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Literature summary extracted from

  • Rodrigues, J.; Fernandez, A.; Canales, J.; Cabezas, A.; Ribeiro, J.; Costas, M.; Cameselle, J.
    Characterization of Danio rerio Mn2+-dependent ADP-ribose/CDP-alcohol diphosphatase, the structural prototype of the ADPRibase-Mn-like protein family (2012), PLoS ONE, 7, e42249.
    View publication on PubMedView publication on EuropePMC

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.6.1.13 substrate-docking to zebrafish wild-type protein, and H97A mutant point to a role of His-97 in catalysis by orientation, and to a bidentate water bridging the dinuclear metal center as the potential nucleophile Danio rerio
3.6.1.53 substrate-docking studies point to a role of His-97 in catalysis by orientation, and to a bidentate water bridging the dinuclear metal center as the potential nucleophile Danio rerio

Protein Variants

EC Number Protein Variants Comment Organism
3.6.1.13 H97A mutant shows 60fold decrease in activity for substrates ADP-ribose and ADP and 300–500fold for CDP-alcohols. For H97A, 2',3'-cAMP is a better substrate than ADP-ribose Danio rerio
3.6.1.53 H97A severe reduction of activtiy Danio rerio

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.6.1.13 0.053
-
 ADP-ribose wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 0.071
-
 ADP-ribose mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 0.19
-
 cADP-ribose wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 0.76
-
 2',3'-cAMP wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 1.7
-
 2',3'-cAMP mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 2
-
 CDP-glycerol wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 2.65
-
 ADP wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 3.9
-
 CDP-ethanolamine wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 6.3
-
 CDP-glycerol mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 12
-
 CDP-choline wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 19
-
 ADP mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 31
-
 CDP-ethanolamine mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 43
-
 CDP-choline mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 0.053
-
 ADP-ribose wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 0.071
-
 ADP-ribose mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 0.19
-
 cyclic ADP-ribose wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 0.76
-
 2',3'-cAMP wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 1.7
-
 2',3'-cAMP mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 2
-
 CDP-glycerol wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 2.65
-
 ADP wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 3.9
-
 CDP-ethanolamine wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 6.3
-
 CDP-glycerol mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 12
-
 CDP-choline wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 19
-
 ADP mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 31
-
 CDP-ethanolamine mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 43
-
 CDP-choline mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.6.1.13 Mn2+ required for full activity Danio rerio
3.6.1.53 Mg2+ about 25% of the activity with Mn2+ Danio rerio
3.6.1.53 Mn2+ required, similar activatory effects with all the substrates tested. Km values around 1 microM and 2.5 mM Mn2+ for ADP-ribose hydrolysis Danio rerio

Organism

EC Number Organism UniProt Comment Textmining
3.6.1.13 Danio rerio Q7T291
-
-
3.6.1.53 Danio rerio Q7T291
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.6.1.13 2',3'-cAMP + H2O
-
 Danio rerio 3'AMP 95% of products ?
3.6.1.13 ADP + H2O
-
 Danio rerio AMP + phosphate
-
 ?
3.6.1.13 ADP-ribose + H2O
-
 Danio rerio AMP + D-ribose 5-phosphate
-
 ?
3.6.1.13 cADP-ribose + H2O
-
 Danio rerio N1-(5-phosphoribosyl)-AMP + phosphate
-
 ?
3.6.1.13 CDP-choline + H2O
-
 Danio rerio CMP + choline phosphate
-
 ?
3.6.1.13 CDP-ethanolamine + H2O
-
 Danio rerio CMP + ethanolamine phosphate
-
 ?
3.6.1.13 CDP-glycerol + H2O
-
 Danio rerio CMP + glycerol phosphate
-
 ?
3.6.1.13 additional information no or very poor substrates: ADP-glucose, UDP-glucose, CDP-glucose, CDP, CMP, AMP, and 3',5'-cAMP Danio rerio ?
-
 ?
3.6.1.53 2',3'-cAMP + H2O
-
 Danio rerio ?
-
 ?
3.6.1.53 ADP + H2O
-
 Danio rerio AMP + phosphate
-
 ?
3.6.1.53 ADP-ribose + H2O
-
 Danio rerio AMP + D-ribose 5-phosphate
-
 ?
3.6.1.53 CDP-choline + H2O
-
 Danio rerio CMP + phosphocholine
-
 ?
3.6.1.53 CDP-ethanolamine + H2O
-
 Danio rerio CMP + phosphoethanolamine
-
 ?
3.6.1.53 CDP-glycerol + H2O
-
 Danio rerio CMP + phosphoglycerol
-
 ?
3.6.1.53 cyclic ADP-ribose + H2O
-
 Danio rerio N1-(5-phosphoribosyl)-AMP
-
 ?
3.6.1.53 additional information very poor substrate: cyclic ADP-ribose. No substrate: ADP-glucose, UDP-glucose, CDP-glucose, CDP, CMP, AMP or 3',5'-cAMP Danio rerio ?
-
 ?

