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Literature summary extracted from

  • Buchko, G.W.; Litvinova, O.; Robinson, H.; Yakunin, A.F.; Kennedy, M.A.
    Functional and structural characterization of DR_0079 from Deinococcus radiodurans, a novel nudix hydrolase with a preference for cytosine (deoxy)ribonucleoside 5-di- and triphosphates (2008), Biochemistry, 47, 6571-6582.
    View publication on PubMedView publication on EuropePMC

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.6.1.15 determined in the metal-free form at 1.9 A resolution, data collection and structure refinement statistics, molscript ribbon representation of the crystal structure Deinococcus radiodurans

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.6.1.15 0.023
-
dCTP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.034
-
CTP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.046
-
IDP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.051
-
dGDP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.062
-
dATP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.082
-
CDP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.083
-
dGTP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.088
-
dITP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.092
-
GDP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.092
-
dCDP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.105
-
TDP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.124
-
UTP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.137
-
UDP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.138
-
TTP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.145
-
dADP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.147
-
ITP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.217
-
ADP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.317
-
ATP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.394
-
GTP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
3.6.1.15 membrane
-
Deinococcus radiodurans 16020
-

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.6.1.15 Co2+ lower activity in presence of Co2+ than in presence of Mn2+ Deinococcus radiodurans
3.6.1.15 Mg2+ highest value for Mg2+ requirement in metal profile determined Deinococcus radiodurans
3.6.1.15 Mn2+ higher activity in presence of Mn2+ than of Co2+ Deinococcus radiodurans

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.6.1.15 ADP + H2O Deinococcus radiodurans relative substrate activity toward a variety of nucleoside di- and triphosphate substrates AMP + phosphate
-
?
3.6.1.15 ATP + H2O Deinococcus radiodurans relative substrate activity toward a variety of nucleoside di- and triphosphate substrates ADP + phosphate
-
?
3.6.1.15 CDP + H2O Deinococcus radiodurans first nudix hydrolase observed to have a marked preference for CDP and CTP, activity at the site of the phosphodiester bond corroborated using 31P NMR spectroscopy, nucleophilic substitution at the beta-phosphorus CMP + phosphate
-
?
3.6.1.15 CTP + H2O Deinococcus radiodurans first nudix hydrolase observed to have a marked preference for CDP and CTP, activity at the site of the phosphodiester bond corroborated using 31P NMR spectroscopy, nucleophilic substitution at the beta-phosphorus CDP + phosphate
-
?
3.6.1.15 dADP + H2O Deinococcus radiodurans relative substrate activity toward a variety of nucleoside di- and triphosphate substrates dAMP + phosphate
-
?
3.6.1.15 dATP + H2O Deinococcus radiodurans relative substrate activity toward a variety of nucleoside di- and triphosphate substrates dADP + phosphate
-
?
3.6.1.15 dCDP + H2O Deinococcus radiodurans next most preferred substrates with a relative activity of <50% compared to CDP, activity at the site of the phosphodiester bond corroborated using 31P NMR spectroscopy dCMP + phosphate
-
?
3.6.1.15 dCTP + H2O Deinococcus radiodurans next most preferred substrates with a relative activity of <50% compared to CDP, activity at the site of the phosphodiester bond corroborated using 31P NMR spectroscopy dCDP + phosphate
-
?
3.6.1.15 dGDP + H2O Deinococcus radiodurans relative substrate activity toward a variety of nucleoside di- and triphosphate substrates dGMP + phosphate
-
?
3.6.1.15 dGTP + H2O Deinococcus radiodurans relative substrate activity toward a variety of nucleoside di- and triphosphate substrates dGDP + phosphate
-
?
3.6.1.15 dITP + H2O Deinococcus radiodurans
-
dTDP + phosphate
-
?
3.6.1.15 GDP + H2O Deinococcus radiodurans relatively low substrate activity GMP + phosphate
-
?
3.6.1.15 GTP + H2O Deinococcus radiodurans relatively low substrate activity GDP + phosphate
-
?
3.6.1.15 IDP + H2O Deinococcus radiodurans activity at the site of the phosphodiester bond corroborated using 31P NMR spectroscopy, low substrate activity IMP + phosphate
-
?
3.6.1.15 ITP + H2O Deinococcus radiodurans
-
IDP + phosphate
-
?
3.6.1.15 TDP + H2O Deinococcus radiodurans relative substrate activity toward a variety of nucleoside di- and triphosphate substrates TMP + phosphate
-
?
3.6.1.15 TTP + H2O Deinococcus radiodurans relative substrate activity toward a variety of nucleoside di- and triphosphate substrates TDP + phosphate
-
?
3.6.1.15 UDP + H2O Deinococcus radiodurans relative low substrate activity UMP + phosphate
-
?
3.6.1.15 UTP + H2O Deinococcus radiodurans relative low substrate activity UDP + phosphate
-
?

