4KB0

Crystal structure of RNase T in complex with a bluge DNA (Two nucleotide insertion CC )

Summary for 4KB0

• Entry DOI: 10.2210/pdb4kb0/pdb
• Related: 3NGY 3V9W 3V9X 3V9Z 3VA0 3VA3 4KAZ 4KB1
• Descriptor: Ribonuclease T, DNA (5'-D(*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*CP*C)-3'), MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: dnaq, dedd, exonuclease, dna repair, hydrolase-dna complex, hydrolase/dna
• Biological source: Escherichia coli
• Total number of polymer chains: 4
• Total formula weight: 62424.30

Authors

Hsiao, Y.-Y.,Yuan, H.S. (deposition date: 2013-04-23, release date: 2014-03-05, Last modification date: 2023-09-20)

Primary citation

Hsiao, Y.Y.,Fang, W.H.,Lee, C.C.,Chen, Y.P.,Yuan, H.S.
Structural insights into DNA repair by RNase T--an exonuclease processing 3' end of structured DNA in repair pathways.
Plos Biol., 12:e1001803-e1001803, 2014

PubMed Abstract: DNA repair mechanisms are essential for preservation of genome integrity. However, it is not clear how DNA are selected and processed at broken ends by exonucleases during repair pathways. Here we show that the DnaQ-like exonuclease RNase T is critical for Escherichia coli resistance to various DNA-damaging agents and UV radiation. RNase T specifically trims the 3' end of structured DNA, including bulge, bubble, and Y-structured DNA, and it can work with Endonuclease V to restore the deaminated base in an inosine-containing heteroduplex DNA. Crystal structure analyses further reveal how RNase T recognizes the bulge DNA by inserting a phenylalanine into the bulge, and as a result the 3' end of blunt-end bulge DNA can be digested by RNase T. In contrast, the homodimeric RNase T interacts with the Y-structured DNA by a different binding mode via a single protomer so that the 3' overhang of the Y-structured DNA can be trimmed closely to the duplex region. Our data suggest that RNase T likely processes bulge and bubble DNA in the Endonuclease V-dependent DNA repair, whereas it processes Y-structured DNA in UV-induced and various other DNA repair pathways. This study thus provides mechanistic insights for RNase T and thousands of DnaQ-like exonucleases in DNA 3'-end processing.

PubMed: 24594808
DOI: 10.1371/journal.pbio.1001803

Experimental method

X-RAY DIFFRACTION (2.004 Å)