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Information on EC 3.6.1.62 - 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase and Organism(s) Homo sapiens
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3.6.1.62 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolaseIUBMB Comments
Decapping of mRNA is a critical step in eukaryotic mRNA turnover. The enzyme is unable to cleave a free cap structure (m7GpppG) . The enzyme from Vaccinia virus is synergistically activated in the presence of Mg2+ and Mn2+ .
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The taxonomic range for the selected organisms is: Homo sapiens
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
Synonyms
nudt16, dcp1p, hdcp2, dcp2p, mrna decapping enzyme, nudt19, hnudt16, d10 protein, d10 decapping enzyme, nudt17, 
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topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
Nudt16
SYSTEMATIC NAME
IUBMB Comments
5'-(N7-methylguanosine 5'-triphospho)-[mRNA] N7-methylguanosine-5'-diphosphate phosphohydrolase
Decapping of mRNA is a critical step in eukaryotic mRNA turnover. The enzyme is unable to cleave a free cap structure (m7GpppG) [3]. The enzyme from Vaccinia virus is synergistically activated in the presence of Mg2+ and Mn2+ [5].
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
5'-(N7-methylguanosine 5'-triphospho)-mRNA + H2O
m7GDP + 5'-phospho-mRNA
-
luciferase mRNA
-
-
?
a 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] + H2O
N7-methylguanosine 5'-diphosphate + a 5'-phospho-[mRNA]
-
-
-
-
?
ApppG + H2O
?
-
unmethylated dinucleotide ApppG is hydrolyzed by the enzyme with greater efficiency than m7GpppG (94.32% hydrolysis after 100 min)
-
-
?
GpppA-[16nt mRNA] + H2O
?
-
unmethylated oligonucleotide GpppA-16nt is hydrolyzed by the enzyme with greater efficiency than m7GpppG-[16nt RNA] (89.75% hydrolysis after 60 min)
-
-
?
GpppG + H2O
?
-
unmethylated dinucleotide GpppG is hydrolyzed by the enzyme with greater efficiency than m7GpppG (98.79% hydrolysis after 40 min)
-
-
?
GpppG-[16nt mRNA] + H2O
?
-
unmethylated oligonucleotide GpppG-16nt is hydrolyzed by the enzyme with greater efficiency than m7GpppG-16nt (86.9% hydrolysis after 180 min)
-
-
?
m7G5'ppp5'-U3 snoRNA + H2O
m7GDP + 5'-phospho-U3 snoRNA
removes m7G and m227G caps from RNAs, rendering them substrates for 5'-3' exonucleases for degradation in vivo. The metal identity determines both the efficiency of decapping and the RNA substrate specificity. In Mg2+ the protein hydrolyzes the 5' cap from only one RNA substrate: U8 small nucleolar RNA. In the presence of Mn2+ or Co2+ all RNAs are substrates and the decapping efficiency is higher. The metal that binds the X29/H29K proteins in vivo may determine whether these decapping proteins function solely as a negative regulator of ribosome biogenesis or can decap a wider variety of nuclear-limited RNAs
-
-
?
m7G5'ppp5'-U8 snomRNA + H2O
m7GDP + 5'-phospho-U8 snomRNA
-
hNUDT16 relies on divalent cations for its cap-hydrolysis activity to remove m7GDP and m227GDP from RNAs. hNUDT16 without the coordination of metals can not catalyze the hydrolytic reaction since no detectable cleaved products can be observed for either the U8 snoRNA or the mRNA substrate. Both Mg2+ and Mn2+ can effectively switch the protein from apoenzyme to holoenzyme. Mn2+ is more efficient as the activating factor
-
-
?
m7G5'ppp5'-mRNA + H2O
m7GDP + 5'-phospho-mRNA
Dcp2 is involved in mRNA decay
-
-
?
m7G5'ppp5'-mRNA + H2O
m7GDP + 5'-phospho-mRNA
decapping of mRNA is a critical step in eukaryotic mRNA turnover
-
-
?
m7G5'ppp5'-mRNA + H2O
m7GDP + 5'-phospho-mRNA
-
hNUDT16 relies on divalent cations for its cap-hydrolysis activity to remove m7GDP and m227GDP from RNAs
-
-
?
m7G5'ppp5'-mRNA + H2O
m7GDP + 5'-phospho-mRNA
-
mRNA decapping is a critical step in the control of mRNA stability and gene expression
-
-
?
m7G5'ppp5'-mRNA + H2O
m7GDP + 5'-phospho-mRNA
regulation of RNA degradation plays an important role in the control of gene expression. Mammalian cells possess multiple mRNA decapping enzymes to regulate mRNA turnover. Nudt16, like Dcp2, is involved in mRNA stability. Each decapping enzyme can selectively affect the stability of at least a subset of mRNAs
-
-
?
