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PDBsum entry 3dpg
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Hydrolase/DNA
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PDB id
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3dpg
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References listed in PDB file
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Key reference
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Title
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The structure of sgrai bound to DNA; recognition of an 8 base pair target.
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Authors
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P.W.Dunten,
E.J.Little,
M.T.Gregory,
V.M.Manohar,
M.Dalton,
D.Hough,
J.Bitinaite,
N.C.Horton.
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Ref.
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Nucleic Acids Res, 2008,
36,
5405-5416.
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PubMed id
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Abstract
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The three-dimensional X-ray crystal structure of the 'rare cutting' type II
restriction endonuclease SgrAI bound to cognate DNA is presented. SgrAI forms a
dimer bound to one duplex of DNA. Two Ca(2+) bind in the enzyme active site,
with one ion at the interface between the protein and DNA, and the second bound
distal from the DNA. These sites are differentially occupied by Mn(2+), with
strong binding at the protein-DNA interface, but only partial occupancy of the
distal site. The DNA remains uncleaved in the structures from crystals grown in
the presence of either divalent cation. The structure of the dimer of SgrAI is
similar to those of Cfr10I, Bse634I and NgoMIV, however no tetrameric structure
of SgrAI is observed. DNA contacts to the central CCGG base pairs of the SgrAI
canonical target sequence (CR|CCGGYG, | marks the site of cleavage) are found to
be very similar to those in the NgoMIV/DNA structure (target sequence G|CCGGC).
Specificity at the degenerate YR base pairs of the SgrAI sequence may occur via
indirect readout using DNA distortion. Recognition of the outer GC base pairs
occurs through a single contact to the G from an arginine side chain located in
a region unique to SgrAI.
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