5ULJ

Crystal structure of Scheffersomyces stipitis Rai1 in complex with (3'-NADP)+ and calcium ion

Summary for 5ULJ

• Entry DOI: 10.2210/pdb5ulj/pdb
• Descriptor: RAI1, CALCIUM ION, [[(2R,3S,4R,5R)-5-(3-aminocarbonyl-4H-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate, ... (5 entities in total)
• Functional Keywords: hydrolase, nadp
• Biological source: Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) (yeast)
• Total number of polymer chains: 4
• Total formula weight: 188479.84

Authors

Doamekpor, S.K.,Tong, L. (deposition date: 2017-01-24, release date: 2017-05-17, Last modification date: 2024-03-06)

Primary citation

Jiao, X.,Doamekpor, S.K.,Bird, J.G.,Nickels, B.E.,Tong, L.,Hart, R.P.,Kiledjian, M.
5' End Nicotinamide Adenine Dinucleotide Cap in Human Cells Promotes RNA Decay through DXO-Mediated deNADding.
Cell, 168:1015-1027.e10, 2017

PubMed Abstract: Eukaryotic mRNAs generally possess a 5' end N7 methyl guanosine (mG) cap that promotes their translation and stability. However, mammalian mRNAs can also carry a 5' end nicotinamide adenine dinucleotide (NAD) cap that, in contrast to the mG cap, does not support translation but instead promotes mRNA decay. The mammalian and fungal noncanonical DXO/Rai1 decapping enzymes efficiently remove NAD caps, and cocrystal structures of DXO/Rai1 with 3'-NADP illuminate the molecular mechanism for how the "deNADding" reaction produces NAD and 5' phosphate RNA. Removal of DXO from cells increases NAD-capped mRNA levels and enables detection of NAD-capped intronic small nucleolar RNAs (snoRNAs), suggesting NAD caps can be added to 5'-processed termini. Our findings establish NAD as an alternative mammalian RNA cap and DXO as a deNADding enzyme modulating cellular levels of NAD-capped RNAs. Collectively, these data reveal that mammalian RNAs can harbor a 5' end modification distinct from the classical mG cap that promotes rather than inhibits RNA decay.

PubMed: 28283058
DOI: 10.1016/j.cell.2017.02.019

Experimental method

X-RAY DIFFRACTION (1.911 Å)