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Literature summary extracted from

  • Sharma, S.; Grudzien-Nogalska, E.; Hamilton, K.; Jiao, X.; Yang, J.; Tong, L.; Kiledjian, M.
    Mammalian Nudix proteins cleave nucleotide metabolite caps on RNAs (2020), Nucleic Acids Res., 48, 6788-6798.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
3.6.1.62 cloning of Nudt16 residues 1-184 into a modified pET28a vector in-frame with an N-terminal His6-tagged yeast SMT3 SUMO gene recombinant overexpression in Escherichia coli strain BL21(DE3) Homo sapiens
3.6.1.77 expressed in Escherichia coli BL21(DE3) cells Homo sapiens

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.6.1.62 purified human Nudt16 free form or in complex with FAD, sitting-drop vapor diffusion method, mixing of 25 mg/ml protein in 20 mM HEPES, pH 7.5, 250 mM NaCl, 1 mM MnCl2, and 10 mM DTT, with reservoir solution containing 0.2 M ammonium chloride, 20% w/v PEG 3350 and (for free Nudt16) 100 mM MES, pH 5.5, 2 weeks, 20°C, X-ray diffraction structure determination and analysis at 2.3-2.7 A resolution, molecular replacement using PDB ID 3COU as the search model Homo sapiens

Protein Variants

EC Number Protein Variants Comment Organism
3.6.1.62 additional information generation of three CRISPR/Cas9n directed human Nudt16 gene knockout monoclonal cell lines (Nudt16-KO), a statistically significant 1.3fold increase in total NAD-capped RNA is detected by NAD-capQ in cells devoid of Nudt16 compared to the control knockout Homo sapiens

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.6.1.62 Mg2+ required Homo sapiens
3.6.1.62 Mg2+ required Mammalia

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.6.1.62 5'-end (methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + H2O Mammalia
-
 methyl-GDP + 5'-end phospho-ribonucleoside in mRNA + 2 H+
-
 ?
3.6.1.62 5'-end (methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + H2O Homo sapiens
-
 methyl-GDP + 5'-end phospho-ribonucleoside in mRNA + 2 H+
-
 ?
3.6.1.62 5'-end (N7-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + H2O Mammalia
-
 N7-methyl-GDP + 5'-end phospho-ribonucleoside in mRNA + 2 H+
-
 ?
3.6.1.62 5'-end (N7-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + H2O Homo sapiens
-
 N7-methyl-GDP + 5'-end phospho-ribonucleoside in mRNA + 2 H+
-
 ?
3.6.1.62 5'-end CoA-ribonucleoside in mRNA + H2O Mammalia
-
 5'-end phospho-adenosine-phospho-ribonucleoside in mRNA + (R)-4'-phosphopantetheine + 2 H+
-
 ?
3.6.1.62 5'-end CoA-ribonucleoside in mRNA + H2O Homo sapiens
-
 5'-end phospho-adenosine-phospho-ribonucleoside in mRNA + (R)-4'-phosphopantetheine + 2 H+
-
 ?
3.6.1.62 5'-end FAD-phospho-ribonucleoside in mRNA + H2O Mammalia cf. EC 3.6.1.18 5'-end phospho-adenosine-phospho-ribonucleoside in mRNA + FMN + 2 H+
-
 ?
3.6.1.62 5'-end FAD-phospho-ribonucleoside in mRNA + H2O Homo sapiens cf. EC 3.6.1.18 5'-end phospho-adenosine-phospho-ribonucleoside in mRNA + FMN + 2 H+
-
 ?
3.6.1.62 5'-end NAD+-phospho-ribonucleoside in mRNA + H2O Mammalia cf. EC 3.6.1.22 5'-end phospho-adenosine-phospho-ribonucleoside in mRNA + beta-nicotinamide D-ribonucleotide + 2 H+
-
 ?
3.6.1.62 5'-end NAD+-phospho-ribonucleoside in mRNA + H2O Homo sapiens cf. EC 3.6.1.22 5'-end phospho-adenosine-phospho-ribonucleoside in mRNA + beta-nicotinamide D-ribonucleotide + 2 H+
-
 ?
3.6.1.77 coenzyme A + H2O Homo sapiens
-
 adenosine 3',5'-bisphosphate + 4'-phosphopantetheine
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
3.6.1.62 Homo sapiens Q96DE0
-
-
3.6.1.62 Mammalia
-
-
-
3.6.1.62 no activity with mammalian Nudix hydrolase Nudt1
-
-
-
3.6.1.62 no activity with mammalian Nudix hydrolase Nudt11
-
-
-
3.6.1.62 no activity with mammalian Nudix hydrolase Nudt13
-
-
-
3.6.1.62 no activity with mammalian Nudix hydrolase Nudt14
-
-
-
3.6.1.62 no activity with mammalian Nudix hydrolase Nudt18
-
-
-
3.6.1.62 no activity with mammalian Nudix hydrolase Nudt21
-
-
-
3.6.1.62 no activity with mammalian Nudix hydrolase Nudt22
-
-
-
3.6.1.62 no activity with mammalian Nudix hydrolase Nudt4
-
-
-
3.6.1.62 no activity with mammalian Nudix hydrolase Nudt5
-
-
-
3.6.1.62 no activity with mammalian Nudix hydrolase Nudt6
-
-
-
3.6.1.62 no activity with mammalian Nudix hydrolase Nudt9
-
-
-
3.6.1.77 Homo sapiens
-
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
3.6.1.62 recombinant His6/SUMO-tagged Nudt16 residues 1-184 from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, tag removal, heparin affinity chromatography, and gel filtration Homo sapiens
3.6.1.77 Ni-NTA column chromatography, HiTrap column chromatography, and Sephacryl S-200 gel filtration Homo sapiens

