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PDBsum entry 1ae9
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DNA recombination
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PDB id
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1ae9
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Flexibility in DNA recombination: structure of the lambda integrase catalytic core.
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Authors
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H.J.Kwon,
R.Tirumalai,
A.Landy,
T.Ellenberger.
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Ref.
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Science, 1997,
276,
126-131.
[DOI no: ]
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PubMed id
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Abstract
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Lambda integrase is archetypic of site-specific recombinases that catalyze
intermolecular DNA rearrangements without energetic input. DNA cleavage, strand
exchange, and religation steps are linked by a covalent phosphotyrosine
intermediate in which Tyr342 is attached to the 3'-phosphate of the DNA cut
site. The 1.9 angstrom crystal structure of the integrase catalytic domain
reveals a protein fold that is conserved in organisms ranging from
archaebacteria to yeast and that suggests a model for interaction with target
DNA. The attacking Tyr342 nucleophile is located on a flexible loop about 20
angstroms from a basic groove that contains all the other catalytically
essential residues. This bipartite active site can account for several
apparently paradoxical features of integrase family recombinases, including the
capacity for both cis and trans cleavage of DNA.
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Figure 3.
Fig. 3. Theoretical model of the  Int
catalytic core bound to a B-form half-att site. A full att site
contains a pair of inverted^ core-type Int binding sites. An Int
protomer at each site is responsible^ for cleaving one DNA
strand via formation of a covalent 3  phospho-tyrosine^
linkage and a free 5 -hydroxyl.
The two nicks are staggered by seven base pairs with a 5 overhang.
For clarity, only one subunit of the Int c170 dimer that was
modeled on DNA is shown. The catalytic^ Arg-His-Arg triad (cyan)
of Int is docked over one of the scissile^ phosphates (shown as
breaks in the DNA ribbon). The C  trace of^
Int c170 (blue) is displayed with the active site loop
containing the Tyr342 nucleophile shown in two alternative
conformations. The orientation corresponding to cis cleavage
(orange tyrosine) is a theoretical model, whereas that
corresponding to trans cleavage (red tyrosine) is present in one
of two Int protomers in the crystal structure. The segment of
the loop that is disordered in both protomers (Lys334 to Gln341)
is modeled in pink.
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The above figure is
reprinted
by permission from the AAAs:
Science
(1997,
276,
126-131)
copyright 1997.
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