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Information on EC 3.6.1.59 - 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase and Organism(s) Homo sapiens and UniProt Accession Q96C86
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3.6.1.59 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphataseIUBMB Comments
The enzyme removes (decaps) the N7-methylguanosine 5-phosphate cap from an mRNA degraded to a maximal length of 10 nucleotides [3,6]. Decapping is an important process in the control of eukaryotic mRNA degradation. The enzyme functions to clear the cell of cap structure following decay of the RNA body . The nematode enzyme can also decap triply methylated substrates, 5'-(N2,N2,N7-trimethyl 5'-triphosphoguanosine)-[mRNA] .
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Word Map
- 3.6.1.59
- heterodimer
- m7gdp
- disability
- nucleoside
-
hint
-
exosome
-
diauxie
-
craniofacial
- trehalase
-
exonucleolytic
-
intellectual
- medicine
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
scavenger mrna decapping enzyme, ylr270w, ydcps, m7gpppx pyrophosphatase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
a 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] + H2O = N7-methylguanosine 5'-phosphate + a 5'-diphospho-[mRNA]
(1)
SYSTEMATIC NAME
IUBMB Comments
5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] N7-methylguanosine 5'-phosphate phosphohydrolase
The enzyme removes (decaps) the N7-methylguanosine 5-phosphate cap from an mRNA degraded to a maximal length of 10 nucleotides [3,6]. Decapping is an important process in the control of eukaryotic mRNA degradation. The enzyme functions to clear the cell of cap structure following decay of the RNA body [2]. The nematode enzyme can also decap triply methylated substrates, 5'-(N2,N2,N7-trimethyl 5'-triphosphoguanosine)-[mRNA] [4].
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
7-dimethylguanosine 5'-[3-(5'-guanosinyl)-3-boranotriphosphate] + H2O
7-methylguanosine 5'-phosphate + ?
boranophosphate analog of the mRNA cap. 90 Min reaction time, 11% cleavage of S-enantiomer, 98% cleavage of R-enantiomer
-
-
?
7-methylguanosin-5'-yl-[3-(5'-guanosinyl)-2-boranotriphosphate] + H2O
7-methylguanosine 5'-phosphate + ?
boranophosphate analog of the mRNA cap. 90 Min reaction time, 12-19% cleavage
-
-
?
additional information
?
-
Dcps shows no activity with 7-methylguanosine 5'-diphosphate
-
-
?
7-methylguanosine 5'-diphosphate + H2O
7-methylguanosine 5'-phosphate + phosphate
-
-
-
?
7-methylguanosine 5'-diphosphate + H2O
7-methylguanosine 5'-phosphate + phosphate
eukaryotic mRNA degradation proceeds through two main pathways, both involving mRNA cap breakdown. In the 3'-5' mRNA decay pathway, mRNA body degradation generates free m7GpppN that is hydrolyzed by DcpS generating m7GMP. In the 5'-3' pathway, the recently identified human Dcp2 decapping enzyme cleaves the cap of deadenylated mRNAs to produce m7GDP and 5'-phosphorylated mRNA
-
-
?
m7G5'ppp5'N(3'ppp5'N)n + H2O
7-methylguanosine 5'-phosphate + pp5'N(3'ppp5'N)n
eukaryotic cells utilize DcpS, a scavenger decapping enzyme, to degrade the residual cap structure following 30-50 mRNA decay, thereby preventing the premature decapping of the capped long mRNA and misincorporation of methylated nucleotides in nucleic acids
-
-
?
m7G5'ppp5'N(3'ppp5'N)n + H2O
7-methylguanosine 5'-phosphate + pp5'N(3'ppp5'N)n
n = 1-8
-
-
?
m7G5'ppp5'N(3'ppp5'N)n + H2O
7-methylguanosine 5'-phosphate + pp5'N(3'ppp5'N)n
n = 1-8, decapping is an important process in the control of eukaryotic mRNA degradation. The scavenger decapping enzyme DcpS functions to clear the cell of cap structure following decay of the RNA body by catalyzing the hydrolysis of m7GpppN to m7Gp and ppN
-
-
?
