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Enzyme Nomenclature
Information on EC 3.1.4.55 - phosphoribosyl 1,2-cyclic phosphate phosphodiesterase and Organism(s) Escherichia coli and UniProt Accession P16692
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3.1.4.55 phosphoribosyl 1,2-cyclic phosphate phosphodiesteraseIUBMB Comments
Binds Mn2+ and Zn2+. Isolated from the bacterium Escherichia coli, where it participates in the degradation of methylphosphonate.
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The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Reaction Schemes
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
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.
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
5-phospho-alpha-D-ribose 1,2-cyclic phosphate + H2O
alpha-D-ribose 1,5-bisphosphate
-
-
enzyme PhnP regiospecifically converts 5-phospho-alpha-D-ribosyl 1,2-cyclic to alpha-D-ribosyl 1,5-bisphosphate
-
?
alpha-D-ribosyl 1,2-cyclic phosphate + H2O
alpha-D-ribosyl 1-phosphate
-
enzyme PhnP regiospecifically converts alpha-D-ribosyl 1,2-cyclic phosphate to alpha-D-ribosyl 1-phosphate
-
-
?
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
-
-
?
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
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mn2+
Ni2+
Mn2+
distinct preference for Mn2+ and Ni2+ for catalysis. 0.13 mol per mol of monomer
Mn2+
inhibitor orthovanadate binds in a tetrahedral geometry by the two catalytic manganese ions and the putative general acid residue H200
Ni2+
preference for Mn2+ and Ni2+ for catalysis. 1.3 mol per mol of monomer
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
15
thymidine 5'-monophosphate p-nitrophenyl ester
pH 7.2, 25°C, presence of Mn2+
2.4
bis(p-nitrophenyl)phosphate
mutant D54A, pH 7.1, 25°C, presence of Mn2+
3
bis(p-nitrophenyl)phosphate
mutant H222A, pH 7.1, 25°C, presence of Mn2+
3.4
bis(p-nitrophenyl)phosphate
mutant D187A, pH 7.1, 25°C, presence of Mn2+
3.5
bis(p-nitrophenyl)phosphate
wild-type, pH 7.1, 25°C, presence of Mn2+
3.7
bis(p-nitrophenyl)phosphate
mutant D164A, pH 7.1, 25°C, presence of Mn2+
3.7
bis(p-nitrophenyl)phosphate
mutant D80A, pH 7.1, 25°C, presence of Mn2+
3.8
bis(p-nitrophenyl)phosphate
mutant H78A, pH 7.1, 25°C, presence of Mn2+
18
bis(p-nitrophenyl)phosphate
mutant H200A, pH 7.1, 25°C, presence of Mn2+
28
bis(p-nitrophenyl)phosphate
mutant T75A, pH 7.1, 25°C, presence of Mn2+
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.08
thymidine 5'-monophosphate p-nitrophenyl ester
pH 7.2, 25°C, presence of Mn2+
0.001
bis(p-nitrophenyl)phosphate
mutant D164A, pH 7.1, 25°C, presence of Mn2+
0.001
bis(p-nitrophenyl)phosphate
mutant D54A, pH 7.1, 25°C, presence of Mn2+
0.001
bis(p-nitrophenyl)phosphate
mutant D80A, pH 7.1, 25°C, presence of Mn2+
0.003
bis(p-nitrophenyl)phosphate
mutant H78A, pH 7.1, 25°C, presence of Mn2+
0.13
bis(p-nitrophenyl)phosphate
mutant H222A, pH 7.1, 25°C, presence of Mn2+
0.25
bis(p-nitrophenyl)phosphate
mutant T75A, pH 7.1, 25°C, presence of Mn2+
0.55
bis(p-nitrophenyl)phosphate
mutant H200A, pH 7.1, 25°C, presence of Mn2+
0.88
bis(p-nitrophenyl)phosphate
mutant D187A, pH 7.1, 25°C, presence of Mn2+
1.07
bis(p-nitrophenyl)phosphate
wild-type, pH 7.1, 25°C, presence of Mn2+
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.124
methyl 2,4-dichlorophenyl phosphate
wild-type, pH 7.1, 25°C, presence of Mn2+
0.22
methyl 2,4-dinitrophenyl phosphate
wild-type, pH 7.1, 25°C, presence of Mn2+
0.68
methyl 2,5-dinitrophenyl phosphate
wild-type, pH 7.1, 25°C, presence of Mn2+
0.29
methyl 2-chloro-4-nitrophenyl phosphate
wild-type, pH 7.1, 25°C, presence of Mn2+
0.041
methyl 3-nitrophenyl phosphate
wild-type, pH 7.1, 25°C, presence of Mn2+
0.0024
methyl 4-chlorophenyl phosphate
wild-type, pH 7.1, 25°C, presence of Mn2+
0.006
methyl 4-cyanophenyl phosphate
wild-type, pH 7.1, 25°C, presence of Mn2+
0.047
methyl 4-nitrophenyl phosphate
wild-type, pH 7.1, 25°C, presence of Mn2+
0.009
methyl phenyl phosphate
wild-type, pH 7.1, 25°C, presence of Mn2+
0.005
thymidine 5'-monophosphate p-nitrophenyl ester
pH 7.2, 25°C, presence of Mn2+
0.001
bis(p-nitrophenyl)phosphate
mutant H78A, pH 7.1, 25°C, presence of Mn2+
0.009
bis(p-nitrophenyl)phosphate
mutant T75A, pH 7.1, 25°C, presence of Mn2+
0.03
bis(p-nitrophenyl)phosphate
mutant H200A, pH 7.1, 25°C, presence of Mn2+
0.043
bis(p-nitrophenyl)phosphate
mutant H222A, pH 7.1, 25°C, presence of Mn2+
0.25
bis(p-nitrophenyl)phosphate
mutant D187A, pH 7.1, 25°C, presence of Mn2+
0.3
bis(p-nitrophenyl)phosphate
wild-type, pH 7.1, 25°C, presence of Mn2+
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
-
mutants grown in the presence of alkylphosphonic acid or phosphite display the accumulation of alpha-D-ribosyl 1,2-cyclic phosphate and alpha-D-ribosyl 1-alkylphosphonate
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
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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D80A
H200A
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
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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
J. Biol. Chem.
284
17216-17226
2009
Escherichia coli, Escherichia coli (P16692)
He, S.M.; Wathier, M.; Podzelinska, K.; Wong, M.; McSorley, F.R.; Asfaw, A.; Hove-Jensen, B.; Jia, Z.; Zechel, D.L.
Structure and mechanism of PhnP, a phosphodiesterase of the carbon-phosphorus lyase pathway
Biochemistry
50
8603-8615
2011
Escherichia coli (P16692)
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