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Information on EC 3.6.1.61 - diadenosine hexaphosphate hydrolase (ATP-forming) and Organism(s) Thermus thermophilus and UniProt Accession Q75UV1

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EC Tree
IUBMB Comments
The enzyme requires the presence of the divalent cations (Mn2+, Mg2+, Zn2+, and Co2+). It hydrolyses P1,P4-bis(5-guanosyl) tetraphosphate very slowly [cf. EC 3.6.1.17, bis(5-nucleosyl)-tetraphosphatase (asymmetrical)].
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This record set is specific for:
Thermus thermophilus
UNIPROT: Q75UV1
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The taxonomic range for the selected organisms is: Thermus thermophilus
The expected taxonomic range for this enzyme is: Bacteria, Archaea
Synonyms
Ndx1, ygdP, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
P1,P6-bis(5'-adenosyl)hexaphosphate + H2O = 2 ATP
show the reaction diagram
(1)
P1,P5-bis(5'-adenosyl)pentaphosphate + H2O = ATP + ADP
show the reaction diagram
(2)
P1,P4-bis(5'-adenosyl)tetraphosphate + H2O = ATP + AMP
show the reaction diagram
nucleophilic double, not single, displacement catalytic forward reaction mechanism via oxocarbenium ion intermediate, detailed overview
PATHWAY SOURCE
PATHWAYS
SYSTEMATIC NAME
IUBMB Comments
P1,P6-bis(5'-adenosyl)hexaphosphate nucleotidohydrolase (ATP-forming)
The enzyme requires the presence of the divalent cations (Mn2+, Mg2+, Zn2+, and Co2+). It hydrolyses P1,P4-bis(5-guanosyl) tetraphosphate very slowly [cf. EC 3.6.1.17, bis(5-nucleosyl)-tetraphosphatase (asymmetrical)].
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
P1,P4-bis(5'-adenosyl)tetraphosphate + H2O
ATP + AMP
show the reaction diagram
-
-
-
?
P1,P5-bis(5'-adenosyl)pentaphosphate + H2O
ATP + ADP
show the reaction diagram
-
-
-
?
P1,P6-bis(5'-adenosyl)hexaphosphate + H2O
2 ATP
show the reaction diagram
additional information
?
-
-
homology modeling techniques shows Glu46, Arg88, and Glu90 are three important determinant residues in binding as they have strong hydrogen bonding interactions and electrostatic interactions with P1,P6-bis(5'-adenosyl)hexaphosphate
-
-
?
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
P1,P6-bis(5'-adenosyl)hexaphosphate + H2O
2 ATP
show the reaction diagram
-
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
Ndx1 activity requires the presence of the divalent cations Mn2+, Mg2+, Zn2+, and Co2+
Mg2+
Ndx1 activity requires the presence of the divalent cations Mn2+, Mg2+, Zn2+, and Co2+
Mn2+
Ndx1 activity requires the presence of the divalent cations Mn2+, Mg2+, Zn2+, and Co2+
Zn2+
Ndx1 activity requires the presence of the divalent cations Mn2+, Mg2+, Zn2+, and Co2+
Mg2+
-
homology modeling techniques shows that Ser38, Leu39 and Glu46, coordinate enzyme-bound Mg2+ ions in the complex of Ndx1 with P1,P6-bis(5'-adenosyl)hexaphosphate
additional information
Ca2+, Ni2+, and Cu2+ are not able to activate Ndx1
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
fluoride
non-competitive inhibition
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0014
P1,P6-bis(5'-adenosyl)hexaphosphate
pH 7.0, 25°C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
4.1
P1,P6-bis(5'-adenosyl)hexaphosphate
pH 7.0, 25°C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2929
P1,P6-bis(5'-adenosyl)hexaphosphate
pH 7.0, 25°C
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.013
ATP
pH 7.0, 25°C
0.041
dATP
pH 7.0, 25°C
0.424
fluoride
pH 7.0, 25°C
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.08
fluoride
Thermus thermophilus
pH 7.0, 25°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8
hydrolysis of P1,P6-bis(5'-adenosyl)hexaphosphate
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
70
hydrolysis of P1,P6-bis(5'-adenosyl)hexaphosphate
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.8
calculated from sequence
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
SwissProt
Manually annotated by BRENDA team
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
NDX1_THETH
126
0
14170
Swiss-Prot
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
14170
1 * 14170, calculated from sequence
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
1 * 14170, calculated from sequence
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E46Q
2200fold reduction in kcat
E49Q
mutation has very little effect on activity
E50Q
130000fold reduction in kcat
W26S
no decrease in fluorescence intensity upon the addition of ATP
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
2 - 12
25°C, stable
715466
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
95
pH 7.5, stable up to
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
overexpressed in Escherichia coli
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Zheng, Q.C.; Li, Z.S.; Sun, M.; Zhang, Y.; Sun, C.C.
Homology modeling and substrate binding study of Nudix hydrolase Ndx1 from Thermos thermophilus HB8
Biochem. Biophys. Res. Commun.
333
881-887
2005
Thermus thermophilus
Manually annotated by BRENDA team
Iwai, T.; Kuramitsu, S.; Masui, R.
The Nudix hydrolase Ndx1 from Thermus thermophilus HB8 is a diadenosine hexaphosphate hydrolase with a novel activity
J. Biol. Chem.
279
21732-21739
2004
Thermus thermophilus (Q75UV1)
Manually annotated by BRENDA team