m7G5'ppp5'N(3'ppp5'N)n + H2O
7-methylguanosine 5'-phosphate + pp5'N(3'ppp5'N)n
n = 1-8, eukaryotic mRNA degradation proceeds through two main pathways, both involving mRNA cap breakdown. In the 3'-5' mRNA decay pathway, mRNA body degradation generates free m7GpppN that is hydrolyzed by DcpS generating m7GMP. In the 5'-3' pathway, the recently identified human Dcp2 decapping enzyme cleaves the cap of deadenylated mRNAs to produce m7GDP and 5'-phosphorylated mRNA
-
-
?
m7G5'ppp5'N(3'ppp5'N)n + H2O
7-methylguanosine 5'-phosphate + pp5'N(3'ppp5'N)n
n = 1-8, DcpS is capable of acting on an mRNA once it is degraded down to 10 nuceotides
-
-
?
m7G5'ppp5'N(3'ppp5'N)n + H2O
7-methylguanosine 5'-phosphate + pp5'N(3'ppp5'N)n
n = 1-8, the recombinant protein specifically hydrolyzes methylated cap analog but does not hydrolyze unmethylated cap analog nor does it function on intact capped RNA. DcpS is capable of acting on an mRNA once it is degraded down to 10 nucleotides
-
-
?
m7G5'ppp5'N(3'ppp5'N)n + H2O
7-methylguanosine 5'-phosphate + pp5'N(3'ppp5'N)n
Tyr273 seems to play an important role in cap binding and product release
-
-
?
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
7-methylguanosine 5'-diphosphate + H2O
7-methylguanosine 5'-phosphate + phosphate
-
-
-
?
7-methylguanosine 5'-diphosphate + H2O
7-methylguanosine 5'-phosphate + phosphate
eukaryotic mRNA degradation proceeds through two main pathways, both involving mRNA cap breakdown. In the 3'-5' mRNA decay pathway, mRNA body degradation generates free m7GpppN that is hydrolyzed by DcpS generating m7GMP. In the 5'-3' pathway, the recently identified human Dcp2 decapping enzyme cleaves the cap of deadenylated mRNAs to produce m7GDP and 5'-phosphorylated mRNA
-
-
?
m7G5'ppp5'N(3'ppp5'N)n + H2O
7-methylguanosine 5'-phosphate + pp5'N(3'ppp5'N)n
eukaryotic cells utilize DcpS, a scavenger decapping enzyme, to degrade the residual cap structure following 30-50 mRNA decay, thereby preventing the premature decapping of the capped long mRNA and misincorporation of methylated nucleotides in nucleic acids
-
-
?
m7G5'ppp5'N(3'ppp5'N)n + H2O
7-methylguanosine 5'-phosphate + pp5'N(3'ppp5'N)n
n = 1-8
-
-
?
m7G5'ppp5'N(3'ppp5'N)n + H2O
7-methylguanosine 5'-phosphate + pp5'N(3'ppp5'N)n
n = 1-8, decapping is an important process in the control of eukaryotic mRNA degradation. The scavenger decapping enzyme DcpS functions to clear the cell of cap structure following decay of the RNA body by catalyzing the hydrolysis of m7GpppN to m7Gp and ppN
-
-
?
m7G5'ppp5'N(3'ppp5'N)n + H2O
7-methylguanosine 5'-phosphate + pp5'N(3'ppp5'N)n
n = 1-8, eukaryotic mRNA degradation proceeds through two main pathways, both involving mRNA cap breakdown. In the 3'-5' mRNA decay pathway, mRNA body degradation generates free m7GpppN that is hydrolyzed by DcpS generating m7GMP. In the 5'-3' pathway, the recently identified human Dcp2 decapping enzyme cleaves the cap of deadenylated mRNAs to produce m7GDP and 5'-phosphorylated mRNA
-
-
?
