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PDBsum entry 5ffj
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DNA binding protein/DNA
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PDB id
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5ffj
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References listed in PDB file
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Key reference
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Title
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Structural insights into DNA sequence recognition by type isp restriction-Modification enzymes.
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Authors
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M.Kulkarni,
N.Nirwan,
K.Van aelst,
M.D.Szczelkun,
K.Saikrishnan.
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Ref.
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Nucleic Acids Res, 2016,
44,
4396-4408.
[DOI no: ]
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PubMed id
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Abstract
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Engineering restriction enzymes with new sequence specificity has been an
unaccomplished challenge, presumably because of the complexity of target
recognition. Here we report detailed analyses of target recognition by Type ISP
restriction-modification enzymes. We determined the structure of the Type ISP
enzyme LlaGI bound to its target and compared it with the previously reported
structure of a close homologue that binds to a distinct target, LlaBIII. The
comparison revealed that, although the two enzymes use almost a similar set of
structural elements for target recognition, the residues that read the bases
vary. Change in specificity resulted not only from appropriate substitution of
amino acids that contacted the bases but also from new contacts made by
positionally distinct residues directly or through a water bridge. Sequence
analyses of 552 Type ISP enzymes showed that the structural elements involved in
target recognition of LlaGI and LlaBIII were structurally well-conserved but
sequentially less-conserved. In addition, the residue positions within these
structural elements were under strong evolutionary constraint, highlighting the
functional importance of these regions. The comparative study helped decipher a
partial consensus code for target recognition by Type ISP enzymes.
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