1VRR

Crystal structure of the restriction endonuclease BstYI complex with DNA

Replaces:  1YUV

Summary for 1VRR

• Entry DOI: 10.2210/pdb1vrr/pdb
• Related: 1BHM 1DFM 1SDO
• Descriptor: 5'-D(*TP*TP*AP*TP*AP*GP*AP*TP*CP*TP*AP*TP*AP*A)-3', BstYI (3 entities in total)
• Functional Keywords: enzyme-dna complex, double helix, hydrolase-dna complex, hydrolase/dna
• Biological source: Geobacillus stearothermophilus
• Total number of polymer chains: 4
• Total formula weight: 55001.00

Authors

Townson, S.A.,Samuelson, J.C.,Xu, S.Y.,Aggarwal, A.K. (deposition date: 2005-06-02, release date: 2005-06-07, Last modification date: 2023-12-27)

Primary citation

Townson, S.A.,Samuelson, J.C.,Xu, S.Y.,Aggarwal, A.K.
Implications for Switching Restriction Enzyme Specificities from the Structure of BstYI Bound to a BglII DNA Sequence.
Structure, 13:791-801, 2005

PubMed Abstract: 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.

PubMed: 15893669
DOI: 10.1016/j.str.2005.02.018

Experimental method

X-RAY DIFFRACTION (2.7 Å)