Structure and Function of Allophanate Hydrolase

Chen, Fan; Li, Zi; Yin, Huiyong; Xiang, Song

doi:10.1074/jbc.m113.453837

Cited by 21 publications

(30 citation statements)

References 47 publications

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“…The role of the smaller C-terminal domain is less clear, however. Fan et al (37) suggested that the C-terminal domain of AH Kl is catalytic, decarboxylating N-carboxycarbamate to form carbamate and carbon dioxide. On the basis of in silico substrate docking and mutagenesis studies, it was proposed that a histidine residue in the C-terminal domain (His492; Fig.…”

Section: Resultsmentioning

confidence: 99%

“…In a report from Fan et al, the authors proposed that the C-terminal domain of AH Kl is involved in the hydrolysis of N-carboxycarbamate, the unstable product of AH-mediated allophanate deamination ( Fig. 1) (37). Moreover, in silico substrate docking suggested that a C-terminal histidine residue (His492) plays an important catalytic role (37).…”

mentioning

confidence: 99%

“…Structures for AtzB, AtzE, and AtzF have yet to be reported, although structures for the ureolytic allophanate hydrolases (AHs) from Kluyveromyces lactis (AH Kl ) and Granulibacter bethesdensis (AH Gb ) were reported in 2013 (37,38). Unlike the atrazine-degrading AHs, the ureolytic enzymes are found as multidomain enzymes along with a biotin-and ATPdependent urea carboxylase, which is required to generate allophanate from urea (37,(39)(40)(41)(42). The AH components of these complexes have considerable sequence conservation with each other and the triazine-related AHs (Fig.…”

mentioning

confidence: 99%

“…1) (37). Moreover, in silico substrate docking suggested that a C-terminal histidine residue (His492) plays an important catalytic role (37).…”

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confidence: 99%

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X-Ray Structure of the Amidase Domain of AtzF, the Allophanate Hydrolase from the Cyanuric Acid-Mineralizing Multienzyme Complex

Balotra

Newman

Cowieson

et al. 2015

Appl Environ Microbiol

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dThe activity of the allophanate hydrolase from Pseudomonas sp. strain ADP, AtzF, provides the final hydrolytic step for the mineralization of s-triazines, such as atrazine and cyanuric acid. Indeed, the action of AtzF provides metabolic access to two of the three nitrogens in each triazine ring. The X-ray structure of the N-terminal amidase domain of AtzF reveals that it is highly homologous to allophanate hydrolases involved in a different catabolic process in other organisms (i.e., the mineralization of urea). The smaller C-terminal domain does not appear to have a physiologically relevant catalytic function, as reported for the allophanate hydrolase of Kluyveromyces lactis, when purified enzyme was tested in vitro. However, the C-terminal domain does have a function in coordinating the quaternary structure of AtzF. Interestingly, we also show that AtzF forms a large, ca. 660-kDa, multienzyme complex with AtzD and AtzE that is capable of mineralizing cyanuric acid. The function of this complex may be to channel substrates from one active site to the next, effectively protecting unstable metabolites, such as allophanate, from solvent-mediated decarboxylation to a dead-end metabolic product.A trazine (1-chloro-3-ethylamino-5-isopropylamino-2,4,6-triazine; Fig. 1) is one of the most heavily applied herbicides in the world and is registered for use in North and South America, Australia, Africa, Asia, and the Middle East. Atrazine is environmentally persistent (half-life, 4 to 57 weeks, depending on the location) and mobile, leading to the detection of atrazine in surface water, groundwater, and aquifers (1-3). Atrazine has been detected in the environment at concentrations of up to 4.6 M in several countries (2, 3). It has been suggested that atrazine may be a carcinogen and an endocrine disrupter at such concentrations (4-6).Since atrazine was introduced in the 1950s, bacteria have evolved highly efficient catabolic pathways that allow the use of atrazine as a sole nitrogen and carbon source (7-10). These pathways have provided valuable insights into the evolutionary processes that drive the establishment of new enzyme function and new catabolic pathways (11-15). In addition, these pathways and cognate enzymes provide a potential biotechnological solution to atrazine contamination (i.e., bioremediation) (16-19).The most intensively studied atrazine catabolism pathway was discovered in Pseudomonas sp. strain ADP in the mid-1990s and is comprised of six hydrolases: atrazine chlorohydrolase (AtzA; EC 3.8.1.8) (20,21), N-ethylaminohydrolase (AtzB; EC 3.5.99.3) (22,23), N-isopropylammelide isopropylaminohydrolase (AtzC; EC 3.5.99.4) (24, 25), cyanuric acid amidohydrolase (AtzD; EC 3.5.2.15) (15,26,27), biuret amidohydrolase (AtzE; EC 3.5.1.84) (28), and allophanate hydrolase (AtzF; EC 3.5.1.54) (29-31). These hydrolases sequentially dechlorinate (AtzA) and remove the two N-alkyl side groups (AtzB and AtzC) to produce cyanuric acid, which is then further hydrolyzed to biuret, allophanate, and ammonia via AtzD, AtzE, a...

