Mechanistic Inferences from the Crystal Structure of Fumarylacetoacetate Hydrolase with a Bound Phosphorus-based Inhibitor

Bateman, Raynard L.; Bhanumoorthy, P.; Witte, John F.; McClard, Ronald W.; Grompe, Markus; Timm, David E.

doi:10.1074/jbc.m007621200

Cited by 54 publications

(66 citation statements)

References 35 publications

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“…The catalytic domain of these proteins resembles that of the eukaryal fumarylacetoacetate hydrolase; an enzyme that catalyzes the Mg 2ϩ -or Ca 2ϩ -dependent hydrolytic cleavage of fumarylacetoacetate to yield fumarate and acetoacetate as the final step of phenylalanine and tyrosine degradation (53). In humans, several mutations in the fumarylacetoacetate hydrolase gene will lead to hereditary tyrosinemia type I, which is mainly characterized by liver defects (54).…”

Section: Resultsmentioning

confidence: 99%

Identification of the Missing Links in Prokaryotic Pentose Oxidation Pathways

Brouns

Walther

Snijders

et al. 2006

Journal of Biological Chemistry

104

188

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The pentose metabolism of Archaea is largely unknown. Here, we have employed an integrated genomics approach including DNA microarray and proteomics analyses to elucidate the catabolic pathway for D-arabinose in Sulfolobus solfataricus. During growth on this sugar, a small set of genes appeared to be differentially expressed compared with growth on D-glucose. These genes were heterologously overexpressed in Escherichia coli, and the recombinant proteins were purified and biochemically studied. This showed that D-arabinose is oxidized to 2-oxoglutarate by the consecutive action of a number of previously uncharacterized enzymes, including a D-arabinose dehydrogenase, a D-arabinonate dehydratase, a novel 2-keto-3-deoxy-D-arabinonate dehydratase, and a 2,5-dioxopentanoate dehydrogenase. Promoter analysis of these genes revealed a palindromic sequence upstream of the TATA box, which is likely to be involved in their concerted transcriptional control. Integration of the obtained biochemical data with genomic context analysis strongly suggests the occurrence of pentose oxidation pathways in both Archaea and Bacteria, and predicts the involvement of additional enzyme components. Moreover, it revealed striking genetic similarities between the catabolic pathways for pentoses, hexaric acids, and hydroxyproline degradation, which support the theory of metabolic pathway genesis by enzyme recruitment.Pentose sugars are a ubiquitous class of carbohydrates with diverse biological functions. Ribose and deoxyribose are major constituents of nucleic acids, whereas arabinose and xylose are building blocks of several plant cell wall polysaccharides. Many prokaryotes, as well as yeasts and fungi, are able to degrade these polysaccharides, and use the released five-carbon sugars as a sole carbon and energy source. At present, three main catabolic pathways have been described for pentoses. The first is present in Bacteria and uses isomerases, kinases, and epimerases to convert D-and L-arabinose (Ara) and D-xylose (Xyl) into D-xylulose 5-phosphate (Fig. 1A), which is further metabolized by the enzymes of the phosphoketolase or pentose phosphate pathway. The genes encoding the pentose-converting enzymes are often located in gene clusters in bacterial genomes, for example, the araBAD operon for L-Ara (1), the xylAB operon for D-Xyl (2), and the darK-fucPIK gene cluster for D-Ara (3). The second catabolic pathway for pentoses converts D-Xyl into D-xylulose 5-phosphate as well, but the conversions are catalyzed by reductases and dehydrogenases instead of isomerases and epimerases (Fig. 1B). This pathway is commonly found in yeasts, fungi, mammals, and plants, but also in some bacteria (4 -6). In a third pathway, pentoses such as L-Ara, D-Xyl, D-ribose, and D-Ara are metabolized non-phosphorylatively to either 2-oxoglutarate (2-OG) 4 or to pyruvate and glycolaldehyde (Fig. 1C). The conversion to 2-OG, which is a tricarboxylic acid cycle intermediate, proceeds via the subsequent action of a pentose dehydrogenase, a pentonolactonase, a pentoni...

