PDBsum entry 1ik9

Go to PDB code: 
protein Protein-protein interface(s) links
Gene regulation/ligase PDB id
Protein chains
207 a.a. *
195 a.a. *
28 a.a. *
Waters ×224
* Residue conservation analysis
PDB id:
Name: Gene regulation/ligase
Title: Crystal structure of a xrcc4-DNA ligase iv complex
Structure: DNA repair protein xrcc4. Chain: a, b. Fragment: xrcc4 fragment, residues 1-213. Engineered: yes. Mutation: yes. DNA ligase iv. Chain: c. Fragment: linker connecting brct domains, residues 748-784. Synonym: polydeoxyribonucleotide synthase.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: xrcc4. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: lig4.
Biol. unit: Trimer (from PQS)
2.30Å     R-factor:   0.228     R-free:   0.266
Authors: B.L.Sibanda,S.E.Critchlow,J.Begun,X.Y.Pei,S.P.Jackson, T.L.Blundell,L.Pellegrini
Key ref:
B.L.Sibanda et al. (2001). Crystal structure of an Xrcc4-DNA ligase IV complex. Nat Struct Biol, 8, 1015-1019. PubMed id: 11702069 DOI: 10.1038/nsb725
03-May-01     Release date:   21-Nov-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q13426  (XRCC4_HUMAN) -  DNA repair protein XRCC4
336 a.a.
207 a.a.*
Protein chain
Pfam   ArchSchema ?
Q13426  (XRCC4_HUMAN) -  DNA repair protein XRCC4
336 a.a.
195 a.a.*
Protein chain
Pfam   ArchSchema ?
P49917  (DNLI4_HUMAN) -  DNA ligase 4
911 a.a.
28 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 8 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chain C: 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 recombination   2 terms 
  Biochemical function     DNA binding     2 terms  


DOI no: 10.1038/nsb725 Nat Struct Biol 8:1015-1019 (2001)
PubMed id: 11702069  
Crystal structure of an Xrcc4-DNA ligase IV complex.
B.L.Sibanda, S.E.Critchlow, J.Begun, X.Y.Pei, S.P.Jackson, T.L.Blundell, L.Pellegrini.
A complex of two proteins, Xrcc4 and DNA ligase IV, plays a fundamental role in DNA non-homologous end joining (NHEJ), a cellular function required for double-strand break repair and V(D)J recombination. Here we report the crystal structure of human Xrcc4 bound to a polypeptide that corresponds to the DNA ligase IV sequence linking its two BRCA1 C-terminal (BRCT) domains. In the complex, a single ligase chain binds asymmetrically to an Xrcc4 dimer. The helical tails of Xrcc4 undergo a substantial conformational change relative to the uncomplexed protein, forming a coiled coil that unwinds upon ligase binding, leading to a flat interaction surface. A buried network of charged hydrogen bonds surrounded by extensive hydrophobic contacts explains the observed tightness of the interaction. The strong conservation of residues at the interface between the two proteins provides evidence that the observed mode of interaction has been maintained in NHEJ throughout evolution.
  Selected figure(s)  
Figure 1.
Figure 1. Interaction between DNA ligase IV and Xrcc4. a , Analysis of the Xrcc4 region critical for DNA ligase IV binding. Two Xrcc4 fragments, spanning residues 1 -179 and 1 -213, were tested for binding to the C-terminal region of DNA ligase IV (residues 653 -911) by gel filtration chromatography on a Superdex-200 HR 10/30 column (Pharmacia). SDS-PAGE analysis of column fractions shows that only the longer Xrcc4 sequence forms a complex with the ligase. Retention volumes (in ml) for ligase (653 -911), Xrcc4 (1 -179) and the ligase (653 -911) -Xrcc4 (1 -213) complex are indicated. b , Isolation of the Xrcc4 -ligase complex (see Methods). CBD represents the chitin binding domain. c , The electron density of the DNA ligase IV linker. A portion of the 2F[o] - F[c] map relative to the ligase linker polypeptide, contoured at 1.2 , is shown. The refined model of the ligase is superimposed. The N- and C-terminal residues are labeled.
Figure 4.
