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PDBsum entry 4rd5
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Hydrolase/DNA
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PDB id
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4rd5
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References listed in PDB file
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Key reference
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Title
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Crystal structure of the r-Protein of the multisubunit ATP-Dependent restriction endonuclease ngoavii.
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Authors
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G.Tamulaitiene,
A.Silanskas,
S.Grazulis,
M.Zaremba,
V.Siksnys.
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Ref.
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Nucleic Acids Res, 2014,
42,
14022-14030.
[DOI no: ]
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PubMed id
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Abstract
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The restriction endonuclease (REase) NgoAVII is composed of two proteins,
R.NgoAVII and N.NgoAVII, and shares features of both Type II restriction enzymes
and Type I/III ATP-dependent restriction enzymes (see accompanying paper Zaremba
et al., 2014). Here we present crystal structures of the R.NgoAVII apo-protein
and the R.NgoAVII C-terminal domain bound to a specific DNA. R.NgoAVII is
composed of two domains: an N-terminal nucleolytic PLD domain; and a C-terminal
B3-like DNA-binding domain identified previously in BfiI and EcoRII REases, and
in plant transcription factors. Structural comparison of the B3-like domains of
R.NgoAVII, EcoRII, BfiI and the plant transcription factors revealed a conserved
DNA-binding surface comprised of N- and C-arms that together grip the DNA. The
C-arms of R.NgoAVII, EcoRII, BfiI and plant B3 domains are similar in size, but
the R.NgoAVII N-arm which makes the majority of the contacts to the target site
is much longer. The overall structures of R.NgoAVII and BfiI are similar;
however, whilst BfiI has stand-alone catalytic activity, R.NgoAVII requires an
auxiliary cognate N.NgoAVII protein and ATP hydrolysis in order to cleave DNA at
the target site. The structures we present will help formulate future
experiments to explore the molecular mechanisms of intersubunit crosstalk that
control DNA cleavage by R.NgoAVII and related endonucleases.
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