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Section: Resultsmentioning

confidence: 99%

Identification of the Missing Links in Prokaryotic Pentose Oxidation Pathways

Brouns

Walther

Snijders

et al. 2006

Journal of Biological Chemistry

104

188

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“…As described in detail by Timm and co-workers (48,66), the active site of fumarylacetoacetate hydrolase is composed of a catalytic triad consisting of a glutamate carboxylate that stabilizes a histidine base that directly activates a nucleophilic water molecule. Also present is an oxyanion hole, which is positioned to stabilize the proposed tetrahedral alkoxy intermediate, a Ca 2ϩ ion that likely interacts with substrate and product, and a Mg 2ϩ ion.…”

Section: Discussionmentioning

confidence: 99%

“…6, close mechanistic similarities can be visualized between the chemistries of UGL and fumarylacetoacetate hydrolase catalysis. Based on their crystal structures of fumarylacetoacetate hydrolase and of its complexes with products and with a competitive inhibitor, Timm and co-workers (48,66) have proposed that the enzymatic cleavage of the C-C bond in fumarylacetoacetate catalysis proceeds via initial nucleophilic attack on the carbonyl carbon to form a tetrahedral alkoxy intermediate, which then breaks down via ketonization to yield the products fumarate and the enolate of acetoacetate. This mechanism is conceptually very analogous to the mechanism which we have proposed for amidoglycolate lyases (41), which, as illustrated in Fig.…”

Section: Discussionmentioning

confidence: 99%

Catalysis, Stereochemistry, and Inhibition of Ureidoglycolate Lyase

McIninch

May

2003

Journal of Biological Chemistry

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Ureidoglycolate lyase (UGL, EC 4.3.2.3) catalyzes the breakdown of ureidoglycolate to glyoxylate and urea, which is the final step in the catabolic pathway leading from purines to urea. Although the sequence of enzymatic steps was worked out nearly 40 years ago, the stereochemistry of the uric acid degradation pathway and the catalytic properties of UGL have remained very poorly described. We now report the first direct investigation of the absolute stereochemistry of UGL catalysis. Using chiral chromatographic analyses with substrate enantiomers, we demonstrate that UGL catalysis is stereospecific for substrates with the (S)-hydroxyglycine configuration. The first potent competitive inhibitors for UGL are reported here. These inhibitors are compounds which contain a 2,4-dioxocarboxylate moiety, designed to mimic transient species produced during lyase catalysis. The most potent inhibitor, 2,4-dioxo-4-phenylbutanoic acid, exhibits a K I value of 2.2 nM and is therefore among the most potent competitive inhibitors ever reported for a lyase enzyme. New synthetic alternate substrates for UGL, which are acyl-␣-hydroxyglycine compounds, are described. Based on these alternate substrates, we introduce the first assay method for monitoring UGL activity directly. Finally, we report the first putative primary nucleotide and derived peptide sequence for UGL. This sequence exhibits a high level of similarity to the fumarylacetoacetate hydrolase family of proteins. Close mechanistic similarities can be visualized between the chemistries of ureidoglycolate lyase and fumarylacetoacetate hydrolase catalysis.Ureidoglycolate lyase (UGL, 1 EC 4.3.2.3) and allantoicase (Acase, EC 3.5.3.4) are the enzymes that catalyze the final steps in the catabolic pathway leading from purines to urea. In this pathway ( Fig. 1), allantoic acid is formed from allantoin by allantoinase, Acase then converts allantoic acid to ureidoglycolate and urea, and, finally, UGL catalyzes the breakdown of ureidoglycolate to glyoxylate and urea. Acase was first found independently in frog liver by Krebs and Weil (1) and in the mycelium of Aspergillus niger by Brunel (2). UGL was first described by Valentine et al. (3,4) in Streptococcus allantoicus and in a strain of Pseudomonas. It has since been established that UGL and Acase are both functional in many bacteria, yeast, fish, and rat (5-16), whereas in some species only one of these activities has been detected (2, 17-23).The stereochemistry of UGL catalysis, and indeed of the uric acid degradation pathway as a whole, has remained poorly described for many years. Conflicting results have been reported as to whether UGL reacts preferentially with (Ϫ)-ureidoglycolate (5, 6, 9, 10, 18) or with (ϩ)-ureidoglycolate (17). Moreover, allantoinase reacts with both enantiomers of allantoin, and Acase has been reported to produce ureidoglycolate exhibiting a negative rotation, but, paradoxically, to also convert ureidoglycolate exhibiting a positive rotation to glyoxylate and urea (11). Thus, the stereospecificity of U...

