, P.Ahnesorg, R.S.Pitcher, C.K.Bruce, B.Kysela, A.J.Green, J.Bianchi, T.E.Wilson, S.P.Jackson, and A.J.Doherty (2006).
Evolutionary and functional conservation of the DNA non-homologous end-joining protein, XLF/Cernunnos.
  J Biol Chem, 281, 37517-37526.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.