BRENDA - Enzyme Database
show all sequences of 3.5.3.12

Mechanistic studies of agmatine deiminase from multiple bacterial species

Jones, J.E.; Dreyton, C.J.; Flick, H.; Causey, C.P.; Thompson, P.R.; Biochemistry 49, 9413-9423 (2010)

Data extracted from this reference:

Inhibitors
Inhibitors
Commentary
Organism
Structure
2-chloroacetamidine
-
Helicobacter pylori
2-chloroacetamidine
-
Porphyromonas gingivalis
2-chloroacetamidine
-
Streptococcus mutans
iodoacetamide
-
Helicobacter pylori
iodoacetamide
-
Porphyromonas gingivalis
iodoacetamide
-
Streptococcus mutans
N-(4-aminobutyl)-2-chloroethanimidamide
-
Helicobacter pylori
N-(4-aminobutyl)-2-chloroethanimidamide
-
Porphyromonas gingivalis
N-(4-aminobutyl)-2-chloroethanimidamide
-
Streptococcus mutans
N-(4-aminobutyl)-2-fluoroethanimidamide
inactivation proceeds via a multistep mechanism that requires general acid catalysis
Helicobacter pylori
N-(4-aminobutyl)-2-fluoroethanimidamide
inactivation proceeds via a multistep mechanism that requires general acid catalysis
Porphyromonas gingivalis
N-(4-aminobutyl)-2-fluoroethanimidamide
inactivation proceeds via a multistep mechanism that requires general acid catalysis
Streptococcus mutans
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Helicobacter pylori
-
-
-
Porphyromonas gingivalis
-
-
-
Streptococcus mutans
-
-
-
Purification (Commentary)
Commentary
Organism
the protein is recombinantly expressed, lysed by sonication, and then purified by a combination of anion exchange, heparin affinity, and gel filtration
Helicobacter pylori
the protein is recombinantly expressed, lysed by sonication, and then purified by a combination of anion exchange, heparin affinity, and gel filtration
Porphyromonas gingivalis
the protein is recombinantly expressed, lysed by sonication, and then purified by a combination of anion exchange, heparin affinity, and gel filtration
Streptococcus mutans
Reaction
Reaction
Commentary
Organism
agmatine + H2O = N-carbamoylputrescine + NH3
like other GME hydrolases the enzyme possesses a high pKa active site Cys, suggesting that the enzyme employs a reverse protonation mechanism
Helicobacter pylori
agmatine + H2O = N-carbamoylputrescine + NH3
like other GME hydrolases the enzyme possesses a high pKa active site Cys, suggesting that the enzyme employs a reverse protonation mechanism
Porphyromonas gingivalis
agmatine + H2O = N-carbamoylputrescine + NH3
like other GME hydrolases the enzyme possesses a high pKa active site Cys, suggesting that the enzyme employs a reverse protonation mechanism
Streptococcus mutans
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
agmatine + H2O
-
718884
Helicobacter pylori
N-carbamoylputrescine + NH3
-
-
-
?
agmatine + H2O
-
718884
Porphyromonas gingivalis
N-carbamoylputrescine + NH3
-
-
-
?
agmatine + H2O
-
718884
Streptococcus mutans
N-carbamoylputrescine + NH3
-
-
-
?