Figure 4. The protein -protein interface of the human Xrcc4 -DNA ligase IV complex. a , Polar interactions. The protein backbone is magenta for Xrcc4 and green for the ligase. Relevant side chains are drawn in light gray as ball-and-stick models. Yellow dashed lines represent hydrogen bonds. b , Hydrophobic interactions. The ligase is green, with relevant side chains drawn as yellow sticks. Xrcc4 is represented as a solvent-accessible molecular surface, with its electrostatic potential mapped onto it. c , Local ligase-induced asymmetry at the Xrcc4 -ligase interface determines the Xrcc4:DNA ligase IV stoichiometry. Leu 774 and Phe 778 of the ligase form a wedge that points towards the middle of the coiled coil of Xrcc4, forcing the side chains of Tyr 177, Phe 180 and Leu 184 to adopt rotamers that would sterically clash with a second ligase molecule trying to bind to the other face of the coil. Backbone is green and side chains cyan for the ligase, and magenta and orange, respectively, for Xrcc4. van der Waals surfaces are shown for Leu 774 and Phe 778 of DNA ligase IV, and for Phe 180 of Xrcc4.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 1015-1019) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20935051 K.Bahmed, A.Seth, K.C.Nitiss, and J.L.Nitiss (2011).
End-processing during non-homologous end-joining: a role for exonuclease 1.
  Nucleic Acids Res, 39, 970-978.  
21273447 M.van Breugel, M.Hirono, A.Andreeva, H.A.Yanagisawa, S.Yamaguchi, Y.Nakazawa, N.Morgner, M.Petrovich, I.O.Ebong, C.V.Robinson, C.M.Johnson, D.Veprintsev, and B.Zuber (2011).
Structures of SAS-6 suggest its organization in centrioles.
  Science, 331, 1196-1199.
PDB codes: 2y3v 2y3w
20975951 A.Demogines, A.M.East, J.H.Lee, S.R.Grossman, P.C.Sabeti, T.T.Paull, and S.L.Sawyer (2010).
Ancient and recent adaptive evolution of primate non-homologous end joining genes.
  PLoS Genet, 6, e1001169.  
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.  
20192759 M.R.Lieber (2010).
The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway.
  Annu Rev Biochem, 79, 181-211.  
20813000 M.Shen, I.Menashe, L.M.Morton, Y.Zhang, B.Armstrong, S.S.Wang, Q.Lan, P.Hartge, M.P.Purdue, J.R.Cerhan, A.Grulich, W.Cozen, M.Yeager, T.R.Holford, C.M.Vajdic, S.Davis, B.Leaderer, A.Kricker, R.K.Severson, S.H.Zahm, N.Chatterjee, N.Rothman, S.J.Chanock, and T.Zheng (2010).
Polymorphisms in DNA repair genes and risk of non-Hodgkin lymphoma in a pooled analysis of three studies.
  Br J Haematol, 151, 239-244.  
19133841 B.L.Mahaney, K.Meek, and S.P.Lees-Miller (2009).
Repair of ionizing radiation-induced DNA double-strand breaks by non-homologous end-joining.
  Biochem J, 417, 639-650.  
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
19332554 P.Y.Wu, P.Frit, S.Meesala, S.Dauvillier, M.Modesti, S.N.Andres, Y.Huang, J.Sekiguchi, P.Calsou, B.Salles, and M.S.Junop (2009).
Structural and functional interaction between the human DNA repair proteins DNA ligase IV and XRCC4.
  Mol Cell Biol, 29, 3163-3172.
PDB code: 3ii6
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.  
18166980 E.Weterings, and D.J.Chen (2008).
The endless tale of non-homologous end-joining.
  Cell Res, 18, 114-124.  
18335491 K.Dahm (2008).
Role and regulation of human XRCC4-like factor/cernunnos.
  J Cell Biochem, 104, 1534-1540.  
18832348 P.L.Palmbos, D.Wu, J.M.Daley, and T.E.Wilson (2008).
Recruitment of Saccharomyces cerevisiae Dnl4-Lif1 Complex to a Double-Strand Break Requires Interactions With Yku80 and the Xrs2 FHA Domain.
  Genetics, 180, 1809-1819.  
18518823 T.Ellenberger, and A.E.Tomkinson (2008).
Eukaryotic DNA ligases: structural and functional insights.
  Annu Rev Biochem, 77, 313-338.  
18046455 Y.Li, D.Y.Chirgadze, V.M.Bolanos-Garcia, B.L.Sibanda, O.R.Davies, P.Ahnesorg, S.P.Jackson, and T.L.Blundell (2008).
Crystal structure of human XLF/Cernunnos reveals unexpected differences from XRCC4 with implications for NHEJ.
  EMBO J, 27, 290-300.
PDB code: 2qm4
18165945 Y.Liu, K.Zhou, H.Zhang, Y.Y.Shugart, L.Chen, Z.Xu, Y.Zhong, H.Liu, L.Jin, Q.Wei, F.Huang, D.Lu, and L.Zhou (2008).