Source Tissue

EC Number Source Tissue Comment Organism Textmining
3.6.1.77 HEK-293T cell
-
 Homo sapiens
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.6.1.62 5'-end (methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + H2O
-
 Mammalia methyl-GDP + 5'-end phospho-ribonucleoside in mRNA + 2 H+
-
 ?
3.6.1.62 5'-end (methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + H2O
-
 Homo sapiens methyl-GDP + 5'-end phospho-ribonucleoside in mRNA + 2 H+
-
 ?
3.6.1.62 5'-end (N7-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + H2O
-
 Mammalia N7-methyl-GDP + 5'-end phospho-ribonucleoside in mRNA + 2 H+
-
 ?
3.6.1.62 5'-end (N7-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + H2O
-
 Homo sapiens N7-methyl-GDP + 5'-end phospho-ribonucleoside in mRNA + 2 H+
-
 ?
3.6.1.62 5'-end CoA-ribonucleoside in mRNA + H2O
-
 Mammalia 5'-end phospho-adenosine-phospho-ribonucleoside in mRNA + (R)-4'-phosphopantetheine + 2 H+
-
 ?
3.6.1.62 5'-end CoA-ribonucleoside in mRNA + H2O
-
 Homo sapiens 5'-end phospho-adenosine-phospho-ribonucleoside in mRNA + (R)-4'-phosphopantetheine + 2 H+
-
 ?
3.6.1.62 5'-end FAD-phospho-ribonucleoside in mRNA + H2O cf. EC 3.6.1.18 Mammalia 5'-end phospho-adenosine-phospho-ribonucleoside in mRNA + FMN + 2 H+
-
 ?
3.6.1.62 5'-end FAD-phospho-ribonucleoside in mRNA + H2O cf. EC 3.6.1.18 Homo sapiens 5'-end phospho-adenosine-phospho-ribonucleoside in mRNA + FMN + 2 H+
-
 ?
3.6.1.62 5'-end NAD+-phospho-ribonucleoside in mRNA + H2O cf. EC 3.6.1.22 Mammalia 5'-end phospho-adenosine-phospho-ribonucleoside in mRNA + beta-nicotinamide D-ribonucleotide + 2 H+
-
 ?
3.6.1.62 5'-end NAD+-phospho-ribonucleoside in mRNA + H2O cf. EC 3.6.1.22 Homo sapiens 5'-end phospho-adenosine-phospho-ribonucleoside in mRNA + beta-nicotinamide D-ribonucleotide + 2 H+
-
 ?
3.6.1.62 additional information binding and metal-coordinated hydrolysis of FAD by Nudt16, overview Homo sapiens ?
-
-
3.6.1.77 CoA ester + H2O
-
 Homo sapiens ?
-
 ?
3.6.1.77 coenzyme A + H2O
-
 Homo sapiens adenosine 3',5'-bisphosphate + 4'-phosphopantetheine
-
 ?
3.6.1.77 dephospho-CoA + H2O
-
 Homo sapiens ?
-
 ?