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
37
-
assay at
Helicobacter pylori
37
-
assay at
Porphyromonas gingivalis
37
-
assay at
Streptococcus mutans
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
8
-
assay at
Helicobacter pylori
8
-
assay at
Porphyromonas gingivalis
8
-
assay at
Streptococcus mutans
IC50 Value
IC50 Value
IC50 Value Maximum
Commentary
Organism
Inhibitor
Structure
0.00026
-
pH 8.0, 37°C
Streptococcus mutans
N-(4-aminobutyl)-2-chloroethanimidamide
0.00027
-
pH 8.0, 37°C
Streptococcus mutans
N-(4-aminobutyl)-2-fluoroethanimidamide
0.00087
-
pH 8.0, 37°C
Helicobacter pylori
N-(4-aminobutyl)-2-chloroethanimidamide
0.0068
-
pH 8.0, 37°C
Helicobacter pylori
N-(4-aminobutyl)-2-fluoroethanimidamide
0.015
-
pH 8.0, 37°C
Porphyromonas gingivalis
N-(4-aminobutyl)-2-chloroethanimidamide
0.091
-
pH 8.0, 37°C
Porphyromonas gingivalis
N-(4-aminobutyl)-2-fluoroethanimidamide
IC50 Value (protein specific)
IC50 Value
IC50 Value Maximum
Commentary
Organism
Inhibitor
Structure
0.00026
-
pH 8.0, 37°C
Streptococcus mutans
N-(4-aminobutyl)-2-chloroethanimidamide
0.00027
-
pH 8.0, 37°C
Streptococcus mutans
N-(4-aminobutyl)-2-fluoroethanimidamide
0.00087
-
pH 8.0, 37°C
Helicobacter pylori
N-(4-aminobutyl)-2-chloroethanimidamide
0.0068
-
pH 8.0, 37°C
Helicobacter pylori
N-(4-aminobutyl)-2-fluoroethanimidamide
0.015
-
pH 8.0, 37°C
Porphyromonas gingivalis
N-(4-aminobutyl)-2-chloroethanimidamide
0.091
-
pH 8.0, 37°C
Porphyromonas gingivalis
N-(4-aminobutyl)-2-fluoroethanimidamide
Inhibitors (protein specific)
Inhibitors
Commentary
Organism
Structure
2-chloroacetamidine
-
Helicobacter pylori
2-chloroacetamidine
-
Porphyromonas gingivalis
2-chloroacetamidine
-
Streptococcus mutans
iodoacetamide
-
Helicobacter pylori
iodoacetamide
-
Porphyromonas gingivalis
iodoacetamide
-
Streptococcus mutans
N-(4-aminobutyl)-2-chloroethanimidamide
-
Helicobacter pylori
N-(4-aminobutyl)-2-chloroethanimidamide
-
Porphyromonas gingivalis
N-(4-aminobutyl)-2-chloroethanimidamide
-
Streptococcus mutans
N-(4-aminobutyl)-2-fluoroethanimidamide
inactivation proceeds via a multistep mechanism that requires general acid catalysis
Helicobacter pylori
N-(4-aminobutyl)-2-fluoroethanimidamide
inactivation proceeds via a multistep mechanism that requires general acid catalysis
Porphyromonas gingivalis
N-(4-aminobutyl)-2-fluoroethanimidamide
inactivation proceeds via a multistep mechanism that requires general acid catalysis
Streptococcus mutans
Purification (Commentary) (protein specific)
Commentary
Organism
the protein is recombinantly expressed, lysed by sonication, and then purified by a combination of anion exchange, heparin affinity, and gel filtration
Helicobacter pylori
the protein is recombinantly expressed, lysed by sonication, and then purified by a combination of anion exchange, heparin affinity, and gel filtration
Porphyromonas gingivalis
the protein is recombinantly expressed, lysed by sonication, and then purified by a combination of anion exchange, heparin affinity, and gel filtration
Streptococcus mutans
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
agmatine + H2O
-
718884
Helicobacter pylori
N-carbamoylputrescine + NH3
-
-
-
?
agmatine + H2O
-
718884
Porphyromonas gingivalis
N-carbamoylputrescine + NH3
-
-
-
?
agmatine + H2O
-
718884
Streptococcus mutans
N-carbamoylputrescine + NH3
-
-
-
?
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
37
-
assay at
Helicobacter pylori
37
-
assay at
Porphyromonas gingivalis
37
-
assay at
Streptococcus mutans
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
8
-
assay at
Helicobacter pylori
8
-
assay at
Porphyromonas gingivalis
8
-
assay at
Streptococcus mutans
Other publictions for EC 3.5.3.12
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
733200
del Rio
Putrescine production via the ...
Lactococcus lactis subsp. cremoris, Lactococcus lactis subsp. cremoris CECT 8666
Appl. Microbiol. Biotechnol.
99
897-905
2015
-
-
-
-
-
-
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1
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4
-
3
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1
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4
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1
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4
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1
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4
-
-
-
-
-
-
-
-
-
-
1
1
-
-
-
733510
Marchenko
Development of a clickable act ...
Streptococcus mutans, Streptococcus mutans UA159
Bioorg. Med. Chem.
