One Protein, Two Enzymes Revisited: A Structural Entropy Switch Interconverts the Two Isoforms of Acireductone Dioxygenase

Ju, Tingting; Goldsmith, Rachel Beaulieu; Chai, Sergio C.; Maroney, Michael J.; Pochapsky, Susan Sondej; Pochapsky, Thomas C.

doi:10.1016/j.jmb.2006.08.060

Cited by 58 publications

(140 citation statements)

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“…They found that substitution of the Fe(II) by Ni(II) or Co(II) significantly increased the reaction energy barrier and thus deterred the oxidization reaction (50). In the only known nickel-containing dioxygenase, Ni-ARD, the nickel is not redox-active and serves only to coordinate the substrate and facilitate ligand oxidation by O 2 (51).…”

Section: Discussionmentioning

confidence: 99%

Nickel Ions Inhibit Histone Demethylase JMJD1A and DNA Repair Enzyme ABH2 by Replacing the Ferrous Iron in the Catalytic Centers

Chen

Giri

Zhang

et al. 2010

Journal of Biological Chemistry

132

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Iron-and 2-oxoglutarate-dependent dioxygenases are a diverse family of non-heme iron enzymes that catalyze various important oxidations in cells. A key structural motif of these dioxygenases is a facial triad of 2-histidines-1-carboxylate that coordinates the Fe(II) at the catalytic site. Using histone demethylase JMJD1A and DNA repair enzyme ABH2 as examples, we show that this family of dioxygenases is highly sensitive to inhibition by carcinogenic nickel ions. We find that, with iron, the 50% inhibitory concentrations of nickel (IC 50 Nickel compounds are human respiratory carcinogens (1), causing a very high incidence of lung and nasal cancers in nickel refinery workers (2). Over 20 years ago, our group reported that cells phagocytosed particulate nickel compounds, and the dissolution of these particles inside of the cells generated high concentrations of free nickel ions in the cytoplasm and nucleus (3). Using a dye that fluoresces when intracellular nickel ion binds to it, we showed that both soluble and insoluble nickel compounds were able to elevate the levels of nickel ions in the cytoplasmic and nuclear compartments (4). A strong correlation was found between the uptake of particulate nickel compounds by cells and subsequent cell transformation (5), suggesting that intracellular nickel ion concentration is a major determinant of toxicity and carcinogenicity of nickel compounds. Identifying the intracellular targets of nickel ions is therefore crucial to understand the underlying mechanism for the carcinogenic effects of nickel compounds.Silencing of tumor suppressor gene(s) by epigenetic mechanisms represents one of the potential mechanisms of nickel carcinogenesis. Epigenetic events, which include DNA methylation and histone modifications, are ubiquitously involved in the regulation of gene expression. By using a transgenic cell model with the target gene placed near heterochromatin, we were the first to demonstrate that nickel exposure caused a very high frequency of transgene silencing by increasing DNA methylation and repressive histone marks at the promoter of the silenced transgene (6 -8). In animal experiments, injection of particulate nickel compounds (nickel sulfide or nickel subsulfide) into mice induced formation of malignant fibrous histiocytomas and sarcomas, with the p16 and Fhit genes often found to be epigenetically silenced in these cancers (9,10). Additional studies have demonstrated that nickel exposure caused truncation of histone H2B and H2A as well as global alterations of a variety of histone modifications, such as histone acetylation, methylation, phosphorylation, and ubiquitination (11)(12)(13)(14)(15)(16)(17)(18)(19)(20). However, the underlying mechanisms responsible for these nickel-induced epigenetic alterations are poorly understood. In our recent study, we reported that nickel increases the global levels of mono-and di-methylated histone H3 lysine 9 (H3K9me1 and H3K9me2) not by affecting histone methyltransferases but rather by inhibiting a group of unidentified iron-and...

