1VRR: Crystal structure of the restriction endonuclease BstYI complex with DNA

The type II restriction endonuclease BstYI recognizes the degenerate sequence 5'-RGATCY-3' (where R = A/G and Y = C/T), which overlaps with both BamHI (GGATCC) and BglII (AGATCT), and thus raises the question of whether BstYI DNA recognition will be more BamHI-like or BglII-like. We present here the structure of BstYI bound to a cognate DNA sequence (AGATCT). We find the complex to be more BglII-like with similarities mapping to DNA conformation, domain organization, and residues involved in catalysis. However, BstYI is unique in containing an extended arm subdomain, and the mechanism of DNA capture has both BglII-like and BamHI-like elements. Further, DNA recognition is more minimal than BglII and BamHI, where only two residues mediate recognition of the entire core sequence. Taken together, the structure reveals a mechanism of degenerate DNA recognition and offers insights into the possibilities and limitations in altering specificities of closely related restriction enzymes.
PDB ID: 1VRRDownload
MMDB ID: 74385
PDB Deposition Date: 2005/6/2
Updated in MMDB: 2009/07
Experimental Method:
x-ray diffraction
Resolution: 2.7  Å
Source Organism:
Geobacillus stearothermophilus
Similar Structures:
Biological Unit for 1VRR: tetrameric; determined by author
Molecular Components in 1VRR
Label Count Molecule
Proteins (2 molecules)
Molecule annotation
Nucleotide(1 molecule)
Molecule annotation
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Citing MMDB