6WRE

Crystal structure of mouse DXO in complex with 5'-OH RNA substrate mimic and calcium ion

Summary for 6WRE

• Entry DOI: 10.2210/pdb6wre/pdb
• Descriptor: Decapping and exoribonuclease protein, RNA (5'-R(*UP*(U37)P*(U37)P*UP)-3'), CALCIUM ION, ... (5 entities in total)
• Functional Keywords: 5'-oh, rna, cap, hydrolase
• Biological source: Mus musculus (Mouse); More
• Total number of polymer chains: 2
• Total formula weight: 45320.96

Authors

Doamekpor, S.K.,Tong, L. (deposition date: 2020-04-29, release date: 2020-05-13, Last modification date: 2023-10-18)

Primary citation

Doamekpor, S.K.,Gozdek, A.,Kwasnik, A.,Kufel, J.,Tong, L.
A novel 5'-hydroxyl dinucleotide hydrolase activity for the DXO/Rai1 family of enzymes.
Nucleic Acids Res., 48:349-358, 2020

PubMed Abstract: Modifications at the 5'-end of RNAs play a pivotal role in determining their fate. In eukaryotes, the DXO/Rai1 family of enzymes removes numerous 5'-end RNA modifications, thereby regulating RNA turnover. Mouse DXO catalyzes the elimination of incomplete 5'-end caps (including pyrophosphate) and the non-canonical NAD+ cap on mRNAs, and possesses distributive 5'-3' exoribonuclease activity toward 5'-monophosphate (5'-PO4) RNA. Here, we demonstrate that DXO also catalyzes the hydrolysis of RNAs bearing a 5'-hydroxyl group (5'-OH RNA). The crystal structure of DXO in complex with a 5'-OH RNA substrate mimic at 2.0 Å resolution provides elegant insight into the molecular mechanism of this activity. More importantly, the structure predicts that DXO first removes a dinucleotide from 5'-OH RNA. Our nuclease assays confirm this prediction and demonstrate that this 5'-hydroxyl dinucleotide hydrolase (HDH) activity for DXO is higher than the subsequent 5'-3' exoribonuclease activity for selected substrates. Fission yeast Rai1 also has HDH activity although it does not have 5'-3' exonuclease activity, and the Rat1-Rai1 complex can completely degrade 5'-OH RNA. An Arabidopsis DXO1 variant is active toward 5'-OH RNA but prefers 5'-PO4 RNA. Collectively, these studies demonstrate the diverse activities of DXO/Rai1 and expands the collection of RNA substrates that can undergo 5'-3' mediated decay.

PubMed: 31777937
DOI: 10.1093/nar/gkz1107

Experimental method

X-RAY DIFFRACTION (2 Å)