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Information on EC 3.6.1.62 - 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase and Organism(s) Saccharomyces cerevisiae and UniProt Accession P53550

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EC Tree
IUBMB 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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Saccharomyces cerevisiae
UNIPROT: P53550
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Word Map
The taxonomic range for the selected organisms is: Saccharomyces cerevisiae
The enzyme appears in selected viruses and cellular organisms
Synonyms
nudt16, dcp1p, hdcp2, dcp2p, mrna decapping enzyme, nudt19, hnudt16, d10 protein, d10 decapping enzyme, nudt17, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Dcp1p
-
regulatory subunit
Dcp2p
-
catalytic subunit
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) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
m7G5'ppp5'-mRNA + H2O
m7GDP + 5'-phospho-mRNA
show the reaction diagram
a 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] + H2O
N7-methylguanosine 5'-diphosphate + a 5'-phospho-[mRNA]
show the reaction diagram
-
-
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
m7G5'ppp5'-mRNA + H2O
m7GDP + 5'-phospho-mRNA
show the reaction diagram
Dcp2 has role in mRNA decay
-
-
?
a 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] + H2O
N7-methylguanosine 5'-diphosphate + a 5'-phospho-[mRNA]
show the reaction diagram
-
-
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
conserved glutamate residues E152, E153, and E198 coordinate a magnesium ion through a water mediated contact, while E149 directly contacts the metal
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Hedls protein
-
also known as Edc4 or Ge-1
-
Lsm1p-7p complex
-
-
-
tristetraprolin
-
-
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
many long noncoding RNAs degraded by DCP2 are expressed proximal to inducible genes. Of these, several genes required for galactose utilization are associated with long noncoding RNAs that have expression patterns inversely correlated with their mRNA counterpart. Decapping of these lncRNAs is critical for rapid and robust induction of GAL gene expression
physiological function
-
the enzyme regulates mRNA stability in cells
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
structures of wild-type, and E198Q and E153Q catalytic glutamate mutants of the Dcp2 Nudix domain, to 2.1A, 1.8 A and 1.7 A resolution, respectively. Conserved glutamate residues E152, E153, and E198 coordinate a magnesium ion through a water mediated contact, while E149 directly contacts the metal. A conserved metal binding loop on the catalytic domain undergoes conformational changes during the catalytic cycle
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E153Q
mutant has 3 molecules in the asymmetric unit. There is clear electron density for an octahedrally coordinated Mg2+ in the structure, similar to wild-type. Mutant is severely catalytically compromised and displays a linear dependence on pH over the range studied (pH 7–9.5)
E198Q
mutant lacks clear density for a metal ion in the active site and fails to crystallize in the presence of any divalent cation
W50A
Mutation in subunit Dcp2. While the wild-type Dcp1-Dcp2 complex is stimulated by enhancer of decapping Edc1CTR by a factor of 13, it only enhances catalysis in the W50A mutant by a factor of three. Coactivation of decapping by Dcp2 is linked to formation of the composite active site
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of a fragment of the yeast Dcp2 protein in Escherichia coli. This fragment contains the MutT/Nudix domain but lacks the non-conserved C-terminal tail and is also active in decapping
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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
Manually annotated by BRENDA team
Geisler, S.; Lojek, L.; Khalil, A.; Baker, K.; Coller, J.
Decapping of long noncoding RNAs regulates inducible genes
Mol. Cell.
45
279-291
2012
Saccharomyces cerevisiae (P53550)
Manually annotated by BRENDA team
Floor, S.; Borja, M.; Gross, J.
Interdomain dynamics and coactivation of the mRNA decapping enzyme Dcp2 are mediated by a gatekeeper tryptophan
Proc. Natl. Acad. Sci. USA
109
2872-2877
2012
Saccharomyces cerevisiae (P53550), Saccharomyces cerevisiae, Schizosaccharomyces pombe (O13828), Schizosaccharomyces pombe, Schizosaccharomyces pombe ATCC 24843 (O13828)
Manually annotated by BRENDA team
Aglietti, R.A.; Floor, S.N.; McClendon, C.L.; Jacobson, M.P.; Gross, J.D.
Active site conformational dynamics are coupled to catalysis in the mRNA decapping enzyme Dcp2
Structure
21
1571-1580
2013
Saccharomyces cerevisiae (P53550)
Manually annotated by BRENDA team
Grudzien-Nogalska, E.; Kiledjian, M.
New insights into decapping enzymes and selective mRNA decay
Wiley Interdiscip. Rev. RNA
8
e1379
2017
Saccharomyces cerevisiae, Homo sapiens
Manually annotated by BRENDA team