Information on EC 2.4.2.57 - AMP phosphorylase

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The expected taxonomic range for this enzyme is: Thermococcus kodakarensis

EC NUMBER
COMMENTARY
2.4.2.57
-
RECOMMENDED NAME
GeneOntology No.
AMP phosphorylase
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
AMP + phosphate = adenine + alpha-D-ribose 1,5-bisphosphate
show the reaction diagram
(1)
-
AMP + phosphate = adenine + alpha-D-ribose 1,5-bisphosphate
show the reaction diagram
-
-
-
-
CMP + phosphate = cytosine + alpha-D-ribose 1,5-bisphosphate
show the reaction diagram
(2)
-
CMP + phosphate = cytosine + alpha-D-ribose 1,5-bisphosphate
show the reaction diagram
-
-
-
-
UMP + phosphate = uracil + alpha-D-ribose 1,5-bisphosphate
show the reaction diagram
(3)
-
UMP + phosphate = uracil + alpha-D-ribose 1,5-bisphosphate
show the reaction diagram
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
adenosine nucleotides degradation IV
-
-
purine metabolism
-
-
SYSTEMATIC NAME
IUBMB Comments
AMP:phosphate alpha-D-ribosyl 5'-phosphate-transferase
The enzyme from archaea is involved in AMP metabolism and CO2 fixation through type III RubisCO enzymes. The activity with CMP and UMP requires activation by cAMP [2].
SYNONYMS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
nucleoside monophosphate phosphorylase
-
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
AMP + phosphate
adenine + alpha-D-ribose 1,5-bisphosphate
show the reaction diagram
-
-
?
AMP + phosphate
adenine + alpha-D-ribose 1,5-bisphosphate
show the reaction diagram
-
-
-
?
AMP + phosphate
adenine + alpha-D-ribose 1,5-bisphosphate
show the reaction diagram
the archaeal enzyme is involved in AMP metabolism and CO2 fixation through type III RubisCO enzymes, the enzyme is involved in AMP metabolism and CO2 fixation through type III RubisCO enzymes
-
?
AMP + phosphate
adenine + alpha-D-ribose 1,5-bisphosphate
show the reaction diagram
-
the enzyme is involved in AMP metabolism and CO2 fixation through type III RubisCO enzymes
-
?
AMP + phosphate
adenine + alpha-D-ribose 1,5-bisphosphate
show the reaction diagram
-
the enzyme is involved in archaeal AMP degradation pathway
-
?
CMP + phosphate
cytosine + alpha-D-ribose 1,5-bisphosphate
show the reaction diagram
-
-
?
CMP + phosphate
cytosine + alpha-D-ribose 1,5-bisphosphate
show the reaction diagram
-
-
-
?
GMP + phosphate
guanine + alpha-D-ribose 1,5-bisphosphate
show the reaction diagram
-
-
?
UMP + phosphate
uracil + alpha-D-ribose 1,5-bisphosphate
show the reaction diagram
-
-
?
UMP + phosphate
uracil + alpha-D-ribose 1,5-bisphosphate
show the reaction diagram
-
-
-
?
GMP + phosphate
guanine + phosphate
show the reaction diagram
-
-
?
additional information
?
-
the use of dAMP, dGMP, or dUMP results in the generation of only trace amounts of their corresponding nucleobases, adenine, guanine, or uracil, respectivelyno activity with: TMP, ADP, ATP, dCMP, dAMP, dGMP, dUMP
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
AMP + phosphate
adenine + alpha-D-ribose 1,5-bisphosphate
show the reaction diagram
Q5JCX3
the archaeal enzyme is involved in AMP metabolism and CO2 fixation through type III RubisCO enzymes, the enzyme is involved in AMP metabolism and CO2 fixation through type III RubisCO enzymes
-
?
AMP + phosphate
adenine + alpha-D-ribose 1,5-bisphosphate
show the reaction diagram
-
the enzyme is involved in AMP metabolism and CO2 fixation through type III RubisCO enzymes
-
?