Polymorphisms of LIG4 and XRCC4 involved in the NHEJ pathway interact to modify risk of glioma.
  Hum Mutat, 29, 381-389.  
18066085 D.C.van Gent, and M.van der Burg (2007).
Non-homologous end-joining, a sticky affair.
  Oncogene, 26, 7731-7740.  
17296606 I.Muylaert, and P.Elias (2007).
Knockdown of DNA ligase IV/XRCC4 by RNA interference inhibits herpes simplex virus type I DNA replication.
  J Biol Chem, 282, 10865-10872.  
17693593 P.Burton, D.J.McBride, J.M.Wilkes, J.D.Barry, and R.McCulloch (2007).
Ku heterodimer-independent end joining in Trypanosoma brucei cell extracts relies upon sequence microhomology.
  Eukaryot Cell, 6, 1773-1781.  
18066091 P.Soulas-Sprauel, P.Rivera-Munoz, L.Malivert, G.Le Guyader, V.Abramowski, P.Revy, and Villartay (2007).
V(D)J and immunoglobulin class switch recombinations: a paradigm to study the regulation of DNA end-joining.
  Oncogene, 26, 7780-7791.  
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
16749933 A.Pavlicek, and J.Jurka (2006).
Positive selection on the nonhomologous end-joining factor Cernunnos-XLF in the human lineage.
  Biol Direct, 1, 15.  
16407064 A.Singh, and S.E.Hitchcock-DeGregori (2006).
Dual requirement for flexibility and specificity for binding of the coiled-coil tropomyosin to its target, actin.
  Structure, 14, 43-50.  
16571728 I.Callebaut, L.Malivert, A.Fischer, J.P.Mornon, P.Revy, and Villartay (2006).
Cernunnos interacts with the XRCC4 x DNA-ligase IV complex and is homologous to the yeast nonhomologous end-joining factor Nej1.
  J Biol Chem, 281, 13857-13860.  
17161371 J.Liu, Y.Pan, B.Ma, and R.Nussinov (2006).
"Similarity trap" in protein-protein interactions could be carcinogenic: simulations of p53 core domain complexed with 53BP1 and BRCA1 BRCT domains.
  Structure, 14, 1811-1821.  
16822175 K.Riha, M.L.Heacock, and D.E.Shippen (2006).
The role of the nonhomologous end-joining DNA double-strand break repair pathway in telomere biology.
  Annu Rev Genet, 40, 237-277.  
16905105 N.Furnham, A.S.Doré, D.Y.Chirgadze, Bakker, M.A.Depristo, and T.L.Blundell (2006).
Knowledge-based real-space explorations for low-resolution structure determination.
  Structure, 14, 1313-1320.  
16648486 N.Puebla-Osorio, D.B.Lacey, F.W.Alt, and C.Zhu (2006).
Early embryonic lethality due to targeted inactivation of DNA ligase III.
  Mol Cell Biol, 26, 3935-3941.  
16439205 P.Ahnesorg, P.Smith, and S.P.Jackson (2006).
XLF interacts with the XRCC4-DNA ligase IV complex to promote DNA nonhomologous end-joining.
  Cell, 124, 301-313.  
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.  
17088645 P.Revy, L.Malivert, and Villartay (2006).
Cernunnos-XLF, a recently identified non-homologous end-joining factor required for the development of the immune system.
  Curr Opin Allergy Clin Immunol, 6, 416-420.  
16524830 T.L.Blundell, B.L.Sibanda, R.W.Montalvão, S.Brewerton, V.Chelliah, C.L.Worth, N.J.Harmer, O.Davies, and D.Burke (2006).
Structural biology and bioinformatics in drug design: opportunities and challenges for target identification and lead discovery.
  Philos Trans R Soc Lond B Biol Sci, 361, 413-423.  
16478998 V.Yurchenko, Z.Xue, and M.J.Sadofsky (2006).
SUMO modification of human XRCC4 regulates its localization and function in DNA double-strand break repair.
  Mol Cell Biol, 26, 1786-1794.  
17292118 W.S.Dynan, Y.Takeda, and S.Li (2006).
Modifying the function of DNA repair nanomachines for therapeutic benefit.
  Nanomedicine, 2, 74-81.  
16285867 J.M.Daley, P.L.Palmbos, D.Wu, and T.E.Wilson (2005).
Nonhomologous end joining in yeast.
  Annu Rev Genet, 39, 431-451.  