Synonyms

EC Number Synonyms Comment Organism
3.6.1.62 Dcp2
-
 Mammalia
3.6.1.62 Nudix hydrolase
-
 Mammalia
3.6.1.62 Nudix hydrolase
-
 Homo sapiens
3.6.1.62 Nudt12
-
 Mammalia
3.6.1.62 Nudt15
-
 Mammalia
3.6.1.62 Nudt16
-
 Mammalia
3.6.1.62 Nudt16
-
 Homo sapiens
3.6.1.62 Nudt17
-
 Mammalia
3.6.1.62 Nudt19
-
 Mammalia
3.6.1.62 NUDT2
-
 Mammalia
3.6.1.62 NUDT3
-
 Mammalia
3.6.1.62 Nudt7
-
 Mammalia
3.6.1.62 Nudt8
-
 Mammalia
3.6.1.77 Nudt19
-
 Homo sapiens
3.6.1.77 Nudt7
-
 Homo sapiens
3.6.1.77 Nudt8
-
 Homo sapiens

General Information

EC Number General Information Comment Organism
3.6.1.62 evolution the enzyme belongs to the NUDIX hydrolase family Mammalia
3.6.1.62 evolution the enzyme belongs to the NUDIX hydrolase family Homo sapiens
3.6.1.62 additional information molecular analysis of the binding and metal-coordinated hydrolysis of FAD by Nudt16, overview Homo sapiens
3.6.1.62 physiological function analysis of 5'caps has revealed that in addition to m7GpppN, mGpppN, and NAD, mammalian RNAs also contain other metabolite caps including flavin adenine dinucleotide (FAD) and dephosphoCoA (dpCoA). Systematical screening of mammalian Nudix proteins for their potential deNADing, FAD cap decapping (deFADding) and dpCoA cap decapping (deCoAping) activity, detailed overview. Role for the Nudix hydrolase Nudt2 in decapping FAD-capped RNAs (deFADding) and dpCoA-capped RNAs (deCoAping) in cells Mammalia
3.6.1.62 physiological function analysis of 5'caps has revealed that in addition to m7GpppN, mGpppN, and NAD, mammalian RNAs also contain other metabolite caps including flavin adenine dinucleotide (FAD) and dephosphoCoA (dpCoA). Systematical screening of mammalian Nudix proteins for their potential deNADing, FAD cap decapping (deFADding) and dpCoA cap decapping (deCoAping) activity, detailed overview. Role for the Nudix hydrolase Nudt3 in decapping FAD-capped RNAs (deFADding) and dpCoA-capped RNAs (deCoAping) in cells Mammalia
3.6.1.62 physiological function analysis of 5'caps has revealed that in addition to m7GpppN, mGpppN, and NAD, mammalian RNAs also contain other metabolite caps including flavin adenine dinucleotide (FAD) and dephosphoCoA (dpCoA). Systematical screening of mammalian Nudix proteins for their potential deNADing, FAD cap decapping (deFADding) and dpCoA cap decapping (deCoAping) activity, detailed overview. Role for the Nudix hydrolase Nudt7 in decapping dpCoA-capped RNAs (deCoAping) in cells Mammalia
3.6.1.62 physiological function analysis of 5'caps has revealed that in addition to m7GpppN, mGpppN, and NAD, mammalian RNAs also contain other metabolite caps including flavin adenine dinucleotide (FAD) and dephosphoCoA (dpCoA). Systematical screening of mammalian Nudix proteins for their potential deNADing, FAD cap decapping (deFADding) and dpCoA cap decapping (deCoAping) activity, detailed overview. Role for the Nudix hydrolase Nudt8 in decapping dpCoA-capped RNAs (deCoAping) in cells Mammalia
