Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides. (1st February 2014)

• Record Type: Journal Article
• Authors: Abdur, Rob; Gerlits, Oksana O.; Gan, Jianhua; Jiang, Jiansheng; Salon, Jozef; Kovalevsky, Andrey Y.; Chumanevich, Alexander A.; Weber, Irene T.; Huang, Zhen
• Is Part Of: Acta crystallographica. Volume 70:Part 2(2014:Feb.)
• Page Start: 354
• Page End: 361
• Publication Date: 2014-02-01
• Subjects: Biomolecules -- Structure -- Periodicals; Physical biochemistry -- Periodicals; X-ray crystallography -- Periodicals; Crystallography -- Periodicals; 572
• DOI: 10.1107/S1399004713027922
• Languages: English
• ISSNs: 0907-4449

Abstract

<abstract abstract-type="main" xml:lang="en"> <title> <x xml:space="preserve">Abstract</x> </title> <p>The crystal structures of protein–nucleic acid complexes are commonly determined using selenium‐derivatized proteins <italic>via</italic> 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.</p> </abstract>