Information on EC 3.5.3.12 - agmatine deiminase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
3.5.3.12
-
RECOMMENDED NAME
GeneOntology No.
agmatine deiminase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
agmatine + H2O = N-carbamoylputrescine + NH3
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
amidine hydrolysis
-
-
-
-
C-N bond cleavage
hydrolysis
-
involved in agmatine deiminase system
hydrolysis of C-N bond of an amidino group
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Arginine and proline metabolism
-
-
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)
-
-
Metabolic pathways
-
-
polyamine pathway
-
-
putrescine biosynthesis II
-
-
SYSTEMATIC NAME
IUBMB Comments
agmatine iminohydrolase
The plant enzyme also catalyses the reactions of EC 2.1.3.3 (ornithine carbamoyltransferase), EC 2.1.3.6 (putrescine carbamoyltransferase) and EC 2.7.2.2 (carbamate kinase), thus functioning as a putrescine synthase, converting agmatine and ornithine into putrescine and citrulline, respectively.
CAS REGISTRY NUMBER
COMMENTARY hide
37289-17-1
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
oat, L. var. Black Supreme
-
-
Manually annotated by BRENDA team
Bacillus cereus CECT 148
strain CECT 148
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
brussels sprouts, var. gemmifera Zenker; cabbage, L. var. capitata L.
-
-
Manually annotated by BRENDA team
gene Cj0949c
SwissProt
Manually annotated by BRENDA team
gene CC0211
SwissProt
Manually annotated by BRENDA team
PBCV-1, gene A638R
SwissProt
Manually annotated by BRENDA team
gene DR2359
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
strain ATCC11700
-
-
Manually annotated by BRENDA team
strain SD10
SwissProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
phycobiont/mycobiont, enzyme localized in the mycobiont, growing on Quercus pyrenaica
-
-
Manually annotated by BRENDA team
strain XB
-
-
Manually annotated by BRENDA team
Lactobacillus sakei 23K is unable to produce putrescine since no putrescine carbamoyltransferase can be amplified
-
-
Manually annotated by BRENDA team
gene YrfC
SwissProt
Manually annotated by BRENDA team
formerly Lactococcus lactis subsp. cremoris GE2-14
UniProt
Manually annotated by BRENDA team
formerly Lactococcus lactis subsp. cremoris GE2-14
UniProt
Manually annotated by BRENDA team
formerly Lactococcus lactis subsp. cremoris GE2-14
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
no activity in Malus sylvestris
apple, Mill. var. Lord lambourne
-
-
Manually annotated by BRENDA team
no activity in Pisum sativum
pea, L. var. Meteor
-
-
Manually annotated by BRENDA team
no activity in Secale cereale
rye, L.
-
-
Manually annotated by BRENDA team
no activity in Streptococcus gordonii
-
-
-
Manually annotated by BRENDA team
no activity in Streptococcus sanguinis
genospecies 1
-
-
Manually annotated by BRENDA team
no activity in Triticum aestivum
wheat, var. Atle
-
-
Manually annotated by BRENDA team
C-x
-
-
Manually annotated by BRENDA team
C-x
-
-
Manually annotated by BRENDA team
Soja hispida
-
-
-
Manually annotated by BRENDA team
strain AHT
-
-
Manually annotated by BRENDA team
strain AHT
-
-
Manually annotated by BRENDA team
strain 33748
-
-
Manually annotated by BRENDA team
strain 33748
-
-
Manually annotated by BRENDA team
strain FA-1 and strain BHT
-
-
Manually annotated by BRENDA team
genospecies 2
-
-
Manually annotated by BRENDA team
strain 6715
-
-
Manually annotated by BRENDA team
strain 6715
-
-
Manually annotated by BRENDA team
gene SCC2.08
SwissProt
Manually annotated by BRENDA team
gene XF2442
SwissProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
Ac-SGRGK + H2O
? + NH3
show the reaction diagram
-
-
-
?
agmatine + ADP + phosphate
ATP + putrescine + NH3 + CO2
show the reaction diagram
-
-
-
?
agmatine + H2O
N-carbamoylputrescine + NH3
show the reaction diagram
agmatine + H2O
NH3 + N-carbamoylputrescine
show the reaction diagram
agmatine + H2O
putrescine + ?
show the reaction diagram
25 mM, assay at pH 6.5, 10 min, 40C
-
-
?
agmatine + ornithine + H2O + phosphate
putrescine + citrulline + NH3 + phosphate
show the reaction diagram
carbamoyl phosphate + ADP + H2O
ATP + CO2 + NH3
show the reaction diagram
-
-
-
r
carbamoyl phosphate + ornithine
citrulline + phosphate
show the reaction diagram
-
-
-
r
guanidine + H2O
? + NH3
show the reaction diagram
-
-
-
?