m7G5'ppp5'-mRNA + H2O
m7GDP + 5'-phospho-mRNA
-
a 60 nucleotide element at the 5' end of the mRNA encoding Rrp41 is preferentially bound and decapped by Dcp2. Enhanced decapping of this element is dependent on the structural integrity of its first 33 nt and not its primary sequence. The structure consists of a stem-loop positioned <10 nt from the 5' end of the mRNA
-
-
?
m7G5'ppp5'-mRNA + H2O
m7GDP + 5'-phospho-mRNA
hDcp2 is unable to cleave a free cap structure (m7GpppG) generated by P1 nuclease treatment of a cap-labelled RNA. Preferentially cleaves methylated cap structure
-
-
?
m7G5'ppp5'-mRNA + H2O
m7GDP + 5'-phospho-mRNA
hDcp2-mediated decapping requires a functional Nudix (nucleotide diphosphate linked to an X moiety) pyrophosphatase motif
-
-
?
m7G5'ppp5'-mRNA + H2O
m7GDP + 5'-phospho-mRNA
Nudt16 can only function on capped RNA but not N7-methyl cap structure (m7GpppN)
-
-
?
m7G5'ppp5'-U8 snoRNA + H2O
m7GDP + 5'-phospho-U8 snoRNA
removes m7G and m227G caps from RNAs, rendering them substrates for 5'-3' exonucleases for degradation in vivo
-
-
?
m7G5'ppp5'-U8 snoRNA + H2O
m7GDP + 5'-phospho-U8 snoRNA
removes m7G and m227G caps from RNAs, rendering them substrates for 5'-3' exonucleases for degradation in vivo. The metal identity determines both the efficiency of decapping and the RNA substrate specificity. In Mg2+ the protein hydrolyzes the 5' cap from only one RNA substrate: U8 small nucleolar RNA. In the presence of Mn2+ or Co2+ all RNAs are substrates and the decapping efficiency is higher. The metal that binds the X29/H29K proteins in vivo may determine whether these decapping proteins function solely as a negative regulator of ribosome biogenesis or can decap a wider variety of nuclear-limited RNAs
-
-
?
additional information
?
-
-
X29 has decapping activity and releases m7GDP from full-length U8 RNA. The NUDIX domain in X29 is required for cap cleavage and release of m7GDP from U8 RNA. X29 can cleave the m227G cap present on U8 RNA in vivo
-
-
?
additional information
?
-
-
dinucleotide cap analogs and capped oligonucleotides containing guanine base in the first transcribed nucleotide are more susceptible to enzymatic digestion by the enzyme than their counterparts containing adenine
-
-
-
additional information
?
-
-
no hydrolysis of dinucleotide m7Gpppm7G after 100 min
-
-
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
a 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] + H2O
N7-methylguanosine 5'-diphosphate + a 5'-phospho-[mRNA]
-
-
-
-
?
m7G5'ppp5'-U8 snoRNA + H2O
m7GDP + 5'-phospho-U8 snoRNA
removes m7G and m227G caps from RNAs, rendering them substrates for 5'-3' exonucleases for degradation in vivo
-
-
?
m7G5'ppp5'-mRNA + H2O
m7GDP + 5'-phospho-mRNA
Dcp2 is involved in mRNA decay
-
-
?
m7G5'ppp5'-mRNA + H2O
m7GDP + 5'-phospho-mRNA
decapping of mRNA is a critical step in eukaryotic mRNA turnover
-
-
?
m7G5'ppp5'-mRNA + H2O
m7GDP + 5'-phospho-mRNA
-
hNUDT16 relies on divalent cations for its cap-hydrolysis activity to remove m7GDP and m227GDP from RNAs
-
-
?
m7G5'ppp5'-mRNA + H2O
m7GDP + 5'-phospho-mRNA
-
mRNA decapping is a critical step in the control of mRNA stability and gene expression
-
-
?
