3V9U

Crystal structure of RNase T in complex with a preferred ssDNA (AAT) with two Mg in the active site

Summary for 3V9U

• Entry DOI: 10.2210/pdb3v9u/pdb
• Related: 3NGY 3NGZ 3NH0 3NH1 3NH2 3V9S 3V9W 3V9X 3V9Z 3VA0 3VA3
• Descriptor: Ribonuclease T, DNA (5'-D(*TP*TP*AP*CP*AP*AP*T)-3'), MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: dedd nucleases family, exo-nucleases, hydrolase-dna complex, hydrolase/dna
• Biological source: Escherichia coli; More
• Total number of polymer chains: 8
• Total formula weight: 111414.08

Authors

Hsiao, Y.-Y.,Yuan, H.S. (deposition date: 2011-12-28, release date: 2012-07-11, Last modification date: 2024-10-30)

Primary citation

Hsiao, Y.-Y.,Duh, Y.,Chen, Y.P.,Wang, Y.T.,Yuan, H.S.
How an exonuclease decides where to stop in trimming of nucleic acids: crystal structures of RNase T-product complexes
Nucleic Acids Res., 40:8144-8154, 2012

PubMed Abstract: Exonucleases are key enzymes in the maintenance of genome stability, processing of immature RNA precursors and degradation of unnecessary nucleic acids. However, it remains unclear how exonucleases digest nucleic acids to generate correct end products for next-step processing. Here we show how the exonuclease RNase T stops its trimming precisely. The crystal structures of RNase T in complex with a stem-loop DNA, a GG dinucleotide and single-stranded DNA with different 3'-end sequences demonstrate why a duplex with a short 3'-overhang, a dinucleotide and a ssDNA with a 3'-end C cannot be further digested by RNase T. Several hydrophobic residues in RNase T change their conformation upon substrate binding and induce an active or inactive conformation in the active site that construct a precise machine to determine which substrate should be digested based on its sequence, length and structure. These studies thus provide mechanistic insights into how RNase T prevents over digestion of its various substrates, and the results can be extrapolated to the thousands of members of the DEDDh family of exonucleases.

PubMed: 22718982
DOI: 10.1093/nar/gks548

Experimental method

X-RAY DIFFRACTION (2.298 Å)