15221026 D.S.Daniels, T.T.Woo, K.X.Luu, D.M.Noll, N.D.Clarke, A.E.Pegg, and J.A.Tainer (2004).
DNA binding and nucleotide flipping by the human DNA repair protein AGT.
  Nat Struct Mol Biol, 11, 714-720.
PDB codes: 1t38 1t39
15242402 F.Le Deist, C.Poinsignon, D.Moshous, A.Fischer, and Villartay (2004).
Artemis sheds new light on V(D)J recombination.
  Immunol Rev, 200, 142-155.  
15466438 G.Siligardi, B.Hu, B.Panaretou, P.W.Piper, L.H.Pearl, and C.Prodromou (2004).
Co-chaperone regulation of conformational switching in the Hsp90 ATPase cycle.
  J Biol Chem, 279, 51989-51998.  
15501676 J.N.Glover, R.S.Williams, and M.S.Lee (2004).
Interactions between BRCT repeats and phosphoproteins: tangled up in two.
  Trends Biochem Sci, 29, 579-585.  
14561766 J.W.Lee, L.Blanco, T.Zhou, M.Garcia-Diaz, K.Bebenek, T.A.Kunkel, Z.Wang, and L.F.Povirk (2004).
Implication of DNA polymerase lambda in alignment-based gap filling for nonhomologous DNA end joining in human nuclear extracts.
  J Biol Chem, 279, 805-811.  
15242401 K.Meek, S.Gupta, D.A.Ramsden, and S.P.Lees-Miller (2004).
The DNA-dependent protein kinase: the director at the end.
  Immunol Rev, 200, 132-141.  
15611176 M.McVey, D.Radut, and J.J.Sekelsky (2004).
End-joining repair of double-strand breaks in Drosophila melanogaster is largely DNA ligase IV independent.
  Genetics, 168, 2067-2076.  
15133503 R.S.Williams, M.S.Lee, D.D.Hau, and J.N.Glover (2004).
Structural basis of phosphopeptide recognition by the BRCT domain of BRCA1.
  Nat Struct Mol Biol, 11, 519-525.
PDB codes: 1t2u 1t2v
15194694 Y.G.Wang, C.Nnakwe, W.S.Lane, M.Modesti, and K.M.Frank (2004).
Phosphorylation and regulation of DNA ligase IV stability by DNA-dependent protein kinase.
  J Biol Chem, 279, 37282-37290.  
15539075 Z.Dudásová, A.Dudás, and M.Chovanec (2004).
Non-homologous end-joining factors of Saccharomyces cerevisiae.
  FEMS Microbiol Rev, 28, 581-601.  
12682039 B.Kysela, A.J.Doherty, M.Chovanec, T.Stiff, S.M.Ameer-Beg, B.Vojnovic, P.M.Girard, and P.A.Jeggo (2003).
Ku stimulation of DNA ligase IV-dependent ligation requires inward movement along the DNA molecule.
  J Biol Chem, 278, 22466-22474.  
12554653 J.B.Mascarenhas, M.A.Rüegg, U.Winzen, W.Halfter, J.Engel, and J.Stetefeld (2003).
Mapping of the laminin-binding site of the N-terminal agrin domain (NtA).
  EMBO J, 22, 529-536.  
  14704177 M.M.Gorski, J.C.Eeken, Jong, I.Klink, M.Loos, R.J.Romeijn, B.L.van Veen, L.H.Mullenders, W.Ferro, and A.Pastink (2003).
The Drosophila melanogaster DNA Ligase IV gene plays a crucial role in the repair of radiation-induced DNA double-strand breaks and acts synergistically with Rad54.
  Genetics, 165, 1929-1941.  
12473094 A.V.Cherepanov, and Vries (2002).
Dynamic mechanism of nick recognition by DNA ligase.
  Eur J Biochem, 269, 5993-5999.  
12110597 D.J.Derbyshire, B.P.Basu, L.C.Serpell, W.S.Joo, T.Date, K.Iwabuchi, and A.J.Doherty (2002).
Crystal structure of human 53BP1 BRCT domains bound to p53 tumour suppressor.
  EMBO J, 21, 3863-3872.
PDB code: 1gzh
  11983065 I.V.Martin, and S.A.MacNeill (2002).
ATP-dependent DNA ligases.
  Genome Biol, 3, REVIEWS3005.  
11839498 K.P.Hopfner, C.D.Putnam, and J.A.Tainer (2002).
DNA double-strand break repair from head to tail.
  Curr Opin Struct Biol, 12, 115-122.  
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.