23
2159-2167
2015
-
-
-
-
-
-
-
-
-
-
1
2
-
18
-
-
-
-
-
-
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2
1
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-
-
-
-
-
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1
2
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-
2
1
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-
-
-
-
-
-
-
-
-
-
-
-
-
734228
Cheng
Listeria monocytogenes aguA1, ...
Listeria monocytogenes 10403S, Listeria monocytogenes
J. Biol. Chem.
288
26606-26615
2013
-
-
1
-
11
-
4
1
-
-
1
2
-
8
-
-
1
-
-
-
-
2
4
1
1
1
-
1
1
1
-
-
-
-
3
-
-
1
-
-
11
-
3
4
-
1
-
-
1
2
-
-
-
1
-
-
-
2
4
1
1
1
-
1
1
1
-
-
1
2
2
1
1
1
734787
Chen
Prevalence of the lmo0036-0043 ...
Listeria monocytogenes
New Microbiol.
36
187-192
2013
-
-
-
-
-
-
-
-
-
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1
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2
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1
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1
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1
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-
-
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-
1
1
-
-
-
735102
Suarez
Expression of the agmatine dei ...
Enterococcus faecalis, Enterococcus faecalis JH2-2
PLoS ONE
8
e76170
2013
1
-
-
-
-
-
-
-
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2
-
9
-
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2
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1
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2
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2
-
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-
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-
-
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-
1
-
-
1
-
-
711375
Jones
Characterization and inactivat ...
Helicobacter pylori
Bioorg. Chem.
38
62-73
2010
-
-
1
1
-
-
5
2
-
-
-
-
-
3
-
-
-
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-
-
-
-
8
-
-
-
-
2
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-
-
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-
5
-
-
1
-
1
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-
5
5
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2
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-
-
-
-
-
-
-
-
-
-
8
-
-
-
-
2
-
-
-
-
-
-
-
-
16
16
712057
Coton
Occurrence of biogenic amine-f ...
Bacteria
Food Microbiol.
27
1078-1085
2010
-
2
-
-
-
-
-
-
-
-
-
-
-
6
-
-
-
-
-
-
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2
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-
-
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-
-
-
-
-
-
-
-
713057
Williams
Discovery of an operon that pa ...
Pseudomonas aeruginosa PA14
Mol. Microbiol.
76
104-119
2010
-
-
1
-
2
-
-
-
1
-
1
-
-
4
-
1
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-
-
-
2
-
2
1
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1
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-
2
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1
-
1
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-
1
-
-
-
2
-
2
1
-
-
-
-
-
-
-
-
2
1
2
2
2
2
718884
Jones
Mechanistic studies of agmatin ...
Helicobacter pylori, Porphyromonas gingivalis, Streptococcus mutans
Biochemistry
49
9413-9423
2010
-
-
-
-
-
-
12
-
-
-
-
-
-
8
-
-
3
3
-
-
-
-
3
-
3
-
-
-
3
-
-
-
-
-
6
-
-
-
-
-
-
-
6
12
-
-
-
-
-
-
-
-
-
3
-
-
-
-
3
-
3
-
-
-
3
-
-
-
-
-
-
-
-
-
719620
Landete
The role of two families of ba ...
Bacillus cereus, Bacillus cereus ATCC 14579, Enterococcus faecalis, Enterococcus faecalis ATCC 11700, Lactobacillus hilgardii, Lactobacillus hilgardii X1B, Lactobacillus sakei, Pseudomonas aeruginosa
Int. Microbiol.
13
169-177
2010
-
-
-
-
-
-
-
-
-
-
-
-
-
23
-
-
-
-
-
-
-
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-
-
5
-
-
-
5
-
-
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-
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-
-
-
-
-
-
5
-
-
-
5
-
-
-
-
-
-
-
-
-
695768
Liu
AguR is required for induction ...
Streptococcus mutans
Appl. Environ. Microbiol.
75
2629-2637
2009
1
-
-
-
-
-
-
-
-
-
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2
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1
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1
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1
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-
1
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
700535
Griswold
Distribution, regulation and r ...
no activity in Streptococcus gordonii, no activity in Streptococcus sanguinis, Streptococcus criceti, Streptococcus criceti AHT, Streptococcus downei, Streptococcus downei 33748, Streptococcus mutans, Streptococcus oralis, Streptococcus ratti, Streptococcus salivarius, Streptococcus sanguinis, Streptococcus sobrinus, Streptococcus sobrinus 6715
Oral Microbiol. Immunol.