Organism

EC Number Organism UniProt Comment Textmining
3.6.1.15 Deinococcus radiodurans Q9RXX6
-
-

Specific Activity [micromol/min/mg]

EC Number Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
3.6.1.15 additional information
-
identification of residues involved in metal and substrate binding using NMR chemical shift mapping experiments, results mapped onto the crystal structure, substrate binding possibilities and biological function discussed, further biochemical studies necessary to determine if the specificity for CDP and CTP is part of its housekeeping duties Deinococcus radiodurans

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.6.1.15 ADP + H2O relative substrate activity toward a variety of nucleoside di- and triphosphate substrates Deinococcus radiodurans AMP + phosphate
-
?
3.6.1.15 ATP + H2O relative substrate activity toward a variety of nucleoside di- and triphosphate substrates Deinococcus radiodurans ADP + phosphate
-
?
3.6.1.15 CDP + H2O first nudix hydrolase observed to have a marked preference for CDP and CTP, activity at the site of the phosphodiester bond corroborated using 31P NMR spectroscopy, nucleophilic substitution at the beta-phosphorus Deinococcus radiodurans CMP + phosphate
-
?
3.6.1.15 CTP + H2O first nudix hydrolase observed to have a marked preference for CDP and CTP, activity at the site of the phosphodiester bond corroborated using 31P NMR spectroscopy, nucleophilic substitution at the beta-phosphorus Deinococcus radiodurans CDP + phosphate
-
?
3.6.1.15 dADP + H2O relative substrate activity toward a variety of nucleoside di- and triphosphate substrates Deinococcus radiodurans dAMP + phosphate
-
?
3.6.1.15 dATP + H2O relative substrate activity toward a variety of nucleoside di- and triphosphate substrates Deinococcus radiodurans dADP + phosphate
-
?
3.6.1.15 dCDP + H2O next most preferred substrates with a relative activity of <50% compared to CDP, activity at the site of the phosphodiester bond corroborated using 31P NMR spectroscopy Deinococcus radiodurans dCMP + phosphate
-
?
3.6.1.15 dCTP + H2O next most preferred substrates with a relative activity of <50% compared to CDP, activity at the site of the phosphodiester bond corroborated using 31P NMR spectroscopy Deinococcus radiodurans dCDP + phosphate
-
?
3.6.1.15 dGDP + H2O relative substrate activity toward a variety of nucleoside di- and triphosphate substrates Deinococcus radiodurans dGMP + phosphate
-
?
3.6.1.15 dGTP + H2O relative substrate activity toward a variety of nucleoside di- and triphosphate substrates Deinococcus radiodurans dGDP + phosphate
-
?
3.6.1.15 dITP + H2O
-
Deinococcus radiodurans dTDP + phosphate
-
?
3.6.1.15 GDP + H2O relatively low substrate activity Deinococcus radiodurans GMP + phosphate
-
?
3.6.1.15 GTP + H2O relatively low substrate activity Deinococcus radiodurans GDP + phosphate
-
?
3.6.1.15 IDP + H2O activity at the site of the phosphodiester bond corroborated using 31P NMR spectroscopy, low substrate activity Deinococcus radiodurans IMP + phosphate
-
?
3.6.1.15 ITP + H2O
-
Deinococcus radiodurans IDP + phosphate
-
?
3.6.1.15 TDP + H2O relative substrate activity toward a variety of nucleoside di- and triphosphate substrates Deinococcus radiodurans TMP + phosphate
-
?
3.6.1.15 TTP + H2O relative substrate activity toward a variety of nucleoside di- and triphosphate substrates Deinococcus radiodurans TDP + phosphate
-
?
3.6.1.15 UDP + H2O relative low substrate activity Deinococcus radiodurans UMP + phosphate
-
?
3.6.1.15 UTP + H2O relative low substrate activity Deinococcus radiodurans UDP + phosphate
-
?

Synonyms

EC Number Synonyms Comment Organism
3.6.1.15 DR_0079
-
Deinococcus radiodurans

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.6.1.15 0.06
-
IDP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.18
-
ITP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.22
-
dITP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.29
-
ATP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.29
-
ADP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.3
-
dCTP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.31
-
dATP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.32
-
GTP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.39
-
GDP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.4
-
dGTP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.51
-
dGDP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.52
-
dADP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.53
-
UTP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.59
-
CTP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 0.69
-
TTP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 1.03
-
TDP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 1.12
-
dCDP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 1.35
-
UDP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans
3.6.1.15 1.67
-
CDP substrate concentration between 0.01 and 4.0 mM, 37°C Deinococcus radiodurans

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.6.1.15 9
-
hydrolysis of CDP Deinococcus radiodurans

pH Range

EC Number pH Minimum pH Maximum Comment Organism
3.6.1.15 9 9.5 optimal range for hydrolysis of CDP between Deinococcus radiodurans