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3.5.3.15: protein-arginine deiminase

This is an abbreviated version!
For detailed information about protein-arginine deiminase, go to the full flat file.

Word Map on EC 3.5.3.15

Reaction

protein L-arginine
+
H2O
=
protein L-citrulline
 +
NH3

Synonyms

deiminase, protein (arginine), HL-60 PAD, hPADI2, hPADI4, hPADVI, PAD, PAD 1, PAD 2, PAD 3, PAD 4, PAD II, PAD IV, PAD type 2, PAD-4, PAD-H19, PAD-R11, PAD-R4, PAD1, PAD2, PAD3, PAD4, PAD6, PADI1, Padi2, PADI3, PADI4, peptidyl arginine deiminas 4, peptidyl arginine deiminase, peptidyl arginine deiminase 2, peptidyl-arginine deiminase, peptidylarginine deiminase, peptidylarginine deiminase 1, peptidylarginine deiminase 2, peptidylarginine deiminase 3, peptidylarginine deiminase 4, peptidylarginine deiminase 6, peptidylarginine deiminase isoform VI, peptidylarginine deiminase IV, peptidylarginine deiminase type 4, Peptidylarginine deiminase type alpha, peptidylarginine deiminase type I, peptidylarginine deiminase type II, peptidylarginine deiminase type III, peptidylarginine deiminase type VI, peptidylarginine deiminase-4, PPAD, protein arginine deiminase, protein arginine deiminase 2, protein arginine deiminase 3, protein arginine deiminase 4

ECTree

     3 Hydrolases
         3.5 Acting on carbon-nitrogen bonds, other than peptide bonds
             3.5.3 In linear amidines
                3.5.3.15 protein-arginine deiminase

Crystallization

Crystallization on EC 3.5.3.15 - protein-arginine deiminase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
Ca2+-free enzyme
crystal structures of a Ca2+-bound PAD4 mutant C645A in complex with three histone N-terminal peptides, each consisting of 10 amino acid residues that include one target arginine residue for the enzyme (H3/Arg-8, H3/Arg-17, and H4/Arg-3). hanging-drop vapor-diffusion method
hanging drop vapor diffusion method, using 0.2 M CaCl2, 20% (w/v) polyethylene glycol 3350
hanging drop vapor diffusion method, using 20 mM imidazole buffer pH 7.0, 0.2 M Li2SO4, 15% (w/v) polyethylene glycol monomethylether 5000
purified recombinant GST-tagged PAD4 mutant C645A in complex with Ca2+ and histone-derived N-terminal peptide substrates, hanging-drop vapor-diffusion method, soaking of Ca2+-free crystals in crystallization buffer containing 5 mM CaCl2 and each histone N-terminal peptide for 8 h at 20°C, X-ray diffraction structure determination and anaylsis at 2.0-2.225 A resolution, molecular replacement
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
structure of isoform Pad1, in presence of Ca2+, to 3.2 A resolution. The asymmetric unit containes two PAD1 molecules, with an elongated N-terminal loop that appears to prevent the formation of a homodimer. The N-terminal loop occupies the substrate binding site of the adjacent PAD1 molecules in the crystal
in complex with inhibitor Cl-amidine, to 1.6 A resolution
structures of wild-type and mutant C351A, to 1.46 and 1.48 A resolution. Catalysis is mediated by residues Asp130, His236, Asp238, Asn297 and Cys351. Arg152 and Arg154 may determine the substrate specificity