Information on EC 3.5.3.11 - agmatinase

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea

EC NUMBER
COMMENTARY
3.5.3.11
-
RECOMMENDED NAME
GeneOntology No.
agmatinase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
agmatine + H2O = putrescine + urea
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
amidine hydrolysis
-
-
-
-
PATHWAY
KEGG Link
MetaCyc Link
Arginine and proline metabolism
-
arginine degradation III (arginine decarboxylase/agmatinase pathway)
-
Metabolic pathways
-
putrescine biosynthesis I
-
putrescine biosynthesis IV
-
SYSTEMATIC NAME
IUBMB Comments
agmatine amidinohydrolase
-
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
AGMAT
Q9BSE5
-
agmatinase
-
-
agmatinase
-
-
agmatinase-like protein
-
-
agmatine ureohydrolase
-
-
-
-
agmatine ureohydrolase
-
-
AUH
-
-
-
-
N130D variant of arginase type I
-
-
Proclavaminic acid amidino hydrolase
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
37289-16-0
-
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
metabolism
-
the gene agmatine ureohydrolase is involved in polyamine biosynthesis
physiological function
-
agmatinase-like protein plays a role in the regulation of intracellular concentrations of the neurotransmitter/neuromodulator agmatine
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
agmatine + H2O
putrescine + urea
show the reaction diagram
-
-
-
-
-
agmatine + H2O
putrescine + urea
show the reaction diagram
-
-
-
-
?
agmatine + H2O
putrescine + urea
show the reaction diagram
-
-
-
?
agmatine + H2O
putrescine + urea
show the reaction diagram
-
-
-
-
?
agmatine + H2O
putrescine + urea
show the reaction diagram
-
-
-
-
?
agmatine + H2O
putrescine + urea
show the reaction diagram
-
-
-
-
?
agmatine + H2O
putrescine + urea
show the reaction diagram
-
-
-
-
?
agmatine + H2O
putrescine + urea
show the reaction diagram
-
-
-
-
?
agmatine + H2O
putrescine + urea
show the reaction diagram
-
-
-
-
?
agmatine + H2O
putrescine + urea
show the reaction diagram
Q9BSE5
-
-
-
?
agmatine + H2O
putrescine + urea
show the reaction diagram
-
the N130D mutant of arginase type I is able to cleave not only arginine but also agmatine (1-amino-4-guanidinobutane)
-
-
?
additional information
?
-
-
no activity with arginine
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
agmatine + H2O
putrescine + urea
show the reaction diagram
-
-
-
-
?
agmatine + H2O
putrescine + urea
show the reaction diagram
-
-
-
-
?
agmatine + H2O
putrescine + urea
show the reaction diagram
-
-
-
-
?
agmatine + H2O
putrescine + urea
show the reaction diagram
-
-
-
-
?
agmatine + H2O
putrescine + urea
show the reaction diagram
-
-
-
-
?
agmatine + H2O
putrescine + urea
show the reaction diagram
-
-
-
-
?
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Ca2+
-
enzyme loses activity by dialysis against a buffer without cations, but the activity is recovered by the addition of divalent cations. CoCl2 is the most effective, and CaCl2, MnCl2, ZnCl2 or MgCl2 is replaced to some extent instead of CoCl2
Co2+
-
enzyme loses activity by dialysis against a buffer without cations, but the activity is recovered by the addition of divalent cations. CoCl2 is the most effective, and CaCl2, MnCl2, ZnCl2 or MgCl2 is replaced to some extent instead of CoCl2
Mg2+
-
enzyme loses activity by dialysis against a buffer without cations, but the activity is recovered by the addition of divalent cations. CoCl2 is the most effective, and CaCl2, MnCl2, ZnCl2 or MgCl2 is replaced to some extent instead of CoCl2
Mn2+
-
a binuclear metal center is suggested
Mn2+
-
0.85 Mn2+ per subunit
Mn2+
-
required
Mn2+
-
enzyme loses activity by dialysis against a buffer without cations, but the activity is recovered by the addition of divalent cations. CoCl2 is the most effective, and CaCl2, MnCl2, ZnCl2 or MgCl2 is replaced to some extent instead of CoCl2
Mn2+
-
activates
Mn2+
-
totally dependent on Mn2+ for catalytic activity
Zn2+
-
enzyme loses activity by dialysis against a buffer without cations, but the activity is recovered by the addition of divalent cations. CoCl2 is the most effective, and CaCl2, MnCl2, ZnCl2 or MgCl2 is replaced to some extent instead of CoCl2
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
1,6-diaminohexane
-
inhibition arises from the displacement of the metal-bridging water
arginine
-
competitive inhibitor
Chloroatranorin
-
12.6 mM
diethyldicarbonate
-
-
EDTA
-
1 mM causes 53% inhibition
EGTA
-
1 mM causes 74% inhibition
everinic acid
-
18.5 mM
guanidinium ion
-
competitive
ornithine
-
noncompetitive inhibitor
putrescine
-
competitive inhibitor
-
putrescine
-
competitive
-
putrescine
-
-
-
putrescine
-
-
-
putrescine
-
linear competitive inhibitor
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
L-arginine
-
but it inhibits at concentrations about 14 mM agmatine
L-ornithine
-
but it inhibits at concentrations about 14 mM agmatine
putrescine
-
but it inhibits at concentrations about 14 mM agmatine
-
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.53
-
agmatine
-
50C, pH 11.3
1.1
-
agmatine
-
wild type
1.2
-
agmatine
-
-
1.4
-
agmatine
-
-
5.3
-
agmatine
-
-
6.3
-
agmatine
-
mutant E274A
6.4
-
agmatine
-
-
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
3
-
agmatine
-
-
Ki VALUE [mM]
Ki VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
15
-
guanidinium ion
-
wild type
44.2
-
guanidinium ion
-
mutant E274A
1.3
-
putrescine
-
-
-
1.8
-
putrescine
-
50C, pH 11.3
