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Information on EC 3.5.3.6 - arginine deiminase and Organism(s) Homo sapiens and UniProt Accession Q9Y2J8

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EC Tree
     3 Hydrolases
         3.5 Acting on carbon-nitrogen bonds, other than peptide bonds
             3.5.3 In linear amidines
                3.5.3.6 arginine deiminase
IUBMB Comments
Also acts on canavanine.
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This record set is specific for:
Homo sapiens
UNIPROT: Q9Y2J8
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Word Map
The taxonomic range for the selected organisms is: Homo sapiens
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
Synonyms
arginine deiminase, arginine dihydrolase, ppadi, arginine-degrading enzyme, l-arginine deiminase, arca-1, lymphocyte blastogenesis inhibitory factor, paadi, streptococcal acid glycoprotein, l-arginine iminohydrolase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
arginine deiminase
-
-
arginine dihydrolase
-
-
-
-
arginine-degrading enzyme
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citrulline iminase
-
-
-
-
deiminase, arginine
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-
-
-
L-arginine deiminase
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-
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Streptococcal acid glycoprotein
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-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
amidine hydrolysis
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
L-arginine iminohydrolase
Also acts on canavanine.
CAS REGISTRY NUMBER
COMMENTARY hide
9027-98-9
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
N-alpha-benzoyl-L-arginine ethyl ester + H2O
N-alpha-benzoyl-L-citrulline methyl ester + NH3
show the reaction diagram
-
-
-
?
L-Arg + H2O
citrulline + NH3
show the reaction diagram
-
-
-
-
?
L-arginine + H2O
L-citrulline + NH3
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
L-arginine + H2O
L-citrulline + NH3
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
the concentration of calcium required for in vitro activity is at least 10 times higher than cellular calcium concentrations (i.e., 0.0001-0.010 mM). Calcium binding occurs in an ordered fashion. A calcium switch (calcium binding sites 3, 4, and 5) controls the overall calcium dependence of the enzyme
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
N-[(1S)-1-(2-tert-butyl-2H-tetrazol-5-yl)-4-[(2-fluoroethanimidoyl)amino]butyl]benzamide
preferentially inhibits protein-arginine deiminase 2 by 3fold with the highest selectivity being observed for PAD2 over PAD4. Highly selective protein-arginine deiminase 2 inhibitor relative to the other protein-arginine deiminases
N-[(1S)-1-(2-tert-butyl-2H-tetrazol-5-yl)-4-[(2-fluoroethanimidoyl)amino]butyl][1,1'-biphenyl]-4-carboxamide
preferentially inhibits protein-arginine deiminase 2 by 25fold with the highest selectivity being observed for PAD2 over PAD4. Highly selective protein-arginine deiminase 2 inhibitor relative to the other protein-arginine deiminases
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.1 - 30
N-alpha-benzoyl-L-arginine ethyl ester
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.03 - 2.65
N-alpha-benzoyl-L-arginine ethyl ester
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.005 - 18
N-alpha-benzoyl-L-arginine ethyl ester
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50
-
purified rcombinant enzyme
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37
-
assay at
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
SwissProt
Manually annotated by BRENDA team
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
lymphatic
Manually annotated by BRENDA team
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retinoblastoma cell line
Manually annotated by BRENDA team
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retinoblastoma cell line
Manually annotated by BRENDA team
additional information
PAD2 is expressed in most tissues and cell types
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
calcium-dependent histone-modifying enzymes whose activity is dysregulated in inflammatory diseases and cancer
metabolism
protein arginine deiminases are calcium-dependent histone-modifying enzymes whose activity is dysregulated in inflammatory diseases and cancer. PAD2 functions as an estrogen receptor (ER) coactivator in breast cancer cells via the citrullination of histone tail arginine residues at ER binding sites
malfunction
physiological function
-
ADI induces excessive synthesis of reactive oxygen species, and activates caspase 8-, but not caspase 9-, dependent apoptosis in endothelial cells
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
PADI2_HUMAN
665
0
75564
Swiss-Prot
-
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
sitting-drop vapor-diffusion technique at 23°C, apoPAD2 crystals with increasing concentrations of calcium (0-10 mM), 16 structures are solved at eight different calcium concentrations to 1.66-1.97 A
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D123N
2.5fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate
D125A
2.75fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate
D166A
85fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate
D169A
2fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate
D177A
15fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate
D370A
220fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate
D374A
145fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate
D389A
20fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate
E352A
1250fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate
E412A
3300fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate
F221A/F222A
1.1fold increase in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate
Q350A
2350fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate
R347A
fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate
W373A
50fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli strain BL21(DE3) in inclusion bodies
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
drug development
the enzyme is a particularly attractive therapeutic target for breast cancer because it is recruited by the estrogen receptor to endoplasmic reticulum target gene promoters where it citrullinates histone H3 at R26, leading to ER-target gene activation
drug development
-
ADI is a potential anti-tumor drug for the treatment of argine-auxotrophic tumors, e.g. hepatocellular carcinoma and melanoma
medicine
pharmacology
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ADI is a potential anti-angiogenic agent and is effective in the treatment of leukemia, ADI in clinical studies, overview
additional information
-
human serum albumin is an effective fusion partner for chemically modifying the enzyme resulting in a longer half-life in serum of two weeks, human serum albumin is more suitable than PEG, overview
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Ni, Y.; Schwaneberg, U.; Sun, Z.
