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77 a.a.
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237 a.a.
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45 a.a.
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37 a.a.
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30 a.a.
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20 a.a.
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13 a.a.
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* Residue conservation analysis
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PDB id:
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Ligase
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Title:
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Co-crystal structure of lif1p-lig4p
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Structure:
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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.
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Source:
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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.
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Resolution:
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3.92Å
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R-factor:
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0.403
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R-free:
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0.467
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Authors:
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A.S.Dore,N.Furnham,O.R.Davies,B.L.Sibanda,D.Y.Chirgadze, S.P.Jackson,L.Pellegrini,T.L.Blundell
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Key ref:
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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:
DOI:
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Date:
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17-Mar-05
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Release date:
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31-Jan-06
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PROCHECK
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Headers
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References
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P53150
(LIF1_YEAST) -
Ligase-interacting factor 1
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Seq:
Struc:
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421 a.a.
77 a.a.
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Q08387
(DNLI4_YEAST) -
DNA ligase 4
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Seq:
Struc:
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944 a.a.
237 a.a.
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No UniProt id for this chain
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No UniProt id for this chain
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No UniProt id for this chain
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Enzyme class:
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Chain C:
E.C.6.5.1.1
- Dna ligase (ATP).
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Reaction:
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ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m)
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ATP
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+
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(deoxyribonucleotide)(n)
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+
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(deoxyribonucleotide)(m)
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=
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AMP
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+
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diphosphate
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+
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(deoxyribonucleotide)(n+m)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Gene Ontology (GO) functional annotation
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Cellular component
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intracellular
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2 terms
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Biological process
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DNA recombination
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2 terms
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Biochemical function
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protein binding
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2 terms
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DOI no:
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Dna Repair (amst)
5:362-368
(2006)
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PubMed id:
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| |
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Structure of an Xrcc4-DNA ligase IV yeast ortholog complex reveals a novel BRCT interaction mode.
|
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A.S.Doré,
N.Furnham,
O.R.Davies,
B.L.Sibanda,
D.Y.Chirgadze,
S.P.Jackson,
L.Pellegrini,
T.L.Blundell.
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ABSTRACT
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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.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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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.
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Microbiol Immunol, 55,
34-43.
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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.
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J Nucleic Acids, 2010,
0.
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A.M.Karmali,
T.L.Blundell,
and
N.Furnham
(2009).
Model-building strategies for low-resolution X-ray crystallographic data.
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Acta Crystallogr D Biol Crystallogr, 65,
121-127.
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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.
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Curr Genet, 55,
381-389.
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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.
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Cell, 139,
100-111.
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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.
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Cancer, 115,
2939-2948.
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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.
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J Virol, 82,
8849-8862.
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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.
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Genetics, 178,
1237-1249.
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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.
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Genetics, 179,
213-225.
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T.Ellenberger,
and
A.E.Tomkinson
(2008).
Eukaryotic DNA ligases: structural and functional insights.
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Annu Rev Biochem, 77,
313-338.
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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.
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Cancer Epidemiol Biomarkers Prev, 17,
2366-2373.
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M.Chovanec,
and
T.E.Wilson
(2007).
Restricting the ligation step of non-homologous end-joining.
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DNA Repair (Amst), 6,
1890-1893.
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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.
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DNA Repair (Amst), 6,
1507-1516.
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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.
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Mol Cell, 28,
1093-1101.
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PDB code:
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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.
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Proc Natl Acad Sci U S A, 103,
14871-14876.
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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.
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Structure, 14,
1313-1320.
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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.
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J Biol Chem, 281,
37517-37526.
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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
code is
shown on the right.
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Links