24
79-82
2009
5
5
-
-
-
-
1
-
-
-
-
-
-
18
-
-
-
-
-
-
18
-
11
-
-
-
-
-
8
-
-
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5
5
-
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-
-
-
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1
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-
-
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-
-
18
-
11
-
-
-
-
-
8
-
-
-
-
-
-
-
-
-
712291
Liu
Multiple two-component systems ...
Streptococcus mutans
J. Bacteriol.
191
7363-7366
2009
-
-
-
-
-
-
-
-
-
-
-
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-
2
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-
-
-
-
-
-
-
-
1
-
-
1
-
-
685687
Liao
Occurrence of agmatine pathway ...
Selenomonas ruminantium
Biosci. Biotechnol. Biochem.
72
445-455
2008
-
-
1
-
1
-
9
1
-
-
1
-
-
5
-
-
1
-
-
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-
-
1
1
1
-
1
-
1
-
1
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-
1
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-
1
-
-
9
-
1
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1
-
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-
-
1
-
-
-
-
1
1
1
-
1
-
1
-
1
-
-
-
-
-
-
-
687349
Arena
Factors affecting the producti ...
Lactobacillus hilgardii, Lactobacillus hilgardii XB
J. Appl. Microbiol.
105
158-165
2008
3
-
-
-
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5
-
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2
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1
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1
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1
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1
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3
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-
-
-
-
-
2
-
1
-
1
-
1
-
1
-
-
-
-
-
-
-
692430
Landete
Comparative survey of putresci ...
Bacillus cereus, Bacillus cereus CECT 148, Enterococcus faecalis, Enterococcus faecalis ATCC 11700, Lactobacillus hilgardii, Lactobacillus hilgardii X1B, Pseudomonas aeruginosa
Food Microbiol.
25
882-887
2008
9
-
-
-
-
-
20
-
-
-
-
1
-
15
-
-
-
-
-
-
1
-
9
-
4
-
-
-
4
-
-
-
-
-
-
9
-
-
-
-
-
-
-
20
-
-
-
-
-
1
-
-
-
-
-
-
1
-
9
-
5
-
-
-
5
-
-
-
-
-
-
-
-
-
674316
Llacer
The gene cluster for agmatine ...
Enterococcus faecalis, Enterococcus faecalis ATCC 700802
J. Bacteriol.
189
1254-1265
2007
-
-
1
1
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1
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1
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4
-
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1
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-
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4
1
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-
1
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-
1
-
1
-
-
-
1
1
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-
-
1
-
-
-
-
1
-
-
-
-
4
1
-
-
-
-
-
-
-
-
-
-
-
-
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653166
Nakada
Identification of the putresci ...
Pseudomonas aeruginosa
Microbiology
149
707-714
2003
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2
1
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1
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655571
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Identification and characteriz ...
Arabidopsis thaliana
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258-261
2003
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2
1
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657259
Sakakibara
Agmatine deiminase from cucumb ...
Cucumis sativus
Protein Expr. Purif.
30
88-93
2003
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1
1
1
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1
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669081
Nakada
Molecular characterization and ...
Arabidopsis thaliana, Campylobacter jejuni, Caulobacter vibrioides, Chlorella virus, Deinococcus radiodurans, Helicobacter pylori, Lactococcus lactis, Pseudomonas aeruginosa, Streptomyces coelicolor, Xylella fastidiosa
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1
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1
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1
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-
1
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-
-
-
-
-
-
-
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-
-
-
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670510
Yanagisawa
Agmatine deiminase from maize ...
Zea mays
Phytochemistry
56
643-647
2001
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-
-
-
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1
1
-
-
3
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2
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1
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2
3
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1
1
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1
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1
2
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1
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1
1
1
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-
3
-
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1
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2
3
-
1
1
-
-
1
-
1
2
-
-
-
-
-
-
-
-
209405
Shoeb
-
Differential enzymatic measure ...
Rhodococcus sp., Rhodococcus sp. C-x
Biosci. Biotechnol. Biochem.
