6aix | pdb_00006aix
Crystal structure of DXO in complex with adenosine 3', 5' bisphosphate and two magnesium ions
Structural highlights
Function[DXO_MOUSE] Ribonuclease that specifically degrades pre-mRNAs with a defective 5' end cap and is part of a pre-mRNA capping quality control. Has decapping, pyrophosphohydrolase and 5'-3' exonuclease activities. Has decapping activity toward incomplete 5' end cap mRNAs such as unmethylated 5' end-capped RNA to release GpppN and 5' end monophosphate RNA. The 5' end monophosphate RNA is then degraded by the 5'-3' exoribonuclease activity, enabling this enzyme to decap and degrade incompletely capped mRNAs. Also possesses RNA 5'-pyrophosphohydrolase activity by hydrolyzing the 5' end triphosphate to release pyrophosphates.[1] Publication Abstract from PubMedThe decapping exoribonuclease DXO functions in pre-mRNA capping quality control, and shows multiple biochemical activities such as decapping, deNADding, pyrophosphohydrolase, and 5'-3' exoribonuclease activities. Previous studies revealed the molecular mechanisms of DXO based on the structures in complexes with a product, substrate mimic, cap analogue, and 3'-NADP(+). Despite several reports on the substrate-specific reaction mechanism, the inhibitory mechanism of DXO remains elusive. Here, we demonstrate that adenosine 3', 5'-bisphosphate (pAp), a known inhibitor of the 5'-3' exoribonuclease Xrn1, inhibits the nuclease activity of DXO based on the results of structural and biochemical experiments. We determined the crystal structure of the DXO-pAp-Mg(2+) complex at 1.8A resolution. In comparison with the DXO-RNA product complex, the position of pAp is well superimposed with the first nucleotide of the product RNA in the vicinity of two magnesium ions. Furthermore, biochemical assays showed that the inhibition by pAp is comparable between Xrn1 and DXO. Collectively, these structural and biochemical studies reveal that pAp inhibits the activities of DXO by occupying the active site to act as a competitive inhibitor. Molecular mechanism for the inhibition of DXO by adenosine 3',5'-bisphosphate.,Yun JS, Yoon JH, Choi YJ, Son YJ, Kim S, Tong L, Chang JH Biochem Biophys Res Commun. 2018 Sep 26;504(1):89-95. doi:, 10.1016/j.bbrc.2018.08.135. Epub 2018 Sep 1. PMID:30180947[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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