Synonyms

EC Number Synonyms Comment Organism
3.6.1.13 ADP-ribose/CDP-alcohol diphosphatase
-
 Danio rerio
3.6.1.13 Adprm
-
 Danio rerio
3.6.1.13 zgc:64213
-
 Danio rerio
3.6.1.53 ADPRibase-Mn
-
 Danio rerio
3.6.1.53 Adprm
-
 Danio rerio

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.6.1.13 0.0005
-
 cADP-ribose wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 0.2
-
 ADP mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 0.4
-
 ADP-ribose mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 0.8
-
 CDP-choline mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 0.8
-
 CDP-glycerol mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 1.8
-
 ADP wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 2.1
-
 CDP-ethanolamine mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 16.9
-
 2',3'-cAMP wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 18
-
 ADP-ribose wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 29.7
-
 2',3'-cAMP mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 67.2
-
 CDP-choline wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 95.6
-
 CDP-glycerol wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 125.2
-
 CDP-ethanolamine wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 0.005
-
 cyclic ADP-ribose wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 0.2
-
 ADP mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 0.4
-
 ADP-ribose mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 0.8
-
 CDP-choline mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 0.8
-
 CDP-glycerol mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 1.8
-
 ADP wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 2.1
-
 CDP-ethanolamine mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 16.9
-
 2',3'-cAMP wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 18
-
 ADP-ribose wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 29.7
-
 2',3'-cAMP mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 67.2
-
 CDP-choline wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 95.6
-
 CDP-glycerol wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 125.2
-
 CDP-ethanolamine wild-type, pH 7.5, temperature not specified in the publication Danio rerio

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.6.1.53 8.5
-
-
 Danio rerio

pH Range

EC Number pH Minimum pH Maximum Comment Organism
3.6.1.53 7.6
-
 half-maximum activity Danio rerio
3.6.1.53 9.2
-
 half-maximum activity Danio rerio

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
3.6.1.13 0.0011
-
 ADP mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 0.002
-
 CDP-choline mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 0.007
-
 CDP-ethanolamine mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 0.028
-
 cADP-ribose wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 0.12
-
 CDP-glycerol mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 0.66
-
 ADP wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 5.6
-
 CDP-choline wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 5.9
-
 ADP-ribose mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 18
-
 2',3'-cAMP mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 22
-
 2',3'-cAMP wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 32
-
 CDP-ethanolamine wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 48
-
 CDP-glycerol wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.13 340
-
 ADP-ribose wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 0.011
-
 ADP mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 0.02
-
 CDP-choline mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 0.028
-
 cyclic ADP-ribose wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 0.07
-
 CDP-ethanolamine mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 0.12
-
 CDP-glycerol mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 0.66
-
 ADP wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 5.6
-
 CDP-choline wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 5.9
-
 ADP-ribose mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 18
-
 2',3'-cAMP mutant H97A, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 22
-
 2',3'-cAMP wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 32
-
 CDP-ethanolamine wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 48
-
 CDP-glycerol wild-type, pH 7.5, temperature not specified in the publication Danio rerio
3.6.1.53 340
-
 ADP-ribose wild-type, pH 7.5, temperature not specified in the publication Danio rerio