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
C5-substituted quinazolines
C5-quinazolines potently inhibit DcpS decapping activity. Binding of C5-substituted quinazolines to DcpS holds the enzyme in an open, catalytically incompetent conformation
-
D156844
highly effective at inhibiting recombinant DcpS decapping activity
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
DcpS exhibits different enzymatic kinetics under low and high substrate conditions, negative cooperativity between two wild type subunits, reduced decapping activity is displayed by the DcpSWT/HIT heterodimer under high substrate conditions
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
DcpS is predominantly a nuclear protein, with low levels of in the cytoplasm
DcpS is predominantly a nuclear protein, with low levels of in the cytoplasm
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
physiological function
DcpS is a molecule that modulates cap concentrations for cellular homeostasis of gene expression activities involving at least RNA processing. A nuclear function for DcpS in maintaining proper pre-mRNA splicing
physiological function
eukaryotic cells utilize DcpS, a scavenger decapping enzyme, to degrade the residual cap structure following 30-50 mRNA decay, thereby preventing the premature decapping of the capped long mRNA and misincorporation of methylated nucleotides in nucleic acids
physiological function
eukaryotic mRNA degradation proceeds through two main pathways, both involving mRNA cap breakdown. In the 3'-5' mRNA decay pathway, mRNA body degradation generates free m7GpppN that is hydrolyzed by DcpS generating m7GMP. In the 5'-3' pathway, the human Dcp2 decapping enzyme cleaves the cap of deadenylated mRNAs to produce 7-methylguanosine 5'-diphosphate and 5'-phosphorylated mRNA
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). DCPS_HUMAN
337
0
38609
Swiss-Prot
other Location (Reliability: 1)
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
dimer
in contrast, and similar to the m7GpppG-DcpS complex, DcpS with bound m7GDP is an asymmetric dimer in which the closed state appears to be the substrate-bound complex, whereas the open state mimics the product-bound complex. apo-DcpS is a symmetric dimer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging-drop vapor-diffusion method at 20°C. Structures of DcpS in ligand-free form and in a complex with m7GDP. Examination of the crystallographic B-factors indicates that the N-terminal domain in apo-DcpS is inherently flexible, and in a dynamic state ready for substrate binding and product release
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
medicine
identification of DcpS as a candidate molecular target of the C5-substituted quinazolines for the potential treatment of spinal muscular atrophy
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Singh, J.; Salcius, M.; Liu, S.W.; Staker, B.L.; Mishra, R.; Thurmond, J.; Michaud, G.; Mattoon, D.R.; Printen, J.; Christensen, J.; Bjornsson, J.M.; Pollok, B.A.; Kiledjian, M.; Stewart, L.; Jarecki, J.; Gurney, M.E.
DcpS as a therapeutic target for spinal muscular atrophy
ACS Chem. Biol.
3
711-722
2008
Homo sapiens (Q96C86)
Liu, H.; Rodgers, N.D.; Jiao, X.; Kiledjian, M.
The scavenger mRNA decapping enzyme DcpS is a member of the HIT family of pyrophosphatases
EMBO J.
21
4699-4708
2002
Saccharomyces cerevisiae (Q06151), Homo sapiens (Q96C86)
Liu, S.W.; Rajagopal, V.; Patel, S.S.; Kiledjian, M.
Mechanistic and kinetic analysis of the DcpS scavenger decapping enzyme
J. Biol. Chem.
283
16427-16436
2008
Homo sapiens (Q96C86)
Chen, N.; Walsh, M.A.; Liu, Y.; Parker, R.; Song, H.
Crystal structures of human DcpS in ligand-free and m7GDP-bound forms suggest a dynamic mechanism for scavenger mRNA decapping
J. Mol. Biol.
347
707-718
2005
Homo sapiens (Q96C86)
van Dijk, E.; Le Hir, H.; Sraphin, B.
DcpS can act in the 5'-3' mRNA decay pathway in addition to the 3'-5' pathway
Proc. Natl. Acad. Sci. USA
100
12081-12086
2003
Homo sapiens (Q96C86)
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 (Q96C86)
Shen, V.; Liu, H.; Liu, S.W.; Jiao, X.; Kiledjian, M.
DcpS scavenger decapping enzyme can modulate pre-mRNA splicing
RNA
14
1132-1142
2008
Homo sapiens (Q96C86)
Kowalska, J.; Wypijewska del Nogal, A.; Darzynkiewicz, Z.M.; Buck, J.; Nicola, C.; Kuhn, A.N.; Lukaszewicz, M.; Zuberek, J.; Strenkowska, M.; Ziemniak, M.; Maciejczyk, M.; Bojarska, E.; Rhoads, R.E.; Darzynkiewicz, E.; Sahin, U.; Jemielity, J.
Synthesis, properties, and biological activity of boranophosphate analogs of the mRNA cap: versatile tools for manipulation of therapeutically relevant cap-dependent processes
Nucleic Acids Res.
42
10245-10264
2014
Caenorhabditis elegans (G5EFS4), Homo sapiens (Q96C86)
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