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Information on EC 3.6.1.9 - nucleotide diphosphatase and Organism(s) Escherichia coli and UniProt Accession P25536

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EC Tree
     3 Hydrolases
         3.6 Acting on acid anhydrides
             3.6.1 In phosphorus-containing anhydrides
                3.6.1.9 nucleotide diphosphatase
IUBMB Comments
The enzyme preferentially hydrolyses ATP, but can also hydrolyse other nucleoside 5' triphosphates such as GTP, CTP, TTP and UTP to their corresponding monophosphates. In vitro the enzyme also acts as a nucleotidohydrolase on ADP, NAD+, NADP+, FAD, and CoA.
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This record set is specific for:
Escherichia coli
UNIPROT: P25536
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The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
Synonyms
npp, cd203c, itpase, inosine triphosphatase, inosine triphosphate pyrophosphatase, maf protein, enpp3, nppase, e-npp, nucleoside triphosphate pyrophosphohydrolase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Maf-like protein YhdE
-
nucleotide pyrophosphatase
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nucleoside triphosphate diphosphatase
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-
-
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nucleoside-triphosphate pyrophosphatase
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-
-
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nucleotide pyrophosphatase
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-
-
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nucleotide pyrophosphatase/phosphodiesterase
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nucleotide pyrophosphohydrolase
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-
-
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nucleotide-sugar pyrophosphatase
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-
-
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pyrophosphatase, nucleoside triphosphate
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-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of phosphoric ester
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-
-
-
SYSTEMATIC NAME
IUBMB Comments
dinucleotide nucleotidohydrolase
The enzyme preferentially hydrolyses ATP, but can also hydrolyse other nucleoside 5' triphosphates such as GTP, CTP, TTP and UTP to their corresponding monophosphates. In vitro the enzyme also acts as a nucleotidohydrolase on ADP, NAD+, NADP+, FAD, and CoA.
CAS REGISTRY NUMBER
COMMENTARY hide
9032-64-8
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
dTTP + H2O
dTMP + diphosphate
show the reaction diagram
the enzyme possesses dTTP-specific activity at a substrate concentration of 0.1 mM
-
-
?
dUTP + H2O
dUMP + diphosphate
show the reaction diagram
weakest substrate
-
-
?
TTP + H2O
TMP + diphosphate
show the reaction diagram
the enzyme exhibits significant activity for TTP only when substrate concentration reaches 0.5 mM
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-
?
UTP + H2O
UMP + diphosphate
show the reaction diagram
the enzyme exhibits significant activity for UTP only when substrate concentration reaches 0.5 mM
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-
?
additional information
?
-
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
additional information
?
-
-
hydrolysis of MpNPP- in solution, diester hydrolysis reactions with the SCC-DFTBPR based implicit solvent model, overview
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-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
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required
Zn2+
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effects of Zn2+ binding on enzyme structure, binding structure, overview
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.09
dTTP
at pH 7.0 and 25°C
0.5
UTP
at pH 7.0 and 25°C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
43
dTTP
at pH 7.0 and 25°C
95
UTP
at pH 7.0 and 25°C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
503
dTTP
at pH 7.0 and 25°C
191
UTP
at pH 7.0 and 25°C
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
enzyme overexpression results in filamentous cells. The enzyme plays a role in in cell growth inhibition under stress conditions, cell-division arrest and cell-shape maintenance
physiological function
emzyme-knockout cells transform the normal rod shape of wild type cells to a more spherical form, and the cell wall appears to become more flexible
additional information
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active site structure, and MgNPP- enzyme structure modeling of wild-type and mutant enzymes using the crystal structure, QM/MM calculations and simulation, overview. Hydrolysis of MpNPP- in solution, diester hydrolysis reactions with the SCC-DFTBPR based implicit solvent model, overview
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
45000
2 * 45000, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
2 * 45000, SDS-PAGE
additional information
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MgNPP- enzyme structure modeling of wild-type and mutant enzymes using the crystal structure, QM/MM calculations and simulation, overview
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
mutant E33A, hanging drop vapor diffusion method, using 0.1 Mmagnesium sulfate, 0.1 M MES buffer (pH 6.5), and 10-15% (w/v) PEG 8000
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E322A
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site-directed mutagenesis
E322Y
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site-directed mutagenesis
R166S
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site-directed mutagenesis
R166S/E332Y
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site-directed mutagenesis
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Ni-charged column chromatography and gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3) cells
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Hou, G.; Cui, Q.
QM/MM analysis suggests that alkaline phosphatase (AP) and nucleotide pyrophosphatase/phosphodiesterase slightly tighten the transition state for phosphate diester hydrolysis relative to solution: implication for catalytic promiscuity in the AP superfamil
J. Am. Chem. Soc.
134
229-246
2012
Escherichia coli, Xanthomonas citri, Xanthomonas citri 306
Manually annotated by BRENDA team
Jin, J.; Wu, R.; Zhu, J.; Yang, S.; Lei, Z.; Wang, N.; Singh, V.K.; Zheng, J.; Jia, Z.
Insights into the cellular function of YhdE, a nucleotide pyrophosphatase from Escherichia coli
PLoS ONE
10
e0117823
2015
Escherichia coli (P25536)
Manually annotated by BRENDA team