Acta Crystallographica Section D

Biological Crystallography

Volume 70, Part 2 (February 2014)

research papers

Acta Cryst. (2014). D70, 354-361    [ doi:10.1107/S1399004713027922 ]

Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides

R. Abdur, O. O. Gerlits, J. Gan, J. Jiang, J. Salon, A. Y. Kovalevsky, A. A. Chumanevich, I. T. Weber and Z. Huang

Abstract: The crystal structures of protein-nucleic acid complexes are commonly determined using selenium-derivatized proteins via MAD or SAD phasing. Here, the first protein-nucleic acid complex structure determined using selenium-derivatized nucleic acids is reported. The RNase H-RNA/DNA complex is used as an example to demonstrate the proof of principle. The high-resolution crystal structure indicates that this selenium replacement results in a local subtle unwinding of the RNA/DNA substrate duplex, thereby shifting the RNA scissile phosphate closer to the transition state of the enzyme-catalyzed reaction. It was also observed that the scissile phosphate forms a hydrogen bond to the water nucleophile and helps to position the water molecule in the structure. Consistently, it was discovered that the substitution of a single O atom by a Se atom in a guide DNA sequence can largely accelerate RNase H catalysis. These structural and catalytic studies shed new light on the guide-dependent RNA cleavage.

PDB reference: 3twh

Keywords: protein-nucleic acid complexes; selenium derivatization and phasing; DNA and modification; RNase H and RNA cleavage.

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