2ABR

Structure of D280A arginine deiminase with L-arginine forming a S-alkylthiouronium reaction intermediate

Summary for 2ABR

• Entry DOI: 10.2210/pdb2abr/pdb
• Related: 1RXX 2A9G 2AAF 2ACI
• Descriptor: Arginine deiminase (1 entity in total)
• Functional Keywords: arginine degradation pathway, l-arginine deiminase, catalytic mechanism, hydrolase
• Biological source: Pseudomonas aeruginosa
• Cellular location: Cytoplasm : P13981
• Total number of polymer chains: 4
• Total formula weight: 186420.24

Authors

Galkin, A.,Lu, X.,Dunaway-Mariano, D.,Herzberg, O. (deposition date: 2005-07-15, release date: 2005-08-09, Last modification date: 2023-08-23)

Primary citation

Galkin, A.,Lu, X.,Dunaway-Mariano, D.,Herzberg, O.
Crystal Structures Representing the Michaelis Complex and the Thiouronium Reaction Intermediate of Pseudomonas aeruginosa Arginine Deiminase.
J.Biol.Chem., 280:34080-34087, 2005

PubMed Abstract: L-arginine deiminase (ADI) catalyzes the irreversible hydrolysis of L-arginine to citrulline and ammonia. In a previous report of the structure of apoADI from Pseudomonas aeruginosa, the four residues that form the catalytic motif were identified as Cys406, His278, Asp280, and Asp166. The function of Cys406 in nucleophilic catalysis has been demonstrated by transient kinetic studies. In this study, the structure of the C406A mutant in complex with L-arginine is reported to provide a snapshot of the enzyme.substrate complex. Through the comparison of the structures of apoenzyme and substrate-bound enzyme, a substrate-induced conformational transition, which might play an important role in activity regulation, was discovered. Furthermore, the position of the guanidinium group of the bound substrate relative to the side chains of His278, Asp280, and Asp166 indicated that these residues mediate multiple proton transfers. His278 and Asp280, which are positioned to activate the water nucleophile in the hydrolysis of the S-alkylthiouronium intermediate, were replaced with alanine to stabilize the intermediate for structure determination. The structures determined for the H278A and D280A mutants co-crystallized with L-arginine provide a snapshot of the S-alkylthiouronium adduct formed by attack of Cys406 on the guanidinium carbon of L-arginine followed by the elimination of ammonia. Asp280 and Asp166 engage in ionic interactions with the guanidinium group in the C406A ADI. L-arginine structure and might orient the reaction center and participate in proton transfer. Structure determination of D166A revealed the apoD166A ADI. The collection of structures is interpreted in the context of recent biochemical data to propose a model for ADI substrate recognition and catalysis.

PubMed: 16091358
DOI: 10.1074/jbc.M505471200

Experimental method

X-RAY DIFFRACTION (2.9 Å)