L-arginine + H2O
? + NH3
show the reaction diagram
-
-
-
?
N-alpha-benzoyl-L-arginine amide + H2O
? + NH3
show the reaction diagram
-
-
-
?
N-alpha-benzoyl-L-arginine ethyl ester + H2O
? + NH3
show the reaction diagram
-
-
-
?
N-alpha-benzoyl-L-arginine methyl ester + H2O
? + NH3
show the reaction diagram
-
-
-
?
N-carbamoylputrescine + phosphate
putrescine + carbamoyl phosphate
show the reaction diagram
-
-
-
r
streptomycin + H2O
? + NH3
show the reaction diagram
-
-
-
?
additional information
?
-
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
N-carbamoylputrescine + NH3
show the reaction diagram
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-chloroacetamidine
8-Azaguanine
-
-
agmatine
arcaine
arginine
Ba2+
-
-
cadaverine
carbohydrate
-
-
-
cationic mercury
-
enzyme 90% inhibited at 0.1 mM
cycloheximide
-
-
fructose
glucose
iodoacetamide
iodoacetoamide
-
enzyme 95% inhibited at 0.1 mM
L-arginine
-
high concentration
Mn2+
-
-
N,N'-diguanidinobutane
N-(4-aminobutyl)-2-chloro-ethanimidamide
i.e. ABCA , haloacetamidine-containing agmatine analogue
N-(4-aminobutyl)-2-chloroethanimidamide
N-(4-aminobutyl)-2-fluoro-ethanimidamide
i.e. ABFA, haloacetamidine-containing agmatine analogue
N-(4-aminobutyl)-2-fluoroethanimidamide
N-ethylmaleimide
NaCN
-
-
p-chloromercuribenzoate
Semicarbazide
spermidine
spermine
succinate
-
at concentration of 0.1 g/l and 1 g/l only about 2% less putrescine production
tryptamine
tyramine
-
at concentration of 0.1 g/l about 2% less putrescine production
additional information
-
no inhibitory effect on isoform AguA1 activity with Fe3+, Mg2+, and Ni2+
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
agmatine
AguR regulator
-
-
-
histamine
L-lactic acid
-
shows a stimulatory effect on activity
spermidine
at concentration of 0.1 g/l about 10% more putrescine production, at concentration of 1 g/l 32% more putrescine production
spermine
at concentration of 0.1 g/l about 2% more putrescine production, at concentration of 1 g/l 23% more putrescine production
succinate
tartaric acid
-
shows a stimulatory effect on activity
tyramine
additional information
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.012 - 15
agmatine
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0047 - 34.28
agmatine
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0000038 - 0.0000235
Ac-SGRGK
0.0283 - 53
agmatine
0.0000678 - 0.0000812
guanidine
0.000017 - 0.000149
L-arginine
0.000072 - 0.0001285
N-alpha-benzoyl-L-arginine amide
0.0000847 - 0.0001383
N-alpha-benzoyl-L-arginine ethyl ester
0.0001038 - 0.0002183
N-alpha-benzoyl-L-arginine methyl ester
0.000033 - 0.0000377
streptomycin
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0033 - 0.028
arcaine
10
spermine
-
-
2.5
tryptamine
-
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.013 - 2.89
Co2+
0.034
Cu2+
Listeria monocytogenes
-
at 25C and pH 7.5
0.00087
N-(4-aminobutyl)-2-chloro-ethanimidamide
Helicobacter pylori
Q9ZN18
wild-type, pH 8.0, 37C
0.00026 - 0.015
N-(4-aminobutyl)-2-chloroethanimidamide
0.0068
N-(4-aminobutyl)-2-fluoro-ethanimidamide
Helicobacter pylori
Q9ZN18
wild-type, pH 8.0, 37C
0.00027 - 0.091
N-(4-aminobutyl)-2-fluoroethanimidamide
0.1
Ni2+
Helicobacter pylori
Q9ZN18
wild-type, pH 8.0, 37C
0.03 - 0.25
Zn2+
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.0002
-
strain FA-1, 25 mM glucose, without agmatine
0.004
-
strain FA-1, 25 mM galactose, without agmatine
0.006
-
25 mM glucose + 10 mM agmatine
0.0097
-
25 mM sorbitol + 10 mM agmatine
0.01
-
crude extract of enzyme
0.01055
Q02J61, Q02J64
pH 9.0, 25C
0.0109
-
25 mM sorbitol + 10 mM agmatine
0.016
-
25 mM glucose + 10 mM agmatine
0.02
-
strain FA-1, 250 mM glucose, without agmatine
0.03
-
strain FA-1, 250 mM glucose + 10 mM agmatine
0.032
-
strain FA-1, 25 mM glucose + 10 mM agmatine
0.034
-
strain FA-1, 25 mM galactose + 10 mM agmatine
0.04
-
strain FA-1, 250 mM galactose, without agmatine
0.052
-
strain BHT, 25 mM glucose + 10 mM agmatine
0.078
-
strain GS-5, 25 mM galactose + 10 mM agmatine
0.102
-
strain FA-1, 25 mM glucose + 10 mM agmatine
0.17
-
strain UA159, 25 mM sorbitol + 10 mM agmatine
0.4762
-
strain UA159, 25 mM galactose + 10 mM agmatine
5.9
-
cells in stationary phase of growth
14.5
-
purified enzyme
26.4