Arginine deiminase, a potential anti-tumor drug
Cancer Lett.
261
1-11
2008
Giardia intestinalis, Halobacterium salinarum, Homo sapiens, Lactococcus lactis ssp. lactis, Mycoplasmopsis arginini, Mycoplasma hominis, Pseudomonas aeruginosa, Pseudomonas putida, Streptococcus sanguinis, Pseudomonas plecoglossicida (A7LKB0), Pseudomonas plecoglossicida CGMCC 2039 (A7LKB0)
Manually annotated by BRENDA team
Izzo, F.; Montella, M.; Orlando, A.P.; Nasti, G.; Beneduce, G.; Castello, G.; Cremona, F.; Ensor, C.M.; Holtzberg, F.W.; Bomalaski, J.S.; Clark, M.A.; Curley, S.A.; Orlando, R.; Scordino, F.; Korba, B.E.
Pegylated arginine deiminase lowers hepatitis C viral titers and inhibits nitric oxide synthesis
J. Gastroenterol. Hepatol.
22
86-91
2007
Homo sapiens
Manually annotated by BRENDA team
Kim, J.H.; Kim, J.H.; Yu, Y.S.; Kim, D.H.; Min, B.H.; Kim, K.W.
Anti-tumor activity of arginine deiminase via arginine deprivation in retinoblastoma
Oncol. Rep.
18
1373-1377
2007
Homo sapiens
Manually annotated by BRENDA team
Bowles, T.L.; Kim, R.; Galante, J.; Parsons, C.M.; Virudachalam, S.; Kung, H.J.; Bold, R.J.
Pancreatic cancer cell lines deficient in argininosuccinate synthetase are sensitive to arginine deprivation by arginine deiminase
Int. J. Cancer
123
1950-1955
2008
Homo sapiens
Manually annotated by BRENDA team
Yu, H.H.; Wu, F.L.; Lin, S.E.; Shen, L.J.
Recombinant arginine deiminase reduces inducible nitric oxide synthase iNOS-mediated neurotoxicity in a coculture of neurons and microglia
J. Neurosci. Res.
86
2963-2972
2008
Homo sapiens
Manually annotated by BRENDA team
Zhuo, W.; Song, X.; Zhou, H.; Luo, Y.
Arginine deiminase modulates endothelial tip cells via excessive synthesis of reactive oxygen species
Biochem. Soc. Trans.
39
1376-1381
2011
Homo sapiens
Manually annotated by BRENDA team
Kelly, M.P.; Jungbluth, A.A.; Wu, B.W.; Bomalaski, J.; Old, L.J.; Ritter, G.
Arginine deiminase PEG20 inhibits growth of small cell lung cancers lacking expression of argininosuccinate synthetase
Br. J. Cancer
106
324-332
2012
Homo sapiens
Manually annotated by BRENDA team
Slade, D.J.; Fang, P.; Dreyton, C.J.; Zhang, Y.; Fuhrmann, J.; Rempel, D.; Bax, B.D.; Coonrod, S.A.; Lewis, H.D.; Guo, M.; Gross, M.L.; Thompson, P.R.
Protein arginine deiminase 2 binds calcium in an ordered fashion implications for inhibitor design
ACS Chem. Biol.
10
1043-1053
2015
Homo sapiens (Q9Y2J8)
Manually annotated by BRENDA team
Subramanian, V.; Knight, J.S.; Parelkar, S.; Anguish, L.; Coonrod, S.A.; Kaplan, M.J.; Thompson, P.R.
Design, synthesis, and biological evaluation of tetrazole analogs of Cl-amidine as protein arginine deiminase inhibitors
J. Med. Chem.
58
1337-1344
2015
Homo sapiens (Q9Y2J8)
Manually annotated by BRENDA team