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Literature summary for 3.1.4.55 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)

Crystallization (Comment) Organism
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

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

KM Value [mM]

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

Metals/Ions

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

Organism

Organism UniProt Comment Textmining
Escherichia coli
-
-
-
Escherichia coli P16692
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2',3'-cAMP + H2O
-
Escherichia coli 3'-AMP
-
?
2',3'-cCMP + H2O
-
Escherichia coli 3'-CMP
-
?
2',3'-cGMP + H2O
-
Escherichia coli 3'-GMP
-
?
bis(p-nitrophenyl)phosphate + H2O
-
Escherichia coli ?
-
?
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 ?
-
?
thymidine 5'-monophosphate p-nitrophenyl ester + H2O
-
Escherichia coli ?
-
?

Synonyms

Synonyms Comment Organism
phnP
-
Escherichia coli

Turnover Number [1/s]

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

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.2
-
-
Escherichia coli

kcat/KM [mM/s]

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