purified recombinant wild-type enzyme
32.2
-
purified enzyme
47.31
-
-
172.2
-
-
876.3
-
-
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.5 - 8.5
-
-
5.5
-
2fold higher actitity compared with enzyme activity at pH 7.0
6.5 - 7.5
-
-
8.8
-
agmatine iminohydrolase function
additional information
-
assay at pH 6.0, 30 min, reaction stopped by 10% trichloroacetic acid
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
3.5 - 10.5
-
more than 85% activity between pH 3.5 and 10.5
4.5 - 10.5
-
-
5 - 9
-
-
5 - 7
-
AgD induction clearly enhanced at low pH values, aguA ca. 3.7fold higher in cells grown at pH 5 than that grown at pH 7, stress response pathway of this organism
6 - 7
-
activity rapidly declining below pH 6.0 and declining less rapidly above pH 7.0
6
-
purified enzyme shows 85% of maximum activity
6.5 - 8
-
89% of maximal activity at pH 6.5, 91% of maximal activity at pH 8.0
8
-
purified enzyme shows 85% of maximum activity
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 35
-
about 65% activity at 5C, about 90% activity at 15C, 100% activity at 25C, less than 40% activity at 35C
37 - 40
-
AgD activity 4fold higher in Streptococcus mutans grown at 42C than at 37C, stress response pathway of this organism
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
Q02J61, Q02J64
isoform Agu2A' contains a twin-arginine translocation signal at its N-terminus and is secreted to the periplasm
-
Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
41190
-
calculated from sequence data
45000
gel filtration; SDS-PAGE
55000
-
gel filtration, PAGE
56000
-
gel filtration, Sephadex G-200
67000
-
gel filtration
70000
-
gel filtration
75000
-
gel filtration
81000
recombinant His-tagged wild-type enzyme, gel filtration
82000
-
gel filtration
89000
-
gel filtration
150000
-
gel filtration
183000
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
heterodimer
-
1 * 43500 + 1 * 44000, SDS-PAGE
homodimer
-
2 * 43000, SDS-PAGE
monomer
oligomer
-
1 * 66000 + 1 * 48000 + 1 * 44000 + 1 * 15000, SDS-PAGE
tetramer
additional information
-
x * 36000, deglycosylated enzyme, SDS-PAGE, x * 47000, glycosylated enzyme, SDS-PAGE, monomer or dimer
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
glycoprotein
-
N-glycosylation
proteolytic modification
Q02J61, Q02J64
cleavage of translocation signal
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging drop vapour diffusion method with in 50 mM Tris-HCl, pH 7.45, 1 mM dithiothreitol and 20 mM NaCl
to 2.1 A resolution. Residue D198 is the key residue for agmatine recognition
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
2.5 - 6
-
agmatine is degraded in a very limited extent when the pH values are close to 2.5, a diminution of activity is observed at pH values above 6.0, at pH values from 3.2 to 3.8, the amount of putrescine formed is 53% and 75% respectively of the maximum amount formed at pH 4.5
687349
6 - 9
30 min, temperature below 40C
685687
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4
-
purified enzyme stable for two months
33
-
50% loss of activity after heating for 15 min
43
-
activity reduced by 50% on heating for 15 min
50
-
exposure for 10 min, decrease of 50% in the activity
55
-
retains 44% activity when exposed for 10 min, completely inactivated at 60C under the same conditions
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
highly unstable
-
highly unstable even in presence of glycerol, dithiothreitol and Mg2+, freeze-thawing and dialysis lead to considerable loss of activity
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C purified enzyme lost 40% activity within 15 days
-
25C, purified enzyme, 6 h, 80% loss of activity
-
4C purified enzyme lost all component activities within 48 h
-
4C, purified enzyme lost 30% of the activity in 3 days
4C, purified enzyme, 2 months, stable
-
4C, purified enzyme, at least 1 month, 15% loss of activity
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2470fold
-
enzyme purified from shoots grown in the dark by DE52 column chromatography, Sephadex G-100 column chromatography and agmatine-epoxy-Sepharose 6B column chromatography
-
HisTrap Ni-affinity column chromatography and Superdex 200 HR gel filtration
nickel-chelated agarose gel column chromatography
-
