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


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.

SUBMITTER: Abdur R 

PROVIDER: S-EPMC3940196 | biostudies-literature | 2014 Feb

REPOSITORIES: biostudies-literature

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

Abdur Rob R   Gerlits Oksana O OO   Gan Jianhua J   Jiang Jiansheng J   Salon Jozef J   Kovalevsky Andrey Y AY   Chumanevich Alexander A AA   Weber Irene T IT   Huang Zhen Z  

Acta crystallographica. Section D, Biological crystallography 20140129 Pt 2


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, th  ...[more]

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