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Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

“…1) (37). Moreover, in silico substrate docking suggested that a C-terminal histidine residue (His492) plays an important catalytic role (37).…”

mentioning

confidence: 99%

See 2 more Smart Citations

X-Ray Structure of the Amidase Domain of AtzF, the Allophanate Hydrolase from the Cyanuric Acid-Mineralizing Multienzyme Complex

Balotra

Newman

Cowieson

et al. 2015

Appl Environ Microbiol

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“…Protein thermodynamic stability, a classic and essential characteristic of the prevalent biopolymer, is frequently investigated in fundamental research, [1][2][3][4][5][6][7][8][9][10][11] drug discovery, [12][13][14][15][16] and protein engineering. [17][18][19][20] Evaluation on protein unfolding/folding energy is one of primary methods to understand protein conformational stability, 21 protein mutation effects, 22 and property changes of small compounds binding to protein.…”

Section: Introductionmentioning

confidence: 99%

Using a second‐order differential model to fit data without baselines in protein isothermal chemical denaturation

Tang

Lew

2016

Protein Science

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In vitro protein stability studies are commonly conducted via thermal or chemical denaturation/renaturation of protein. Conventional data analyses on the protein unfolding/(re)folding require well-defined pre-and post-transition baselines to evaluate Gibbs free-energy change associated with the protein unfolding/(re)folding. This evaluation becomes problematic when there is insufficient data for determining the pre-or post-transition baselines. In this study, fitting on such partial data obtained in protein chemical denaturation is established by introducing second-order differential (SOD) analysis to overcome the limitations that the conventional fitting method has. By reducing numbers of the baseline-related fitting parameters, the SOD analysis can successfully fit incomplete chemical denaturation data sets with high agreement to the conventional evaluation on the equivalent completed data, where the conventional fitting fails in analyzing them. This SOD fitting for the abbreviated isothermal chemical denaturation further fulfills data analysis methods on the insufficient data sets conducted in the two prevalent protein stability studies.

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The urea carboxylase and allophanate hydrolase activities of urea amidolyase are functionally independent

2016

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Urea amidolyase (UAL) is a multifunctional biotin-dependent enzyme that contributes to both bacterial and fungal pathogenicity by catalyzing the ATP-dependent cleavage of urea into ammonia and CO 2 . UAL is comprised of two enzymatic components: urea carboxylase (UC) and allophanate hydrolase (AH). These enzyme activities are encoded on separate but proximally related genes in prokaryotes while, in most fungi, they are encoded by a single gene that produces a fusion enzyme on a single polypeptide chain. It is unclear whether the UC and AH activities are connected through substrate channeling or other forms of direct communication. Here, we use multiple biochemical approaches to demonstrate that there is no substrate channeling or interdomain/intersubunit communication between UC and AH. Neither stable nor transient interactions can be detected between prokaryotic UC and AH and the catalytic efficiencies of UC and AH are independent of one another. Furthermore, an artificial fusion of UC and AH does not significantly alter the AH enzyme activity or catalytic efficiency. These results support the surprising functional independence of AH from UC in both the prokaryotic and fungal UAL enzymes and serve as an important reminder that the evolution of multifunctional enzymes through gene fusion events does not always correlate with enhanced catalytic function.

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Structure and Function of Allophanate Hydrolase

Cited by 21 publications

References 47 publications

X-Ray Structure of the Amidase Domain of AtzF, the Allophanate Hydrolase from the Cyanuric Acid-Mineralizing Multienzyme Complex

X-Ray Structure of the Amidase Domain of AtzF, the Allophanate Hydrolase from the Cyanuric Acid-Mineralizing Multienzyme Complex

Using a second‐order differential model to fit data without baselines in protein isothermal chemical denaturation

The urea carboxylase and allophanate hydrolase activities of urea amidolyase are functionally independent

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