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli by Ni2+-chelate affinity chromatography
strain PAO4495, 21fold purified to near homogeneity, gel filtration
-
the protein is recombinantly expressed, lysed by sonication, and then purified by a combination of anion exchange, heparin affinity, and gel filtration
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
DNA and amino acid sequence determination and analysis, expression as C-terminally His-tagged wild-type and mutant enzymes in Escherichia coli
expressed in Escherichia coli BL21 (DE3) cells
expressed in Escherichia coli Rosetta (DE3) cells
-
expression in Escherichia coli
expression in Escherichia coli DH10B
-
expression in Escherichia coli strain DE3
expression of wild type PAO1 in Escherichia coli XL1-Blue
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
enzyme expression is transcriptionally activated by AguR
induction of the agmatine deiminase system requires agmatine and is optimal at low pH. The VicRK, ComDE, and CiaRH two-component systems influence agmatine deiminase system gene expression in response to acidic and thermal stresses
-
presence of an alternate agmatine operon in the Pseudomonas aeruginosa strain PA14 named agu2ABCA that contains two genes for agmatine deiminases, agu2A and agu2A'. This operon is present in 25% of clinical Pseudomonas aeruginosa isolates. Agmatine induces expression of the operon during the stationary phase of growth and during biofilm growth and agu2ABCA' provides only weak complementation of aguBA, which is induced during log phase
Q02J61, Q02J64
presence of an alternate agmatine operon in the Pseudomonas aeruginosa strain PA14 named agu2ABCA' that contains two genes for agmatine deiminases, agu2A and agu2A'. This operon is present in 25% of clinical Pseudomonas aeruginosa isolates. Agmatine induces expression of the operon during the stationary phase of growth and during biofilm growth and agu2ABCA' provides only weak complementation of aguBA, which is induced during log phase
Q02J61, Q02J64
transcription is significantly induced at pH 5.0
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C180A
site-directed mutagenesis, conserved catalytically relevant Cys, 35% of wild-type activity, inhibition with iodoacetamide is easier abolished by substrate agmatine
C366A
site-directed mutagenesis, conserved catalytically relevant Cys, 15% of wild-type activity, inhibition with iodoacetamide is easier abolished by substrate agmatine
C157G
-
the mutant of inactive isoform AguA2 shows wild type enzyme activity
C356A
-
inactive
D218A
-
inactive
D218E
-
inactive
D94A
-
inactive
D94E
-
inactive
E155A
-
inactive
E155D
-
inactive
G157C
-
inactive
H216A
-
inactive
H216R
-
inactive
D218A
-
inactive
-
D218E
-
inactive
-
D94A
-
inactive
-
D94E
-
inactive
-
H216A
-
inactive
-
C364G
Q02J61, Q02J64
complete loss of activity
R3G/R4S
Q02J61, Q02J64
mutation of the twin-arginine translocation tat-sequence at the N-terminus. Mutant is hardly secreted to periplasm
C361A
20% enzyme activity of wild-type enzyme
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
analysis
-
development of a multiplex PCR method for the simultaneous detection of four genes involved in the production of histamine, i.e. histidine decarboxylase hdc, tyramine, i.e.tyrosine decarboxylase tyrdc, and putrescine, via either ornithine decarboxylase odc, or agmatine deiminase agdi. A collection of 810 lactic acid bacteria strains isolated from wine and cider was screened. The most frequent gene corresponds to the agdi gene detected in 112 strains, 14% of all lactic acid bacteria strains, of 10 different lactic acid bacteria species
food industry
-
development of a multiplex PCR method for the simultaneous detection of four genes involved in the production of histamine, i.e. histidine decarboxylase hdc, tyramine, i.e.tyrosine decarboxylase tyrdc, and putrescine, via either ornithine decarboxylase odc, or agmatine deiminase agdi. A collection of 810 lactic acid bacteria strains isolated from wine and cider was screened. The most frequent gene corresponds to the agdi gene detected in 112 strains, 14% of all lactic acid bacteria strains, of 10 different lactic acid bacteria species
medicine
nutrition
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