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IUBMB Comments The enzyme requires the presence of the divalent cations (Mn2+ 2+ 2+ 2+ P 1 P 4 cf . EC 3.6.1.17 , bis(5′-nucleosyl)-tetraphosphatase (asymmetrical)].
Synonyms ygdP ,
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P1,P4-bis(5'-adenosyl)tetraphosphate + H2O = ATP + AMP
P1,P5-bis(5'-adenosyl)pentaphosphate + H2O = ATP + ADP
P1,P6-bis(5'-adenosyl)hexaphosphate + H2O = 2 ATP
P1,P4-bis(5'-adenosyl)tetraphosphate + H2O = ATP + AMP
nucleophilic double, not single, displacement catalytic forward reaction mechanism via oxocarbenium ion intermediate, detailed overview
P1,P4-bis(5'-adenosyl)tetraphosphate + H2O = ATP + AMP
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P1,P5-bis(5'-adenosyl)pentaphosphate + H2O = ATP + ADP
(2)
P1,P5-bis(5'-adenosyl)pentaphosphate + H2O = ATP + ADP
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P1,P6-bis(5'-adenosyl)hexaphosphate + H2O = 2 ATP
(1)
P1,P6-bis(5'-adenosyl)hexaphosphate + H2O = 2 ATP
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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)].
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P1,P4-bis(5'-adenosyl)tetraphosphate + H2O
ATP + AMP
P1,P5-bis(5'-adenosyl)pentaphosphate + H2O
ATP + ADP
P1,P6-bis(5'-adenosyl)hexaphosphate + H2O
2 ATP
additional information
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P1,P4-bis(5'-adenosyl)tetraphosphate + H2O
ATP + AMP
Substrates: -
?
P1,P4-bis(5'-adenosyl)tetraphosphate + H2O
ATP + AMP
Substrates: -
?
P1,P5-bis(5'-adenosyl)pentaphosphate + H2O
ATP + ADP
Substrates: preferred substrate
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P1,P5-bis(5'-adenosyl)pentaphosphate + H2O
ATP + ADP
Substrates: -
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P1,P6-bis(5'-adenosyl)hexaphosphate + H2O
2 ATP
Substrates: hydrolyzed at about 70% compared to P1,P5-bis(5'-adenosyl)pentaphosphate
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P1,P6-bis(5'-adenosyl)hexaphosphate + H2O
2 ATP
Substrates: -
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P1,P6-bis(5'-adenosyl)hexaphosphate + H2O
2 ATP
Substrates: P1,P6-bis(5'-adenosyl)hexaphosphate is the most preferred substrate. Glu46 and Glu50 are conserved residues in the Nudix motif and are involved in catalysis
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additional information
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Substrates: YgdP does not act on other nucleoside diphosphate derivatives such as ADP-ribose, NADH, UDP-glucose and P1,P3-bis(5'-adenosyl)triphosphate
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additional information
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Substrates: 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
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P1,P6-bis(5'-adenosyl)hexaphosphate + H2O
2 ATP
Substrates: -
?
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Co2+
Ndx1 activity requires the presence of the divalent cations Mn2+, Mg2+, Zn2+, and Co2+
additional information
Ca2+, Ni2+, and Cu2+ are not able to activate Ndx1
Mg2+
divalent cation required, Mg2+, Zn2+ or Mn2+. Maximal activity with 10 mM Mg2+ and to a lesser extent with Zn2+ and Mn2+
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
Mg2+
Ndx1 activity requires the presence of the divalent cations Mn2+, Mg2+, Zn2+, and Co2+
Mn2+
divalent cation required, Mg2+, Zn2+ or Mn2+. Maximal activity with 10 mM Mg2+ and to a lesser extent with Zn2+ and Mn2+
Mn2+
Ndx1 activity requires the presence of the divalent cations Mn2+, Mg2+, Zn2+, and Co2+
Zn2+
divalent cation required, Mg2+, Zn2+ or Mn2+. Maximal activity with 10 mM Mg2+ and to a lesser extent with Zn2+ and Mn2+
Zn2+
Ndx1 activity requires the presence of the divalent cations Mn2+, Mg2+, Zn2+, and Co2+
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fluoride
non-competitive inhibition
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0.07
P1,P4-bis(5'-adenosyl)tetraphosphate
pH 9.0, 37°C
0.36
P1,P5-bis(5'-adenosyl)pentaphosphate
pH 9.0, 37°C
0.0014
P1,P6-bis(5'-adenosyl)hexaphosphate
pH 7.0, 25°C
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0.1
P1,P4-bis(5'-adenosyl)tetraphosphate
pH 9.0, 37°C
1
P1,P5-bis(5'-adenosyl)pentaphosphate
pH 9.0, 37°C
4.1
P1,P6-bis(5'-adenosyl)hexaphosphate
pH 7.0, 25°C
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1.43
P1,P4-bis(5'-adenosyl)tetraphosphate
pH 9.0, 37°C
2.78
P1,P5-bis(5'-adenosyl)pentaphosphate
pH 9.0, 37°C
2929
P1,P6-bis(5'-adenosyl)hexaphosphate
pH 7.0, 25°C
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0.424
fluoride
pH 7.0, 25°C
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0.08
fluoride
Thermus thermophilus
pH 7.0, 25°C
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8
hydrolysis of P1,P6-bis(5'-adenosyl)hexaphosphate
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70
hydrolysis of P1,P6-bis(5'-adenosyl)hexaphosphate
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4.8
calculated from sequence
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SwissProt
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SwissProt
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Highest Expressing Human Cell Lines
Filter by:
Cell Line Links
Gene Links
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NDX1_THETH
126
0
14170
Swiss-Prot
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Y1025_DEIRA
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)
159
0
17569
Swiss-Prot
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RPPH_ECOLI
Escherichia coli (strain K12)
176
0
20795
Swiss-Prot
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14170
1 * 14170, calculated from sequence
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monomer
1 * 14170, calculated from sequence
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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
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expression in Escherichia coli
overexpressed in Escherichia coli
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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
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Bessman, M.J.; Walsh, J.D.; Dunn, C.A.; Swaminathan, J.; Weldon, J.E.; Shen, J.
The gene ygdP, associated with the invasiveness of Escherichia coli K1, designates a Nudix hydrolase, Orf176, active on adenosine (5')-pentaphospho-(5')-adenosine (Ap5A)
J. Biol. Chem.
276
37834-37838
2001
Escherichia coli (P0A776)
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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)
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