The Structure of Allophanate Hydrolase from Granulibacter bethesdensis Provides Insights into Substrate Specificity in the Amidase Signature Family

Journal Article · Wed Jan 02 00:00:00 EST 2013 · Biochemistry

DOI:https://doi.org/10.1021/bi301242m· OSTI ID:1062429

Lin, Yi ^[1]; Maurice, Martin ^[1]

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1. Marquette Univ., Milwaukee, WI (United States)

Allophanate hydrolase (AH) catalyzes the hydrolysis of allophanate, an intermediate in atrazine degradation and urea catabolism pathways, to NH₃ and CO₂. AH belongs to the amidase signature family, which is characterized by a conserved block of 130 amino acids rich in Gly and Ser and a Ser-cis-Ser-Lys catalytic triad. In this study, the first structures of AH fromGranulibacter bethesdensis were determined, with and without the substrate analogue malonate, to 2.2 and 2.8 Å, respectively. The structures confirm the identity of the catalytic triad residues and reveal an altered dimerization interface that is not conserved in the amidase signature family. The structures also provide insights into previously unrecognized substrate specificity determinants in AH. Two residues, Tyr₂₉₉ and Arg₃₀₇, are within hydrogen bonding distance of a carboxylate moiety of malonate. Both Tyr₂₉₉ and Arg₃₀₇ were mutated, and the resulting modified enzymes revealed >3 order of magnitude reductions in both catalytic efficiency and substrate stringency. It is proposed that Tyr₂₉₉ and Arg₃₀₇ serve to anchor and orient the substrate for attack by the catalytic nucleophile, Ser₁₇₂. The structure further suggests the presence of a unique C-terminal domain in AH. While this domain is conserved, it does not contribute to catalysis or to the structural integrity of the core domain, suggesting that it may play a role in mediating transient and specific interactions with the urea carboxylase component of urea amidolyase. Analysis of the AH active site architecture offers new insights into common determinants of catalysis and specificity among divergent members of the amidase signature family.

• Research Organization: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
• Sponsoring Organization: NIGMS
• DOE Contract Number: AC02-06CH11357
• OSTI ID: 1062429
• Journal Information: Biochemistry, Vol. 52, Issue (4) ; 01, 2013; ISSN 0006-2960
• Publisher: American Chemical Society (ACS)
• Country of Publication: United States
• Language: ENGLISH