3TWH

Selenium Derivatized RNA/DNA Hybrid in complex with RNase H Catalytic Domain D132N Mutant

Summary for 3TWH

• Entry DOI: 10.2210/pdb3twh/pdb
• Related: 1ZBI 2G8U
• Descriptor: Ribonuclease H, RNA (5'-R(*UP*CP*GP*AP*CP*A)-3'), DNA (5'-D(*AP*TP*(SDG)P*TP*CP*(SDG))-3'), ... (6 entities in total)
• Functional Keywords: selenium-dna/rna, rnase h, endonuclease, hydrolase, magnesium, manganese, metal-binding, selenium-modification, hydrolase-rna-dna complex, hydrolase/rna/dna
• Biological source: Bacillus halodurans
• Cellular location: Cytoplasm (Potential): Q9KEI9
• Total number of polymer chains: 3
• Total formula weight: 19884.92

Authors

Rob, A.,Gerlits, O.,Jiang, J.S.,Gan, J.H.,Huang, Z. (deposition date: 2011-09-21, release date: 2012-10-03, Last modification date: 2024-02-28)

Primary citation

Abdur, R.,Gerlits, O.O.,Gan, J.,Jiang, J.,Salon, J.,Kovalevsky, A.Y.,Chumanevich, A.A.,Weber, I.T.,Huang, Z.
Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides.
Acta Crystallogr.,Sect.D, 70:354-361, 2014

PubMed 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.

PubMed: 24531469
DOI: 10.1107/S1399004713027922

Experimental method

X-RAY DIFFRACTION (1.79 Å)