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 hide
3.5.3.11
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RECOMMENDED NAME
GeneOntology No.
agmatinase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
agmatine + H2O = putrescine + urea
show the reaction diagram
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
amidine hydrolysis
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Arginine and proline metabolism
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L-arginine degradation III (arginine decarboxylase/agmatinase pathway)
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Metabolic pathways
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polyamine pathway
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putrescine biosynthesis I
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putrescine biosynthesis IV
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SYSTEMATIC NAME
IUBMB Comments
agmatine amidinohydrolase
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CAS REGISTRY NUMBER
COMMENTARY hide
37289-16-0
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
UniProt
Manually annotated by BRENDA team
Anabaena sp. PCC 7120
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UniProt
Manually annotated by BRENDA team
Panus tigrinus (bull. ex. fr.) sing
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Manually annotated by BRENDA team
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UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
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the gene agmatine ureohydrolase is involved in polyamine biosynthesis
physiological function
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agmatinase-like protein plays a role in the regulation of intracellular concentrations of the neurotransmitter/neuromodulator agmatine
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
agmatine + H2O
putrescine + urea
show the reaction diagram
additional information
?
-
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no activity with arginine
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
agmatine + H2O
putrescine + urea
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
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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+
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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
Fe2+
Fe(II)-dependent agmatinase. Requires the presence of 4 equivalents of Fe(II) for maximum activity
Mg2+
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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
Zn2+
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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
COMMENTARY hide
LITERATURE
IMAGE
1,6-diaminohexane
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inhibition arises from the displacement of the metal-bridging water
arginine
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competitive inhibitor
Chloroatranorin
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12.6 mM
diethyldicarbonate
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EGTA
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1 mM causes 74% inhibition
everinic acid
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18.5 mM
guanidinium ion
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competitive
iodoacetic acid
the enzyme is rendered inactive when the purified enzyme is incubated with dithiothreitol followed by excess iodoacetic acid
L-arginine
44% inhibition at at 16.7 mM
N-ethylmaleinimide
the enzyme is rendered inactive when the purified enzyme is incubated with dithiothreitol followed by excess N-ethylmaleimide
ornithine
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noncompetitive inhibitor
putrescine
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
dithiothreitol
the enzyme requires the presence of dithiothreitol for maximum activity
L-arginine
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but it inhibits at concentrations about 14 mM agmatine
L-ornithine
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but it inhibits at concentrations about 14 mM agmatine
putrescine
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but it inhibits at concentrations about 14 mM agmatine
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.53 - 11
agmatine
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0075 - 3
agmatine
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00069 - 0.013
agmatine
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
15 - 44.2
guanidinium ion
1.3 - 1.8
putrescine
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.5 - 10
no activity is detected at pH 6.5 and the measured activity steadily increases to pH 10.0. Higher pH values are tested but the observation of activity is dependent on the buffer used and are not reported here. Agmatine shows no hydrolysis in the pH 10 and 11 buffers and assay conditions used
9.5 - 12.5
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pH 9.5: about 50% of maximal activity, pH 12.5: about 85% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
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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
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in glial cells and arcuate nucleus neurons of the hypothalamus
Manually annotated by BRENDA team
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agmatinase in normal kidneys is restricted to tubulus epithelial cells, while in tumors activity is low and heterogeneous
Manually annotated by BRENDA team
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agmatinase in normal kidneys is restricted to tubulus epithelial cells, while in tumors activity is low and heterogeneous
Manually annotated by BRENDA team
additional information
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the protein is not detected in brain cortex
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Burkholderia thailandensis (strain E264 / ATCC 700388 / DSM 13276 / CIP 106301)
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
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
80000
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gel filtration
120000
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SDS-PAGE
145000
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gel filtration
320000
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gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
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2 * 38000, SDS-PAGE, 2 * 33409, deduced from sequence
tetramer
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4 * 31000, SDS-PAGE
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystal structure of Mn2+ -free, Mn2+ -bound, and Mn2+ -1,6-diaminohexane(inhibitor)-bound forms
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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
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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
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0
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6% of activity retained
70
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20% of activity retained
80
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10 min, stable
90
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10 min, 53% loss of activity
ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimethyl sulfoxide
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10%, no loss of activity at 50C
Ethanol
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10%, no loss of activity at 50C
Methanol
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10%, no loss of activity at 50C
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-80C, at least three months
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
DEAE-cellulose column chromatography
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wild-type and mutant enzymes
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ColE1 plasmids expressed in Escherichia coli
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expressed in Escherichia coli strain JM109
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expression in Escherichia coli as a fusion protein with the C-terminal eight-residue His-tag
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expression in Escherichia coli. Mainly obtained as inactive inclusion body in Escherichia coli
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overexpression in Escherichia coli
residues Ala36-Val352 overexpressed as a fusion with both N- and C-terminal purification tags in Escherichia coli
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
agmatinase expression is up-regulated in hippocampal interneurons of patients with mood disorders
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protein expression increases more than 2fold in morpholino antisense oligonucleotide-ornithine decarboxylase 1-knockdown conceptuses and uteri
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E274A
-
1-2% of wild type activity
C136A
mutant has 90% of the activity compared to wild type in the presence of Fe(II). As the wild-type enzyme the mutant enzyme requires dithiothreitol for activity
C151S
mutant has 6% of the activity compared to wild type in the presence of Fe(II). When dithiothreitol is present in the reaction the mutant shows 24% of the wild type activity
C229A
mutant has 92% of the activity compared to wild type in the presence of Fe(II)
C71S
mutant has 4% of the activity compared to wild type in the presence of Fe(II). When dithiothreitol is present in the reaction the mutant shows 24% of the wild type activity
C136A
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mutant has 90% of the activity compared to wild type in the presence of Fe(II). As the wild-type enzyme the mutant enzyme requires dithiothreitol for activity
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C151S
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mutant has 6% of the activity compared to wild type in the presence of Fe(II). When dithiothreitol is present in the reaction the mutant shows 24% of the wild type activity
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C229A
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mutant has 92% of the activity compared to wild type in the presence of Fe(II)
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C71S
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mutant has 4% of the activity compared to wild type in the presence of Fe(II). When dithiothreitol is present in the reaction the mutant shows 24% of the wild type activity
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