AMP + phosphate
adenine + alpha-D-ribose 1,5-bisphosphate
show the reaction diagram
-
the enzyme is involved in archaeal AMP degradation pathway
-
?
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
cAMP
-
the activity with CMP and UMP requires activation by cAMP
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
6.2
CMP
-
pH 7.5, 85C
18.5
GMP
-
pH 7.5, 85C
2.8
phosphate
-
pH 7.5, 85C; pH 7.5, 85C, cosubstrate: AMP
4.4
UMP
-
pH 7.5, 85C
additional information
AMP
-
the kinetic parameters of the enzyme toward AMP are not determined, because kinetic equations that fit the data well can not be identified
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
39.1
CMP
Thermococcus kodakarensis
-
pH 7.5, 85C
15
phosphate
Thermococcus kodakarensis
-
pH 7.5, 85C; pH 7.5, 85C, cosubstrate: AMP
10.5
UMP
Thermococcus kodakarensis
-
pH 7.5, 85C
additional information
AMP
Thermococcus kodakarensis
-
the kinetic parameters of the AMPpase reaction toward AMP are not determined, because kinetic equations that fit the data well can not be identified
2.7
GMP
Thermococcus kodakarensis
-
pH 7.5, 85C
additional information
additional information
Thermococcus kodakarensis
-
the kinetic parameters of the AMPpase reaction toward AMP are not determined, because kinetic equations that fit the data well can not be identified
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
6.3
CMP
Thermococcus kodakarensis
-
pH 7.5, 85C
100
5.4
phosphate
Thermococcus kodakarensis
-
pH 7.5, 85C, cosubstrate: AMP
16
2.4
UMP
Thermococcus kodakarensis
-
pH 7.5, 85C
133
additional information
AMP
Thermococcus kodakarensis
-
the kinetic parameters of the AMPpase reaction toward AMP are not determined, because kinetic equations that fit the data well can not be identified
30
0.1
GMP
Thermococcus kodakarensis
-
pH 7.5, 85C
162
additional information
additional information
Thermococcus kodakarensis
-
the kinetic parameters of the AMPpase reaction toward AMP are not determined, because kinetic equations that fit the data well can not be identified
2
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.06
-
85C, pH not specified in the publication, substrate: UMP
0.14
-
85C, pH not specified in the publication, substrate: CMP
1.8
-
substrate: GMP, pH 7.5, 85C
2.94
-
60C, pH not specified in the publication
10.8
-
substrate: UMP, pH 7.5, 85C
14.69
-
85C, pH not specified in the publication
15.9
-
substrate: AMP, pH 7.5, 85C
22.3
-
85C, pH not specified in the publication, substrate: AMP
37.5
-
substrate: CMP, pH 7.5, 85C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
85
-
assay; assay at
PDB
SCOP
CATH
ORGANISM
UNIPROT
Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
multimer
-
forms a large macromolecular structure of more than 40 subunits in solution. Structures of two truncated forms of Tk-AMPpase (Tk-AMPpaseDELTAN84 and Tk-AMPpaseDELTAC10) clarify that the multimerization is achieved by two dimer interfaces within a single molecule: one by the central domain and the other by the C-terminal domain, which consists of an unexpected domain-swapping interaction. The N-terminal domain, characteristic of archaeal enzymes, is essential for enzymatic activity, participating in multimerization as well as domain closure of the active site upon substrate binding. Biochemical analysis demonstrates that the macromolecular assembly of the enzyme contributes to its high thermostability
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging-drop vapor diffusion method at 20C. Crystal structures of the enzyme, in the apo-form and in complex with substrates
-
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
the macromolecular assembly of the enzyme contributes to its high thermostability
725719
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
DELTAN1-84
-
mutant enzyme lacking the N-terminal 22 residues aggregates at 75C
additional information
-
all the mutants, forming smaller assemblies, display a decrease in thermostability compared to the wild-type enzyme. Tk-AMPpaseDELTAC10 aggregates at temperatures of 80C or higher, while aggregation of Tk-AMPpaseDELTAN84 is observed at 75C and that of Tk-AMPpase?N84DELTAC10 is observed at 70C