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“…However, if FAH is in the reaction mixture, FAA is converted into fumarate and acetoacetate with a decrease in the absorbance. The reaction mixture contained 50 mM potassium phosphate buffer (pH 7), 1 mM ascorbic acid, 50 M ferrous sulfate, 50 M reduced GSH, 100 M HGA, about 50 g of crude protein extract of Escherichia coli expressing human HGD, and 25 g of purified FAH (recombinant His tag protein in E. coli; a gift of Kara Manning [2]). The reaction was initialized by adding HGA.…”

Section: Methodsmentioning

confidence: 99%

Maleylacetoacetate Isomerase (MAAI/GSTZ)-Deficient Mice Reveal a Glutathione-Dependent Nonenzymatic Bypass in Tyrosine Catabolism

Fernández-Cañón¹,

Baetscher²,

Finegold

et al. 2002

Molecular and Cellular Biology

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In mammals, the catabolic pathway of phenylalanine and tyrosine is found in liver (hepatocytes) and kidney (proximal tubular cells). There are well-described human diseases associated with deficiencies of all enzymes in this pathway except for maleylacetoacetate isomerase (MAAI), which converts maleylacetoacetate (MAA) to fumarylacetoacetate (FAA). MAAI is also known as glutathione transferase zeta (GSTZ1). Here, we describe the phenotype of mice with a targeted deletion of the MAAI (GSTZ1) gene. MAAI-deficient mice accumulated FAA and succinylacetone in urine but appeared otherwise healthy. This observation suggested that either accumulating MAA is not toxic or an alternate pathway for MAA metabolism exists. A complete redundancy of MAAI could be ruled out because substrate overload of the tyrosine catabolic pathway (administration of homogentisic acid, phenylalanine, or tyrosine) resulted in renal and hepatic damage. However, evidence for a partial bypass of MAAI activity was also found. Mice doubly mutant for MAAI and fumarylacetoacetate hydrolase (FAH) died rapidly on a normal diet, indicating that MAA could be isomerized to FAA in the absence of MAAI. Double mutants showed predominant renal injury, indicating that this organ is the primary target for the accumulated compound(s) resulting from MAAI deficiency. A glutathione-mediated isomerization of MAA to FAA independent of MAAI enzyme was demonstrated in vitro. This nonenzymatic bypass is likely responsible for the lack of a phenotype in nonstressed MAAI mutant mice.

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Mechanistic Inferences from the Crystal Structure of Fumarylacetoacetate Hydrolase with a Bound Phosphorus-based Inhibitor

Cited by 54 publications

References 35 publications

Identification of the Missing Links in Prokaryotic Pentose Oxidation Pathways

Identification of the Missing Links in Prokaryotic Pentose Oxidation Pathways

Catalysis, Stereochemistry, and Inhibition of Ureidoglycolate Lyase

Maleylacetoacetate Isomerase (MAAI/GSTZ)-Deficient Mice Reveal a Glutathione-Dependent Nonenzymatic Bypass in Tyrosine Catabolism

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