1S9R

CRYSTAL STRUCTURE OF ARGININE DEIMINASE COVALENTLY LINKED WITH A REACTION INTERMEDIATE

Summary for 1S9R

• Entry DOI: 10.2210/pdb1s9r/pdb
• Related: 1LXY
• Descriptor: Arginine deiminase, ARGININE, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ... (5 entities in total)
• Functional Keywords: deiminase, hydrolase, 5-fold pseudo-symmetric domain, 5-helix bundle domain, raction intermediate
• Biological source: Mycoplasma arginini
• Cellular location: Cytoplasm (Potential): P23793
• Total number of polymer chains: 2
• Total formula weight: 93721.06

Authors

Das, K.,Buttler, G.H.,Kwiatkowski, V.,Clark Jr., A.D.,Yadav, P.,Arnold, E. (deposition date: 2004-02-05, release date: 2004-04-13, Last modification date: 2024-10-30)

Primary citation

Das, K.,Buttler, G.H.,Kwiatkowski, V.,Clark Jr., A.D.,Yadav, P.,Arnold, E.
Crystal Structures of Arginine Deiminase with Covalent Reaction Intermediates: Implications for Catalytic Mechanism
Structure, 12:657-667, 2004

PubMed Abstract: Arginine deiminase (ADI), an enzyme that hydrolyzes arginine to generate energy in many parasitic microorganisms, has potent anticancer activities and can halt growth of solid tumors. We determined the crystal structure of ADI from Mycoplasma arginini in two different forms (1.6 and 2.0 A resolution) using multiple isomorphous replacement. ADI shares common structural features with the arginine-catabolizing enzymes Arg:Gly amidinotransferase and dimethylarginine dimethyl-aminohydrolase; ADI contains an additional domain of five helices. The scissile C-N bonds of the substrates and the catalytic triads (Cys398-His269-Glu213 of ADI) for the three enzymes superimpose on each other. The ADI structure from form I crystals corresponds to a tetrahedral intermediate with four heteroatoms (1S, 2N, 1O) covalently bonded to the reaction-center carbon. The structure from form II crystals represents an amidino-enzyme complex; the reaction-center carbon is covalently bonded to Cys398 sulfur and two nitrogens, and the reacting water molecule is only 2.54 A away.

PubMed: 15062088
DOI: 10.1016/j.str.2004.02.017

Experimental method

X-RAY DIFFRACTION (1.6 Å)