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Information on EC 2.4.2.57 - AMP phosphorylase and Organism(s) Thermococcus kodakarensis and UniProt Accession Q5JCX3

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EC Tree
     2 Transferases
         2.4 Glycosyltransferases
             2.4.2 Pentosyltransferases
                2.4.2.57 AMP phosphorylase
IUBMB Comments
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 .
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This record set is specific for:
Thermococcus kodakarensis
UNIPROT: Q5JCX3
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The taxonomic range for the selected organisms is: Thermococcus kodakarensis
The expected taxonomic range for this enzyme is: Archaea, Bacteria
Synonyms
amp phosphorylase, amppase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
nucleoside monophosphate phosphorylase
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
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
UMP + phosphate = uracil + alpha-D-ribose 1,5-bisphosphate
show the reaction diagram
PATHWAY SOURCE
PATHWAYS
-
-
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].
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
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
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
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
AMP + phosphate
adenine + alpha-D-ribose 1,5-bisphosphate
show the reaction diagram
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
cAMP
the activity with CMP and UMP requires activation by cAMP
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
6.2
CMP
pH 7.5, 85°C
18.5
GMP
pH 7.5, 85°C
2.8
phosphate
4.4
UMP
pH 7.5, 85°C
additional information
AMP
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
39.1
CMP
pH 7.5, 85°C
2.7
GMP
pH 7.5, 85°C
15
phosphate
10.5
UMP
pH 7.5, 85°C
additional information
AMP
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
6.3
CMP
pH 7.5, 85°C
0.1
GMP
pH 7.5, 85°C
5.4
phosphate
pH 7.5, 85°C, cosubstrate: AMP
2.4
UMP
pH 7.5, 85°C
additional information
AMP
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.06
85°C, pH not specified in the publication, substrate: UMP
0.14
85°C, pH not specified in the publication, substrate: CMP
1.8
substrate: GMP, pH 7.5, 85°C
10.8
substrate: UMP, pH 7.5, 85°C
14.69
85°C, pH not specified in the publication
15.9
substrate: AMP, pH 7.5, 85°C
2.94
60°C, pH not specified in the publication
22.3
85°C, pH not specified in the publication, substrate: AMP
37.5
substrate: CMP, pH 7.5, 85°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
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 20°C. Crystal structures of the enzyme, in the apo-form and in complex with substrates
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
DELTAN1-84
mutant enzyme lacking the N-terminal 22 residues aggregates at 75°C
additional information
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Aono, R.; Sato, T.; Yano, A.; Yoshida, S.; Nishitani, Y.; Miki, K.; Imanaka, T.; Atomi, H.
Enzymatic characterization of AMP phosphorylase and ribose-1,5-bisphosphate isomerase functioning in an archaeal AMP metabolic pathway
J. Bacteriol.
194
6847-6855
2012
Thermococcus kodakarensis (Q5JCX3), Thermococcus kodakarensis
Manually annotated by BRENDA team
Nishitani, Y.; Aono, R.; Nakamura, A.; Sato, T.; Atomi, H.; Imanaka, T.; Miki, K.
Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization
J. Mol. Biol.
425
2709-2721
2013
Thermococcus kodakarensis (Q5JCX3), Thermococcus kodakarensis
Manually annotated by BRENDA team
Sato, T.; Atomi, H.; Imanaka, T.
Archaeal type III RuBisCOs function in a pathway for AMP metabolism
Science
315
1003-1006
2007
Thermococcus kodakarensis (Q5JCX3), Thermococcus kodakarensis
Manually annotated by BRENDA team