-
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
pH RANGE
pH RANGE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
9.5
12.5
-
pH 9.5: about 50% of maximal activity, pH 12.5: about 85% of maximal activity
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE
-
agmatinase is localised pre- and postsynaptically, to dendritic spines, spine and non-spine terminals, and dendritic profiles. In dendritic spines, labelling displayed a tendency towards the postsynaptic density
Manually annotated by BRENDA team
-
in astrocytes and neurons of the hippocampus
Manually annotated by BRENDA team
-
agmatinase protein is detected in a subset of hippocampal interneurons. The protein is localized to perikarya, neurites and putative nerve endings contacting hippocampal pyramidal neurons and dentate gyrus granule cells. The number and the numerical density of agmatinase-immunopositive cell bodies are strongly elevated in depressive patients
Manually annotated by BRENDA team
-
in glial cells and arcuate nucleus neurons of the hypothalamus
Manually annotated by BRENDA team
-
agmatinase in normal kidneys is restricted to tubulus epithelial cells, while in tumors activity is low and heterogeneous
Manually annotated by BRENDA team
-
agmatinase in normal kidneys is restricted to tubulus epithelial cells, while in tumors activity is low and heterogeneous
Manually annotated by BRENDA team
-
agmatinase is predominantly detected in distinct populations of neurons, especially cortical interneurons. Principal neurons in limbic regions like the habenula and in the cerebellum robustly express agmatinase protein
Manually annotated by BRENDA team
additional information
-
the protein is not detected in brain cortex
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
Burkholderia thailandensis (strain E264 / ATCC 700388 / DSM 13276 / CIP 106301)
Clostridium difficile (strain 630)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
80000
-
-
gel filtration
120000
-
-
SDS-PAGE
145000
-
-
gel filtration
320000
-
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
dimer
-
2 * 38000, SDS-PAGE, 2 * 33409, deduced from sequence
tetramer
-
4 * 31000, SDS-PAGE
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
crystal structure of Mn2+ -free, Mn2+ -bound, and Mn2+ -1,6-diaminohexane(inhibitor)-bound forms
-
hangimg-drop vapor-diffusion method, crystallized at 297 K using polyethylene glycol 3000 as a precipitant. X-ray diffraction data are collected to 1.8 A from a crystal grown in the presence of Mn2+ and 1,6-hexanediamine. The crystals are orthorhombic, belonging to the space group P2(1)2(1)2(1), with unit-cell parameters a = 81.77 A, b = 131.44 A, c = 168.85 A, alpha = beta = gamma = 90. A hexameric molecule is likely to be present in the asymmetric unit
-
hanging-drop vapour-diffusion method, agmatinase (residues Ala36-Val352) overexpressed as a fusion with both N- and C-terminal purification tags in Escherichia coli and crystallized in the presence of Mn2+ and 1,6-diaminohexane at 297 K using polyethylene glycol 4000 as a precipitant. X-ray diffraction data are collected at 100 K to 2.49 A from a flash-frozen crystal. The crystals are tetragonal, belonging to space group P4(2), with unit-cell parameters a = b = 114.54 A, c =125.65A, alpha = beta = gamma = 90. Three monomers are likely to be present in the asymmetric unit, giving a crystal volume per protein weight of 3.66A
-
TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
0
-
-
6% of activity retained
70
-
-
20% of activity retained
80
-
-
10 min, stable
90
-
-
10 min, 53% loss of activity
ORGANIC SOLVENT
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
dimethyl sulfoxide
-
10%, no loss of activity at 50C
Ethanol
-
10%, no loss of activity at 50C
Methanol
-
10%, no loss of activity at 50C
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
-80C, at least three months
-
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
DEAE-cellulose column chromatography
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expression in Escherichia coli as a fusion protein with the C-terminal eight-residue His-tag
-
ColE1 plasmids expressed in Escherichia coli
-
expressed in Escherichia coli strain JM109
-
residues Ala36-Val352 overexpressed as a fusion with both N- and C-terminal purification tags in Escherichia coli
-
expression in Escherichia coli. Mainly obtained as inactive inclusion body in Escherichia coli
-
EXPRESSION
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
agmatinase expression is up-regulated in hippocampal interneurons of patients with mood disorders
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
E274A
-
1-2% of wild type activity
H126N
-
51% of wild type activity, significant alteration in Mn2+ binding
H126N
-
51% of wild-type activity with Mn2+-activated mutant enzyme. Interaction with the required Mn2+ is significantly altered. Mutation is not accompanied by change in Km-value, Ki-value for putrescine inhibition, molecular weight, tryptophan fluorescence properties or CD spectra of the enzyme
H151N
-
30% of wild type activity, significant alteration in Mn2+ binding
H151N
-
30% of wild-type activity with Mn2+-activated mutant enzyme. Interaction with the required Mn2+ is significantly altered. Mutation is not accompanied by change in Km-value, Ki-value for putrescine inhibition, molecular weight, tryptophan fluorescence properties or CD spectra of the enzyme