Literature summary for 3.5.3.15 extracted from

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 (2015), ACS Chem. Biol., 10, 1043-1053 .

Application

Application	Comment	Organism
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	Homo sapiens

Cloned(Commentary)

Cloned (Comment)	Organism
-	Homo sapiens

Crystallization (Commentary)

Crystallization (Comment)	Organism
27 structures and calcium-titrations by X-ray crystallography to determine order of binding and affinity for the six calcium ions that bind and activate the enzyme	Homo sapiens
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	Homo sapiens

Protein Variants

Protein Variants	Comment	Organism
C647A	loss of activity	Homo sapiens
D123N	2.5fold decrease in activity	Homo sapiens
D123N	2.5fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate	Homo sapiens
D125A	2.75fold decrease in activity	Homo sapiens
D125A	2.75fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate	Homo sapiens
D166A	15fold decrease in activity	Homo sapiens
D166A	85fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate	Homo sapiens
D169A	2fold decrease in activity	Homo sapiens
D169A	2fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate	Homo sapiens
D177A	15fold decrease in activity	Homo sapiens
D177A	15fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate	Homo sapiens
D370A	145fold decrease in activity	Homo sapiens
D370A	220fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate	Homo sapiens
D374A	145fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate	Homo sapiens
D374A	85fold decrease in activity	Homo sapiens
D389A	20fold decrease in activity	Homo sapiens
D389A	20fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate	Homo sapiens
E352A	1250fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate	Homo sapiens
E352A	220fold decrease in activity	Homo sapiens
E354A	2000fold decrease in activity	Homo sapiens
E412A	200fold decrease in activity	Homo sapiens
E412A	3300fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate	Homo sapiens
F221A/F222A	1.1fold increase in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate	Homo sapiens
F221A/F222A	slight increase in activity, mutations do not significantly alter the calcium dependence of the enzyme	Homo sapiens
Q350A	2350fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate	Homo sapiens
Q350A	3000fold decrease in activity	Homo sapiens
R347A	50fold decrease in activity	Homo sapiens
R347A	fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate	Homo sapiens
R373A	2000fold decrease in activity	Homo sapiens
W348A	loss of activity	Homo sapiens
W373A	50fold decrease in kcat/Km compared to wild-type value with N-alpha-benzoyl-L-arginine ethyl ester as substrate	Homo sapiens

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism
0.1	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant F221A/F222A, pH 7.6, 37°C	Homo sapiens
0.1	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme F221A/F222A	Homo sapiens
0.12	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D123N, pH 7.6, 37°C	Homo sapiens
0.12	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D123N	Homo sapiens
0.14	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D125A, pH 7.6, 37°C	Homo sapiens
0.14	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D125A	Homo sapiens
0.16	-	N-alpha-benzoyl-L-arginine ethyl ester	wild-type, pH 7.6, 37°C	Homo sapiens
0.16	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, wild-type enzyme	Homo sapiens
0.25	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D169A, pH 7.6, 37°C	Homo sapiens
0.25	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D169A	Homo sapiens
0.33	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D166A, pH 7.6, 37°C	Homo sapiens
0.33	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D166A	Homo sapiens
0.6	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D389A, pH 7.6, 37°C	Homo sapiens
0.6	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D389A	Homo sapiens
2.4	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D177A, pH 7.6, 37°C	Homo sapiens
2.4	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D177A	Homo sapiens
3.4	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant E352A, pH 7.6, 37°C	Homo sapiens
3.4	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme E352A	Homo sapiens
4.4	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant R347A, pH 7.6, 37°C	Homo sapiens
4.4	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme R347	Homo sapiens
5	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D370A, pH 7.6, 37°C	Homo sapiens
5	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D370A	Homo sapiens
6.3	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant Q350A, pH 7.6, 37°C	Homo sapiens
6.3	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme Q350A	Homo sapiens
8	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D374A, pH 7.6, 37°C	Homo sapiens
8	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D374A	Homo sapiens
13	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant E412A, pH 7.6, 37°C	Homo sapiens
13	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme E412A	Homo sapiens
30	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant R373A, pH 7.6, 37°C	Homo sapiens
30	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme W373A	Homo sapiens

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Ca2+	absolutely required, K0.5 value 0.18 mM. The enzyme binds calcium in a stepwise fashion	Homo sapiens
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	Homo sapiens

Organism

Organism	UniProt	Comment	Textmining
Homo sapiens	Q9Y2J8	-	-

Purification (Commentary)

Purification (Comment)	Organism
-	Homo sapiens

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
N-alpha-benzoyl-L-arginine ethyl ester + H2O	-	Homo sapiens	N-alpha-benzoyl-L-citrulline ethyl ester + NH3	-	?
N-alpha-benzoyl-L-arginine ethyl ester + H2O	-	Homo sapiens	N-alpha-benzoyl-L-citrulline methyl ester + NH3	-	?