m7G5'ppp5'-mRNA + H2O
m7GDP + 5'-phospho-mRNA
regulation of RNA degradation plays an important role in the control of gene expression. Mammalian cells possess multiple mRNA decapping enzymes to regulate mRNA turnover. Nudt16, like Dcp2, is involved in mRNA stability. Each decapping enzyme can selectively affect the stability of at least a subset of mRNAs
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Co2+
Mg2+
Mn2+
Zn2+
-
confer only limited hydrolytic capability on hNUDT16. After 30 min incubation of the RNA substrate with the enzyme, only tiny amounts of m7GDP product are observed on the migration profiles
Co2+
-
confer only limited hydrolytic capability on hNUDT16. After 30 min incubation of the RNA substrate with the enzyme, only tiny amounts of m7GDP product are observed on the migration profiles
Co2+
the metal identity determines both the efficiency of decapping and the RNA substrate specificity. In Mg2+ the protein hydrolyzes the 5' cap from only one RNA substrate: U8 small nucleolar RNA. In the presence of Mn2+ or Co2+ all RNAs are substrates and the decapping efficiency is higher
Mg2+
-
hNUDT16 relies on divalent cations for its cap-hydrolysis activity to remove m7GDP and m227GDP from RNAs. hNUDT16 without the coordination of metals can not catalyze the hydrolytic reaction since no detectable cleaved products can be observed for either the U8 snoRNA or the mRNA substrate. Both Mg2+ and Mn2+ can effectively switch the protein from apoenzyme to holoenzyme. Mn2+ is more efficient as the activating factor
Mg2+
the metal identity determines both the efficiency of decapping and the RNA substrate specificity. In Mg2+ the protein hydrolyzes the 5' cap from only one RNA substrate: U8 small nucleolar RNA. In the presence of Mn2+ or Co2+ all RNAs are substrates and the decapping efficiency is higher. The metal that binds the X29/H29K proteins in vivo may determine whether these decapping proteins function solely as a negative regulator of ribosome biogenesis or can decap a wider variety of nuclear-limited RNAs
Mn2+
-
hNUDT16 relies on divalent cations for its cap-hydrolysis activity to remove m7GDP and m227GDP from RNAs. hNUDT16 without the coordination of metals can not catalyze the hydrolytic reaction since no detectable cleaved products can be observed for either the U8 snoRNA or the mRNA substrate. Both Mg2+ and Mn2+ can effectively switch the protein from apoenzyme to holoenzyme. Mn2+ is more efficient as the activating factor
Mn2+
the metal identity determines both the efficiency of decapping and the RNA substrate specificity. In Mg2+ the protein hydrolyzes the 5' cap from only one RNA substrate: U8 small nucleolar RNA. In the presence of Mn2+ or Co2+ all RNAs are substrates and the decapping efficiency is higher. The metal that binds the X29/H29K proteins in vivo may determine whether these decapping proteins function solely as a negative regulator of ribosome biogenesis or can decap a wider variety of nuclear-limited RNAs
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
poly(A) tail
presence of a poly(A) tail reduces the level of decapping by more than 2fold. The inhibition of decapping is reversed upon the addition of poly(A) competitor
-
additional information
(m7GpppG) is unable to inhibit competitively the hDcp2 reaction
-
additional information
-
(m7GpppG) is unable to inhibit competitively the hDcp2 reaction
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
hDcp2 requires the presence of an mRNA body attached to the cap to be active
-
additional information
-
hDcp2 requires the presence of an mRNA body attached to the cap to be active
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
additional information
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
hDcp2 is predominantly a nuclear protein, with low levels of in the cytoplasm
hDcp2 is predominantly a nuclear protein, with low levels of in the cytoplasm
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
-
reduction of enzyme protein levels in MCF-7 cells promotes increased cell migration and corresponding enhanced filopodia extensions. Enzyme depletion elevates RNA and protein expression of integrin beta6 and fibronectin, which in turn increases MCF-7 cell motility
physiological function
physiological function
-
mRNA decapping is a critical step in the control of mRNA stability and gene expression
physiological function
Nudt16, like Dcp2, is involved in mRNA stability. Each decapping enzyme can selectively affect the stability of at least a subset of mRNAs
physiological function
-
the enzyme is a modulator of MCF-7 breast cancer cell migration
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). DCP1A_HUMAN
582
0
63278
Swiss-Prot
other Location (Reliability: 2)
DCP1B_HUMAN
617
0
67723
Swiss-Prot
other Location (Reliability: 5)
DCP2_HUMAN
420
0
48423
Swiss-Prot
other Location (Reliability: 2)
NUD16_HUMAN
195
0
21273
Swiss-Prot
other Location (Reliability: 3)
A0A087WXD0_HUMAN
102
0
11676
TrEMBL
other Location (Reliability: 2)
A0A0S2Z5I2_HUMAN
307
0
34284
TrEMBL
other Location (Reliability: 2)
A0A0S2Z5K3_HUMAN
546
0
59488
TrEMBL
other Location (Reliability: 2)
F5H4R4_HUMAN
119
0
13544
TrEMBL
other Location (Reliability: 5)
B4DVJ6_HUMAN
153
0
17110
TrEMBL
other Location (Reliability: 5)
A0A087WVE6_HUMAN
191
0
21741
TrEMBL
other Location (Reliability: 2)
Q3LIB4_HUMAN
582
0
63246
TrEMBL
other Location (Reliability: 2)
A0A087WT55_HUMAN
260
0
29056
TrEMBL
other Location (Reliability: 2)
A0A0S2Z5R3_HUMAN
582
0
63309
TrEMBL
other Location (Reliability: 2)
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
apo-form and in complex with IMP and Mg2+, sitting drop vapor diffusion method, using 0.1 MChes pH 9.5 and 20% (w/v) PEG8000
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
A22V
the differences in the kinetic parameters caused by the A22V mutation are small (less than a factor 2)
E76Q
-
mutation totally abolishes the decapping activity under the standard assaying condition
E80Q
-
mutation totally abolishes the decapping activity under the standard assaying condition
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
HisTrap column chromatography, Superdex S200 gel filtration and Superdex S75 gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Ghosh, T.; Peterson, B.; Tomasevic, N.; Peculis, B.A.