3.6.1.62 physiological function analysis of 5'caps has revealed that in addition to m7GpppN, mGpppN, and NAD, mammalian RNAs also contain other metabolite caps including flavin adenine dinucleotide (FAD) and dephosphoCoA (dpCoA). Systematical screening of mammalian Nudix proteins for their potential deNADing, FAD cap decapping (deFADding) and dpCoA cap decapping (deCoAping) activity, detailed overview. Role for the Nudix hydrolase Nudt12 in decapping NAD-capped RNAs (deNADding) and dpCoA-capped RNAs (deCoAping) in cells Mammalia
3.6.1.62 physiological function analysis of 5'caps has revealed that in addition to m7GpppN, mGpppN, and NAD, mammalian RNAs also contain other metabolite caps including flavin adenine dinucleotide (FAD) and dephosphoCoA (dpCoA). Systematical screening of mammalian Nudix proteins for their potential deNADing, FAD cap decapping (deFADding) and dpCoA cap decapping (deCoAping) activity, detailed overview. Role for the Nudix hydrolase Nudt15 in decapping dpCoA-capped RNAs (deCoAping) in cells Mammalia
3.6.1.62 physiological function analysis of 5'caps has revealed that in addition to m7GpppN, mGpppN, and NAD, mammalian RNAs also contain other metabolite caps including flavin adenine dinucleotide (FAD) and dephosphoCoA (dpCoA). Systematical screening of mammalian Nudix proteins for their potential deNADing, FAD cap decapping (deFADding) and dpCoA cap decapping (deCoAping) activity, detailed overview. Role for the Nudix hydrolase Nudt16 in decapping FAD-capped RNAs (deFADding), NAD-capped RNAs (deNADding) and dpCoA-capped RNAs (deCoAping) in cells Mammalia
3.6.1.62 physiological function analysis of 5'caps has revealed that in addition to m7GpppN, mGpppN, and NAD, mammalian RNAs also contain other metabolite caps including flavin adenine dinucleotide (FAD) and dephosphoCoA (dpCoA). Systematical screening of mammalian Nudix proteins for their potential deNADing, FAD cap decapping (deFADding) and dpCoA cap decapping (deCoAping) activity, detailed overview Mammalia
3.6.1.62 physiological function analysis of 5'caps has revealed that in addition to m7GpppN, mGpppN, and NAD, mammalian RNAs also contain other metabolite caps including flavin adenine dinucleotide (FAD) and dephosphoCoA (dpCoA). Systematical screening of mammalian Nudix proteins for their potential deNADing, FAD cap decapping (deFADding) and dpCoA cap decapping (deCoAping) activity, detailed overview. Role for the Nudix hydrolase Nudt19 in decapping dpCoA-capped RNAs (deCoAping) in cells Mammalia
3.6.1.62 physiological function analysis of 5'caps has revealed that in addition to m7GpppN, mGpppN, and NAD, mammalian RNAs also contain other metabolite caps including flavin adenine dinucleotide (FAD) and dephosphoCoA (dpCoA). Systematical screening of mammalian Nudix proteins for their potential deNADing, FAD cap decapping (deFADding) and dpCoA cap decapping (deCoAping) activity, detailed overview. Role for the Nudix hydrolase Nudt16 in decapping FAD-capped RNAs (deFADding), NAD-capped RNAs (deNADding) and dpCoA-capped RNAs (deCoAping) in cells Homo sapiens