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PDBsum entry 2a9g
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References listed in PDB file
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Key reference
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Title
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Crystal structures representing the michaelis complex and the thiouronium reaction intermediate of pseudomonas aeruginosa arginine deiminase.
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Authors
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A.Galkin,
X.Lu,
D.Dunaway-Mariano,
O.Herzberg.
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Ref.
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J Biol Chem, 2005,
280,
34080-34087.
[DOI no: ]
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PubMed id
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Abstract
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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.
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Figure 1.
FIGURE 1. The reactions catalyzed by ADI superfamily
members. A, ADI; B, DDAH; C, PAD; D, arginine:glycine
amidinotransferase (AGAT); E, arginine:inosamine-phosphate
amidinotransferase (IPAT).
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Figure 5.
FIGURE 5. A feasible mechanism of PaADI catalysis of
L-arginine hydrolysis to citrulline and ammonia.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2005,
280,
34080-34087)
copyright 2005.
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