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Section: Discussionmentioning

confidence: 99%

Nickel Ions Inhibit Histone Demethylase JMJD1A and DNA Repair Enzyme ABH2 by Replacing the Ferrous Iron in the Catalytic Centers

Chen

Giri

Zhang

et al. 2010

Journal of Biological Chemistry

132

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“…X-ray absorption spectroscopy (XAS) studies of the structure of the catalytic Ni center in resting NiARD enzyme and the enzyme-substrate (ES) complex have been reported (14). We have also described a structural model for FeARD' and identified a structural entropy switch that interconverts the two isoforms (15) (Figure 1). …”

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confidence: 95%

“…In both cases, the results of XAS studies of NiARD were used to determine Ni-ligand bond lengths and coordination geometry (14). The recently published FeARD' structural model is based on the structure of a stable soluble metal-free mutant of Klebsiella ARD, H98S ARD, after the serendipitous discovery that this mutant is isostructural with FeARD' as determined by multidimensional NMR experiments (15). As with NiARD, Fe-ligand bond lengths and ligation geometry was established using the results of XAS experiments that are detailed here.…”

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confidence: 99%

Characterization of Metal Binding in the Active Sites of Acireductone Dioxygenase Isoforms from Klebsiella ATCC 8724

Chai

Dang

et al. 2008

Biochemistry

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The two acireductone dioxygenase (ARD) isozymes from the methionine salvage pathway of Klebsiella ATCC 8724 present an unusual case in which two enzymes with different structures and distinct activities towards their common substrates (1,2-dihydroxy-3-oxo-5-(methylthio)pent-1-ene and dioxygen) are derived from the same polypeptide chain. Structural and functional differences between the two isozymes are determined by the type of M +2 metal ion bound in the active site. The Ni +2 -bound NiARD catalyzes an off-pathway shunt from the methionine salvage pathway leading to the production of formate, methylthiopropionate and carbon monoxide, while the Fe +2 -bound FeARD' catalyzes the on-pathway formation of methionine precursor 2-keto-4-methylthiobutyrate and formate. Four potential protein-based metal ligands were identified by sequence homology and structural considerations. Based on the results of site-directed mutagenesis experiments, X-ray absorption spectroscopy (XAS) and isothermal calorimetry measurements, it is concluded that the same four residues, His 96, His 98, Glu 102 and His 140, provide the protein-based ligands for the metal in both the Ni-and Fe-containing forms of the enzyme, and subtle differences in the local backbone conformations trigger the observed structural and functional differences between the FeARD' and NiARD isozymes. Furthermore, both forms of the enzyme bind their respective metals with pseudo-octahedral geometry, and both may lose a His ligand upon binding of substrate under anaerobic conditions. However, mutations at two conserved non-ligand acidic residues, Glu 95 and Glu 100, result in low metal contents for the mutant proteins as isolated, suggesting that some of the conserved charged residues may aid in transfer of metal from in vivo sources or prevent the loss of metal to stronger chelators. The Glu 100 mutant reconstitutes readily but has low activity. Mutation of Asp 101 results in an active enzyme that incorporates metal in vivo but shows evidence of mixed forms.* To whom correspondence should be addressed: pochapsk@brandeis.edu, phone 781−736−2559, fax 781−736−2516. e Current address: Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, 70 Ship Street, GE3, Providence, RI, 02912 f Current address: Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Dr., Room 1007, Indianapolis IN 46202 g This work was supported in part by USPHS grant (R01-GM067786 TCP). Acknowledgment is made to the donors of The American Chemical Society Petroleum Research Fund for partial support (MJM). Trainee funding (SCC) was provided by the NIH-Chemistry Biology Interface Program, T32-GM08515. XAS data collection at the National Synchrotron Light Source at Brookhaven National Laboratory was supported by the U.S. Department of Energy, Division of Materials Sciences and Division of Chemical Sciences. Beamline X9B at NSLS is supported in part by the NIH.Supporting information available Fits for resting state and ES...