60
69-72
1996
-
2
-
-
-
-
-
-
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2
-
3
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4
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2
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2
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-
-
4
-
-
-
-
-
-
-
-
-
-
-
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-
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209404
Park
Purification of monomeric agma ...
Glycine max, Oryza sativa, Zea mays
Biochem. Biophys. Res. Commun.
174
32-36
1991
-
-
-
-
-
-
14
3
3
-
3
3
-
6
-
-
3
-
-
4
1
2
5
3
3
-
-
-
3
-
-
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-
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-
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-
-
-
-
-
-
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14
-
3
3
-
3
3
-
-
-
3
-
4
1
2
5
3
3
-
-
-
3
-
-
-
-
-
-
-
-
-
209403
Prasad
-
Purification and characterizat ...
Cucumis sativus, Lathyrus sativus
J. Biosci.
10
373-391
1986
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-
-
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1
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5
2
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2
-
-
2
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3
1
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7
1
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-
-
-
1
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-
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5
2
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-
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2
-
3
1
-
7
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
209402
Chaudhuri
-
Agmatine deiminase in rice see ...
Arachis hypogaea, Helianthus annuus, Hordeum vulgare, Nicotiana tabacum, Oryza sativa, Zea mays
Phytochemistry
24
2433-2435
1985
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13
1
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2
6
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6
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2
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7
1
1
6
2
1
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1
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-
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-
-
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13
-
1
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2
6
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2
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7
1
1
6
2
1
-
-
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1
-
-
-
-
-
-
-
-
-
209401
Legaz
-
Regulation of agmatine iminohy ...
Evernia prunastri, Glycine max, Hordeum vulgare, Lathyrus sativus, Soja hispida, Zea mays
Z. Pflanzenphysiol.
110
53-59
1983
1
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1
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6
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6
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1
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1
1
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6
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1
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6
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1
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6
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1
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1
1
-
6
-
-
-
-
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-
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209400
Simon
-
Enzymes of agmatine degradatio ...
Enterococcus faecalis
J. Bacteriol.
11
676-681
1982
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1
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1
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2
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1
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1
1
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2
-
1
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-
-
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-
-
-
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209398
Yanagisawa
Corn agmatine iminohydrolase. ...
Arachis hypogaea, Helianthus annuus, Zea mays
Plant Physiol.
67
697-700
1981
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-
-
-
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17
2
1
-
2
3
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4
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2
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6
1
1
3
1
1
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1
-
1
1
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-
-
-
-
-
-
-
-
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17
-
2
1
-
2
3
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2
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6
1
1
3
1
1
-
1
-
1
1
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-
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209399
Srivenugopal
Enzymic conversion of agmatine ...
Lathyrus sativus
J. Biol. Chem.
256
9532-9541
1981
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-
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1
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2
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1
1
1
6
1
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3
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1
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2
1
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1
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1
1
1
6
1
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3
-
-
-
-
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209395
Le Rudulier
-
Biogenese de la N-carbamylputr ...
Glycine max, Zea mays
Physiol. Veg.
18
609-616
1980
-
-
-
-
-
-
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2
-
2
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2
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1
1
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2
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-
-
2
-
-
-
-
-
1
1
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-
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-
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209397
Sindhu
-
Purification and properties of ...
Arachis hypogaea, Escherichia coli, Helianthus annuus, Zea mays
Phytochemistry
18
1937-1938
1979
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-
-
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13
1
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4
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4
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1
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6
1
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4
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1
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2
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-
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2
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-
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-
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13
2
1
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4
-
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1
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6
1
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4
-
-
-
1
-
2
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-
-
-
-
-
-
-
-
209396
Smith
-
Agmatine iminohydrolase in mai ...
Avena sativa, Brassica oleracea, Helianthus annuus, Hordeum vulgare, no activity in Malus sylvestris, no activity in Pisum sativum, no activity in Secale cereale, no activity in Triticum aestivum, Zea mays
Phytochemistry
8
2111-2117
1969
-
-
-
-
-
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4
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5
-
9
-
-
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-
5
-
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5
-
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2
-
1
1
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-
-
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-
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-
-
-
-
-
-
4
-
-
-
-
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5
-
-
-
-
-
5
-
-
5
-
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2
-
1
1
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