Information on EC 3.1.4.55 - phosphoribosyl 1,2-cyclic phosphate phosphodiesterase

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The expected taxonomic range for this enzyme is: Escherichia coli

EC NUMBER
COMMENTARY hide
3.1.4.55
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RECOMMENDED NAME
GeneOntology No.
phosphoribosyl 1,2-cyclic phosphate phosphodiesterase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
5-phospho-alpha-D-ribose 1,2-cyclic phosphate + H2O = alpha-D-ribose 1,5-bisphosphate
show the reaction diagram
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
aminomethylphosphonate degradation
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glyphosate degradation III
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methylphosphonate degradation I
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Phosphonate and phosphinate metabolism
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SYSTEMATIC NAME
IUBMB Comments
5-phospho-alpha-D-ribose 1,2-cyclic phosphate 2-phosphohydrolase (alpha-D-ribose 1,5-bisphosphate-forming)
Binds Mn2+ and Zn2+. Isolated from the bacterium Escherichia coli, where it participates in the degradation of methylphosphonate.
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2',3'-cAMP + H2O
3'-AMP
show the reaction diagram
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-
-
?
2',3'-cCMP + H2O
3'-CMP
show the reaction diagram
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-
-
?
2',3'-cGMP + H2O
3'-GMP
show the reaction diagram
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-
-
?
5-phospho-alpha-D-ribose 1,2-cyclic phosphate + H2O
alpha-D-ribose 1,5-bisphosphate
show the reaction diagram
alpha-D-ribosyl 1,2-cyclic phosphate + H2O
alpha-D-ribosyl 1-phosphate
show the reaction diagram
bis(p-nitrophenyl)phosphate + H2O
?
show the reaction diagram
methyl 2,4-dichlorophenyl phosphate + H2O
?
show the reaction diagram
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-
-
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methyl 2,4-dinitrophenyl phosphate + H2O
?
show the reaction diagram
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-
-
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methyl 2,5-dinitrophenyl phosphate + H2O
?
show the reaction diagram
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-
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methyl 2-chloro-4-nitrophenyl phosphate + H2O
?
show the reaction diagram
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methyl 3-nitrophenyl phosphate + H2O
?
show the reaction diagram
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methyl 4-chlorophenyl phosphate + H2O
?
show the reaction diagram
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-
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methyl 4-cyanophenyl phosphate + H2O
?
show the reaction diagram
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methyl 4-nitrophenyl phosphate + H2O
?
show the reaction diagram
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methyl nitrophenyl phosphate + H2O
?
show the reaction diagram
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methyl phenyl phosphate + H2O
?
show the reaction diagram
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thymidine 5'-monophosphate p-nitrophenyl ester + H2O
?
show the reaction diagram
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?
additional information
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Zn2+
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poor activity with Zn2+
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
orthovanadate
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crystallization data
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.11
2',3'-cAMP
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pH 7.2, 25°C, presence of Mn2+
0.14
2',3'-cCMP
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pH 7.2, 25°C, presence of Mn2+
0.31
2',3'-cGMP
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pH 7.2, 25°C, presence of Mn2+
0.68 - 28
bis(p-nitrophenyl)phosphate
15
thymidine 5'-monophosphate p-nitrophenyl ester
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pH 7.2, 25°C, presence of Mn2+
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.71
2',3'-cAMP
Escherichia coli
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pH 7.2, 25°C, presence of Mn2+
0.64
2',3'-cCMP
Escherichia coli
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pH 7.2, 25°C, presence of Mn2+
1.23
2',3'-cGMP
Escherichia coli
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pH 7.2, 25°C, presence of Mn2+
0.001 - 4.1
bis(p-nitrophenyl)phosphate
0.08
thymidine 5'-monophosphate p-nitrophenyl ester
Escherichia coli
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pH 7.2, 25°C, presence of Mn2+
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
15.8
2',3'-cAMP
Escherichia coli
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pH 7.2, 25°C, presence of Mn2+
942
4.22
2',3'-cCMP
Escherichia coli
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pH 7.2, 25°C, presence of Mn2+
7083
3.91
2',3'-cGMP
Escherichia coli
-
pH 7.2, 25°C, presence of Mn2+
5089
0.001 - 1.77
bis(p-nitrophenyl)phosphate
1347
0.124
methyl 2,4-dichlorophenyl phosphate
Escherichia coli
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wild-type, pH 7.1, 25°C, presence of Mn2+
172467
0.22
methyl 2,4-dinitrophenyl phosphate
Escherichia coli
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wild-type, pH 7.1, 25°C, presence of Mn2+
172464
0.68
methyl 2,5-dinitrophenyl phosphate
Escherichia coli
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wild-type, pH 7.1, 25°C, presence of Mn2+
172465
0.29
methyl 2-chloro-4-nitrophenyl phosphate
Escherichia coli
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wild-type, pH 7.1, 25°C, presence of Mn2+
172466
0.041
methyl 3-nitrophenyl phosphate
Escherichia coli
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wild-type, pH 7.1, 25°C, presence of Mn2+
172469
0.0024
methyl 4-chlorophenyl phosphate
Escherichia coli
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wild-type, pH 7.1, 25°C, presence of Mn2+
172470
0.006
methyl 4-cyanophenyl phosphate
Escherichia coli
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wild-type, pH 7.1, 25°C, presence of Mn2+
172468
0.047
methyl 4-nitrophenyl phosphate
Escherichia coli
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wild-type, pH 7.1, 25°C, presence of Mn2+
18163
0.009
methyl phenyl phosphate
Escherichia coli
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wild-type, pH 7.1, 25°C, presence of Mn2+
172471
0.005
thymidine 5'-monophosphate p-nitrophenyl ester
Escherichia coli
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pH 7.2, 25°C, presence of Mn2+
6717
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
complexed with orthovanadate to 1.5 A resolution. Orthovanadate binds in a tetrahedral geometry by the two catalytic manganese ions and the putative general acid residue H200
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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
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D164A
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0.07% of wild-type activity
D187A
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83% of wild-type activity
D54A
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0.09% of wild-type activity
H200A
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10% of wild-type activity, 6.33fold decrease in kcat/KM with substituted methyl phenylphosphate diesters with leaving group pKa values ranging from 4 to 8.4. With bis(pnitrophenyl)phosphate as a substrate, there is a 10fold decrease in kcat/KM, primarily the result of a large increase in KM. The nickel ion-activated H200A mutant displays a bell-shaped pH dependence for kcat/KM with pKa values comparable to those of the wild-type enzyme
H222A
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14% of wild-type activity
H78A
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0.3% of wild-type activity
T75A
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3% of wild-type activity