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Literature summary extracted from

  • Podzelinska, K.; He, S.M.; Wathier, M.; Yakunin, A.; Proudfoot, M.; Hove-Jensen, B.; Zechel, D.L.; Jia, Z.
    Structure of PhnP, a phosphodiesterase of the carbon-phosphorus lyase pathway for phosphonate degradation (2009), J. Biol. Chem., 284, 17216-17226.
    View publication on PubMedView publication on EuropePMC

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.1.4.55 to 1.4 A resolution. The active site of PhnP contains probably two Mn2+ ions surrounded by an array of active site residues that are identical to those observed in the tRNase Z enzymes. A second, remote Zn2+ binding site is also observed, composed of a set of cysteine and histidine residues that are strictly conserved in the PhnP family. This second metal ion site appears to stabilize a structural motif Escherichia coli

Protein Variants

EC Number Protein Variants Comment Organism
3.1.4.55 D80A inactive with substrate bis(p-nitrophenyl)phosphate Escherichia coli

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.1.4.55 0.11
-
 2',3'-cAMP pH 7.2, 25°C, presence of Mn2+ Escherichia coli
3.1.4.55 0.14
-
 2',3'-cCMP pH 7.2, 25°C, presence of Mn2+ Escherichia coli
3.1.4.55 0.31
-
 2',3'-cGMP pH 7.2, 25°C, presence of Mn2+ Escherichia coli
3.1.4.55 0.68
-
 bis(p-nitrophenyl)phosphate pH 7.2, 25°C, presence of Zn2+ Escherichia coli
3.1.4.55 2.3
-
 bis(p-nitrophenyl)phosphate pH 7.2, 25°C, presence of Ni2+ Escherichia coli
3.1.4.55 2.9
-
 bis(p-nitrophenyl)phosphate pH 7.2, 25°C, presence of Mn2+ Escherichia coli
3.1.4.55 15
-
 thymidine 5'-monophosphate p-nitrophenyl ester pH 7.2, 25°C, presence of Mn2+ Escherichia coli

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.1.4.55 Mn2+ distinct preference for Mn2+ and Ni2+ for catalysis. 0.13 mol per mol of monomer Escherichia coli
3.1.4.55 Ni2+ preference for Mn2+ and Ni2+ for catalysis. 1.3 mol per mol of monomer Escherichia coli
3.1.4.55 Zn2+ poor activity with Zn2+ Escherichia coli

Organism

EC Number Organism UniProt Comment Textmining
3.1.4.55 Escherichia coli
-
-
-
3.1.4.55 Escherichia coli P16692
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.1.4.55 2',3'-cAMP + H2O
-
 Escherichia coli 3'-AMP
-
 ?
3.1.4.55 2',3'-cCMP + H2O
-
 Escherichia coli 3'-CMP
-
 ?
3.1.4.55 2',3'-cGMP + H2O
-
 Escherichia coli 3'-GMP
-
 ?
3.1.4.55 bis(p-nitrophenyl)phosphate + H2O
-
 Escherichia coli ?
-
 ?
3.1.4.55 additional information highest activity is observed with 2',3'-cyclic nucleotides. This reaction is regiospecific, with only the 3'-nucleotide product being observed. No activity toward RNA, 3',5'-cyclic nucleotides, p-nitrophenyl phosphate Escherichia coli ?
-
 ?
3.1.4.55 thymidine 5'-monophosphate p-nitrophenyl ester + H2O
-
 Escherichia coli ?
-
 ?

Synonyms

EC Number Synonyms Comment Organism
3.1.4.55 phnP
-
 Escherichia coli

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.1.4.55 0.03
-
 bis(p-nitrophenyl)phosphate pH 7.2, 25°C, presence of Zn2+ Escherichia coli
3.1.4.55 0.08
-
 thymidine 5'-monophosphate p-nitrophenyl ester pH 7.2, 25°C, presence of Mn2+ Escherichia coli
3.1.4.55 0.64
-
 2',3'-cCMP pH 7.2, 25°C, presence of Mn2+ Escherichia coli
3.1.4.55 1.19
-
 bis(p-nitrophenyl)phosphate pH 7.2, 25°C, presence of Mn2+ Escherichia coli
3.1.4.55 1.23
-
 2',3'-cGMP pH 7.2, 25°C, presence of Mn2+ Escherichia coli
3.1.4.55 1.71
-
 2',3'-cAMP pH 7.2, 25°C, presence of Mn2+ Escherichia coli
3.1.4.55 4.1
-
 bis(p-nitrophenyl)phosphate pH 7.2, 25°C, presence of Ni2+ Escherichia coli

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.1.4.55 7.2
-
-
 Escherichia coli

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
3.1.4.55 0.005
-
 thymidine 5'-monophosphate p-nitrophenyl ester pH 7.2, 25°C, presence of Mn2+ Escherichia coli
3.1.4.55 0.044
-
 bis(p-nitrophenyl)phosphate pH 7.2, 25°C, presence of Zn2+ Escherichia coli
3.1.4.55 0.41
-
 bis(p-nitrophenyl)phosphate pH 7.2, 25°C, presence of Mn2+ Escherichia coli
3.1.4.55 1.77
-
 bis(p-nitrophenyl)phosphate pH 7.2, 25°C, presence of Ni2+ Escherichia coli
3.1.4.55 3.91
-
 2',3'-cGMP pH 7.2, 25°C, presence of Mn2+ Escherichia coli
3.1.4.55 4.22
-
 2',3'-cCMP pH 7.2, 25°C, presence of Mn2+ Escherichia coli
3.1.4.55 15.8
-
 2',3'-cAMP pH 7.2, 25°C, presence of Mn2+ Escherichia coli