2P0J

Structure of restriction endonuclease BstYI bound to non-cognate DNA

Summary for 2P0J

• Entry DOI: 10.2210/pdb2p0j/pdb
• Related: 1SD0 1VRR
• Descriptor: 5'-D(*AP*TP*GP*AP*AP*TP*CP*CP*AP*TP*A)-3', 5'-D(*TP*AP*TP*GP*GP*AP*TP*TP*CP*AP*T)-3', BstYI, ... (4 entities in total)
• Functional Keywords: restriction endonuclease, dna recognition, scanning, hydrolase-dna complex, hydrolase/dna
• Biological source: Geobacillus stearothermophilus
• Total number of polymer chains: 4
• Total formula weight: 53149.79

Authors

Townson, S.A.,Samuelson, J.C.,Bao, Y.,Xu, S.Y.,Aggarwal, A.K. (deposition date: 2007-02-28, release date: 2007-05-01, Last modification date: 2024-02-21)

Primary citation

Townson, S.A.,Samuelson, J.C.,Bao, Y.,Xu, S.Y.,Aggarwal, A.K.
BstYI Bound to Noncognate DNA Reveals a "Hemispecific" Complex: Implications for DNA Scanning.
Structure, 15:449-459, 2007

PubMed Abstract: DNA recognition by proteins is essential for specific expression of genes in a living organism. En route to a target DNA site, a protein will often sample noncognate DNA sites through nonspecific protein-DNA interactions, resulting in a variety of conformationally different binding states. We present here the crystal structure of endonuclease BstYI bound to a noncognate DNA. Surprisingly, the structure reveals the enzyme in a "hemispecific" binding state on the pathway between nonspecific and specific recognition. A single base pair change in the DNA abolishes binding of only one monomer, with the second monomer bound specifically. We show that the enzyme binds essentially as a rigid body, and that one end of the DNA is accommodated loosely in the binding cleft while the other end is held tightly. Another intriguing feature of the structure is Ser172, which has a dual role in establishing nonspecific and specific contacts. Taken together, the structure provides a snapshot of an enzyme in a "paused" intermediate state that may be part of a more general mechanism of scanning DNA.

PubMed: 17437717
DOI: 10.1016/j.str.2007.03.002

Experimental method

X-RAY DIFFRACTION (2.1 Å)