Xenopus U8 snoRNA binding protein is a conserved nuclear decapping enzyme
Mol. Cell
13
817-828
2004
Homo sapiens, Xenopus laevis (Q6TEC1)
Zhang, J.; Gao, F.; Zhang, Q.; Chen, Q.; Qi, J.; Yan, J.
Crystallization and crystallographic analysis of human NUDT16
Acta Crystallogr. Sect. F
64
639-640
2008
Homo sapiens
van Dijk, E.; Cougot, N.; Meyer, S.; Babajko, S.; Wahle, E.; Sraphin, B.
Human Dcp2: a catalytically active mRNA decapping enzyme located in specific cytoplasmic structures
EMBO J.
21
6915-6924
2002
Homo sapiens (Q8IU60), Homo sapiens, Saccharomyces cerevisiae (P53550), Saccharomyces cerevisiae
Peculis, B.A.; Reynolds, K.; Cleland, M.
Metal determines efficiency and substrate specificity of the nuclear NUDIX decapping proteins X29 and H29K (Nudt16)
J. Biol. Chem.
282
24792-24805
2007
Homo sapiens (Q96DE0), Homo sapiens, Xenopus laevis (Q6TEC1)
Lykke-Andersen, J.
Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay
Mol. Cell. Biol.
22
8114-8121
2002
Homo sapiens (Q8IU60), Homo sapiens
Song, M.G.; Li, Y.; Kiledjian, M.
Multiple mRNA decapping enzymes in mammalian cells
Mol. Cell.
40
423-432
2010
Homo sapiens (Q8IU60), Homo sapiens (Q96DE0), Homo sapiens, Mus musculus (Q6P3D0), Mus musculus (Q9CYC6), Mus musculus
Li, Y.; Ho, E.S.; Gunderson, S.I.; Kiledjian, M.
Mutational analysis of a Dcp2-binding element reveals general enhancement of decapping by 5'-end stem-loop structures
Nucleic Acids Res.
37
2227-2237
2009
Homo sapiens
Wang, Z.; Jiao, X.; Carr-Schmid, A.; Kiledjian, M.
The hDcp2 protein is a mammalian mRNA decapping enzyme
Proc. Natl. Acad. Sci. USA
99
12663-12668
2002
Homo sapiens (Q8IU60), Homo sapiens
Lu, G.; Zhang, J.; Li, Y.; Li, Z.; Zhang, N.; Xu, X.; Wang, T.; Guan, Z.; Gao, G.F.; Yan, J.
hNUDT16: a universal decapping enzyme for small nucleolar RNA and cytoplasmic mRNA
Protein Cell
2
64-73
2011
Homo sapiens
Liu, S.W.; Jiao, X.; Liu, H.; Gu, M.; Lima, C.D.; Kiledjian, M.
Functional analysis of mRNA scavenger decapping enzymes
RNA
10
1412-1422
2004
Homo sapiens (Q8IU60)
Tresaugues, L.; Lundbaeck, T.; Welin, M.; Flodin, S.; Nyman, T.; Silvander, C.; Graeslund, S.; Nordlund, P.
Structural basis for the specificity of human NUDT16 and its regulation by inosine monophosphate
PLoS ONE
10
e0131507
2015
Homo sapiens (Q96DE0), Homo sapiens
Grudzien-Nogalska, E.; Jiao, X.; Song, M.G.; Hart, R.P.; Kiledjian, M.
Nudt3 is an mRNA decapping enzyme that modulates cell migration
RNA
22
773-781
2016
Homo sapiens
Grzela, R.; Nasilowska, K.; Lukaszewicz, M.; Tyras, M.; Stepinski, J.; Jankowska-Anyszka, M.; Bojarska, E.; Darzynkiewicz, E.
Hydrolytic activity of human Nudt16 enzyme on dinucleotide cap analogs and short capped oligonucleotides
RNA
24
633-642
2018
Homo sapiens
EXTERNAL LINKS (specific for EC-Number 3.6.1.62)
Transporter Classification Database (TCDB): 3.A.18.1.1
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