Enzymes
| UniProtKB help_outline | 569 proteins |
Reaction participants Show >> << Hide
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Namehelp_outline
a 5'-end CoA-ribonucleoside in mRNA
Identifier
RHEA-COMP:17276
Reactive part
help_outline
- Name help_outline a 5'-CoA-ribonucleoside residue Identifier CHEBI:172371 Charge -3 Formula C26H39N7O19P3SR SMILEShelp_outline N1(C2=C(C(=NC=N2)N)N=C1)[C@@H]3O[C@H](COP(OP(OCC(C)([C@H](C(NCCC(NCCS)=O)=O)O)C)(=O)[O-])(=O)[O-])[C@H]([C@H]3O)OP(OC[C@H]4O[C@H]([C@@H]([C@@H]4O*)O)*)(=O)[O-] 2D coordinates Mol file for the small molecule Search links Involved in 2 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
- Name help_outline H2O Identifier CHEBI:15377 (CAS: 7732-18-5) help_outline Charge 0 Formula H2O InChIKeyhelp_outline XLYOFNOQVPJJNP-UHFFFAOYSA-N SMILEShelp_outline [H]O[H] 2D coordinates Mol file for the small molecule Search links Involved in 6,337 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
- Name help_outline 3'-dephospho-CoA Identifier CHEBI:57328 Charge -2 Formula C21H33N7O13P2S InChIKeyhelp_outline KDTSHFARGAKYJN-IBOSZNHHSA-L SMILEShelp_outline CC(C)(COP([O-])(=O)OP([O-])(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n1cnc2c(N)ncnc12)[C@@H](O)C(=O)NCCC(=O)NCCS 2D coordinates Mol file for the small molecule Search links Involved in 7 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
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Namehelp_outline
a 5'-end phospho-ribonucleoside in mRNA
Identifier
RHEA-COMP:15692
Reactive part
help_outline
- Name help_outline 5'-end ribonucleotide residue Identifier CHEBI:138282 Charge -2 Formula C5H7O7PR SMILEShelp_outline [C@@H]1(O[C@H]([C@@H]([C@@H]1O*)O)*)COP([O-])(=O)[O-] 2D coordinates Mol file for the small molecule Search links Involved in 28 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
- Name help_outline H+ Identifier CHEBI:15378 Charge 1 Formula H InChIKeyhelp_outline GPRLSGONYQIRFK-UHFFFAOYSA-N SMILEShelp_outline [H+] 2D coordinates Mol file for the small molecule Search links Involved in 9,717 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Cross-references
| RHEA:67496 | RHEA:67497 | RHEA:67498 | RHEA:67499 | |
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| Reaction direction help_outline | undefined | left-to-right | right-to-left | bidirectional |
| UniProtKB help_outline |
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Publications
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Mammalian Nudix proteins cleave nucleotide metabolite caps on RNAs.
Sharma S., Grudzien-Nogalska E., Hamilton K., Jiao X., Yang J., Tong L., Kiledjian M.
We recently reported the presence of nicotinamide adenine dinucleotide (NAD)-capped RNAs in mammalian cells and a role for DXO and the Nudix hydrolase Nudt12 in decapping NAD-capped RNAs (deNADding) in cells. Analysis of 5'caps has revealed that in addition to NAD, mammalian RNAs also contain othe ... >> More
We recently reported the presence of nicotinamide adenine dinucleotide (NAD)-capped RNAs in mammalian cells and a role for DXO and the Nudix hydrolase Nudt12 in decapping NAD-capped RNAs (deNADding) in cells. Analysis of 5'caps has revealed that in addition to NAD, mammalian RNAs also contain other metabolite caps including flavin adenine dinucleotide (FAD) and dephosphoCoA (dpCoA). In the present study we systematically screened all mammalian Nudix proteins for their potential deNADing, FAD cap decapping (deFADding) and dpCoA cap decapping (deCoAping) activity. We demonstrate that Nudt16 is a novel deNADding enzyme in mammalian cells. Additionally, we identified seven Nudix proteins-Nudt2, Nudt7, Nudt8, Nudt12, Nudt15, Nudt16 and Nudt19, to possess deCoAping activity in vitro. Moreover, our screening revealed that both mammalian Nudt2 and Nudt16 hydrolyze FAD-capped RNAs in vitro with Nudt16 regulating levels of FAD-capped RNAs in cells. All decapping activities identified hydrolyze the metabolite cap substrate within the diphosphate linkage. Crystal structure of human Nudt16 in complex with FAD at 2.7 Å resolution provide molecular insights into the binding and metal-coordinated hydrolysis of FAD by Nudt16. In summary, our study identifies novel cellular deNADding and deFADding enzymes and establishes a foundation for the selective functionality of the Nudix decapping enzymes on non-canonical metabolite caps. << Less
Nucleic Acids Res. 48:6788-6798(2020) [PubMed] [EuropePMC]
This publication is cited by 3 other entries.
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DXO/Rai1 enzymes remove 5'-end FAD and dephospho-CoA caps on RNAs.
Doamekpor S.K., Grudzien-Nogalska E., Mlynarska-Cieslak A., Kowalska J., Kiledjian M., Tong L.
In eukaryotes, the DXO/Rai1 enzymes can eliminate most of the incomplete and non-canonical NAD caps through their decapping, deNADding and pyrophosphohydrolase activities. Here, we report that these enzymes can also remove FAD and dephospho-CoA (dpCoA) non-canonical caps from RNA, and we have name ... >> More
In eukaryotes, the DXO/Rai1 enzymes can eliminate most of the incomplete and non-canonical NAD caps through their decapping, deNADding and pyrophosphohydrolase activities. Here, we report that these enzymes can also remove FAD and dephospho-CoA (dpCoA) non-canonical caps from RNA, and we have named these activities deFADding and deCoAping. The crystal structures of mammalian DXO with 3'-FADP or CoA and fission yeast Rai1 with 3'-FADP provide elegant insight to these activities. FAD and CoA are accommodated in the DXO/Rai1 active site by adopting folded conformations. The flavin of FAD and the pantetheine group of CoA contact the same region at the bottom of the active site tunnel, which undergoes conformational changes to accommodate the different cap moieties. We have developed FAD-capQ to detect and quantify FAD-capped RNAs and determined that FAD caps are present on short RNAs (with less than ∼200 nucleotides) in human cells and that these RNAs are stabilized in the absence of DXO. << Less
Nucleic Acids Res. 48:6136-6148(2020) [PubMed] [EuropePMC]
This publication is cited by 2 other entries.