Synonyms

Synonyms	Comment	Organism
PAD2	-	Homo sapiens
Padi2	-	Homo sapiens

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism
0.03	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant Q350A, pH 7.6, 37°C	Homo sapiens
0.03	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme Q350A	Homo sapiens
0.1	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant E412A, pH 7.6, 37°C	Homo sapiens
0.1	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme E412A	Homo sapiens
0.2	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant R373A, pH 7.6, 37°C	Homo sapiens
0.2	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme W373A	Homo sapiens
0.25	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant E352A, pH 7.6, 37°C	Homo sapiens
0.25	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme E352A	Homo sapiens
0.35	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D166A, pH 7.6, 37°C	Homo sapiens
0.35	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D166A	Homo sapiens
0.51	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D389A, pH 7.6, 37°C	Homo sapiens
0.51	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D389A	Homo sapiens
0.6	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D370A, pH 7.6, 37°C	Homo sapiens
0.6	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D370A	Homo sapiens
0.8	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D123N, pH 7.6, 37°C	Homo sapiens
0.8	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D125A, pH 7.6, 37°C	Homo sapiens
0.8	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D123N	Homo sapiens
0.8	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D125A	Homo sapiens
1.53	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant R347A, pH 7.6, 37°C	Homo sapiens
1.53	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme R347	Homo sapiens
1.55	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D374A, pH 7.6, 37°C	Homo sapiens
1.55	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D374A	Homo sapiens
1.8	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D169A, pH 7.6, 37°C	Homo sapiens
1.8	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant F221A/F222A, pH 7.6, 37°C	Homo sapiens
1.8	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D169A	Homo sapiens
1.8	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme F221A/F222A	Homo sapiens
2.65	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, wild-type enzyme	Homo sapiens
2.65	-	N-alpha-benzoyl-L-arginine ethyl ester	wild-type, pH 7.6, 37°C	Homo sapiens
2.65	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D177A, pH 7.6, 37°C	Homo sapiens
2.65	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D177A	Homo sapiens

General Information

General Information	Comment	Organism
malfunction	calcium-dependent histone-modifying enzymes whose activity is dysregulated in inflammatory diseases and cancer	Homo sapiens
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	Homo sapiens

kcat/KM [mM/s]

kcat/KM Value [1/mMs^-1]	kcat/KM Value Maximum [1/mMs^-1]	Substrate	Comment	Organism
0.005	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme Q350A	Homo sapiens
0.007	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant E412A, pH 7.6, 37°C	Homo sapiens
0.007	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant R373A, pH 7.6, 37°C	Homo sapiens
0.007	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme E412A	Homo sapiens
0.007	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme W373A	Homo sapiens
0.05	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant Q350A, pH 7.6, 37°C	Homo sapiens
0.075	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant E352A, pH 7.6, 37°C	Homo sapiens
0.075	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme E352A	Homo sapiens
0.115	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D370A, pH 7.6, 37°C	Homo sapiens
0.115	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D370A	Homo sapiens
0.195	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D374A, pH 7.6, 37°C	Homo sapiens
0.195	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D374A	Homo sapiens
0.35	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant R347A, pH 7.6, 37°C	Homo sapiens
0.35	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme R347	Homo sapiens
0.845	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D389A, pH 7.6, 37°C	Homo sapiens
0.845	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D389A	Homo sapiens
1.065	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D166A, pH 7.6, 37°C	Homo sapiens
1.065	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D166A	Homo sapiens
1.1	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D177A, pH 7.6, 37°C	Homo sapiens
1.1	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D177A	Homo sapiens
6	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D125A, pH 7.6, 37°C	Homo sapiens
6	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D125A	Homo sapiens
6.8	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D123N, pH 7.6, 37°C	Homo sapiens
6.8	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D123N	Homo sapiens
7.9	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant D169A, pH 7.6, 37°C	Homo sapiens
7.9	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme D169A	Homo sapiens
16.5	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, wild-type enzyme	Homo sapiens
16.5	-	N-alpha-benzoyl-L-arginine ethyl ester	wild-type, pH 7.6, 37°C	Homo sapiens
18	-	N-alpha-benzoyl-L-arginine ethyl ester	mutant F221A/F222A, pH 7.6, 37°C	Homo sapiens
18	-	N-alpha-benzoyl-L-arginine ethyl ester	pH 7.6, 37°C, mutant enzyme F221A/F222A	Homo sapiens