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“…The only gene displaying an elevated mRNA transcript was At4g14716 (Arabidopsis Genome Initiative accession). To show that increased expression of At4g14716 was responsible (28,41). AdoMet is recycled into methionine via the intermediates MTA, 5-methylthioribose (MTR), and acireductone.…”

Section: Overexpression Of the Coding Region Of At4g14716 (Formally Smentioning

confidence: 99%

“…This pathway is important in that it provides the organism with a source of methionine under limiting conditions, regulates the production of polyamines, and in plants allows for the production of ethylene (26). KoARD proteins catalyze two distinct reactions dependent upon which divalent metal ion is bound in the active site (27,28). Fe-bound ARD catalyzes the on-pathway reaction that converts acireductone to the keto acid ␣-keto-␥-methylthiobutyrate (the methionine precursor).…”

Section: ϫ65mentioning

confidence: 99%

Acireductone Dioxygenase 1 (ARD1) Is an Effector of the Heterotrimeric G Protein β Subunit in Arabidopsis

Friedman

Jiang

et al. 2011

Journal of Biological Chemistry

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Heterotrimeric G protein complexes are conserved from plants to mammals, but the complexity of each system varies. Arabidopsis thaliana contains one G␣, one G␤ (AGB1), and at least three G␥ subunits, allowing it to form three versions of the heterotrimer. This plant model is ideal for genetic studies because mammalian systems contain hundreds of unique heterotrimers. The activation of these complexes promotes interactions between both the G␣ subunit and the G␤␥ dimer with enzymes and scaffolds to propagate signaling to the cytoplasm. However, although effectors of G␣ and G␤ are known in mammals, no G␤ effectors were previously known in plants. Toward identifying AGB1 effectors, we genetically screened for dominant mutations that suppress G␤-null mutant (agb1-2) phenotypes. We found that overexpression of acireductone dioxygenase 1 (ARD1) suppresses the 2-day-old etiolated phenotype of agb1-2. ARD1 is homologous to prokaryotic and eukaryotic ARD proteins; one function of ARDs is to operate in the methionine salvage pathway. We show here that ARD1 is an active metalloenzyme, and AGB1 and ARD1 both control embryonic hypocotyl length by modulating cell division; they also may contribute to the production of ethylene, a product of the methionine salvage pathway. ARD1 physically interacts with AGB1, and ARD enzymatic activity is stimulated by AGB1 in vitro. The binding interface on AGB1 was deduced using a comparative evolutionary approach and tested using recombinant AGB1 mutants. A possible mechanism for AGB1 activation of ARD1 activity was tested using directed mutations in a loop near the substrate-binding site.One way that cells communicate with one another and perceive and respond to both intercellular and extracellular signals is through heterotrimeric guanine nucleotide-binding protein (G protein) signaling. As known for animal cells, G protein signaling begins when an extracellular ligand binds to a seventransmembrane receptor that is physically coupled to an inactive heterotrimeric complex consisting of G␣-GDP, G␤, and G␥ subunits located on the cytoplasmic side of the cell membrane. Upon activation by the receptor, the G␣ exchanges GDP for GTP and dissociates from the receptor and the obligate G␤␥ dimer, allowing free G␣ and free G␤␥ to participate in downstream signaling processes through concomitant interactions with proteins called effectors. This signaling ceases when G␣ hydrolyzes GTP to GDP and the heterotrimer reforms (1, 2). Mammalian species possess a complex array of possible G protein heterotrimer combinations as there are 16 G␣, 5 G␤, and 12 G␥ genes, making genetic studies difficult. However, the Arabidopsis thaliana genome encodes one G␣ (GPA1), one G␤ (AGB1), and three G␥ (AGG1, AGG2, and AGG3) genes (3) and thus three heterotrimeric combinations (2). As a result, all G protein signaling in Arabidopsis can be abolished by mutating only a few genes, making this an ideal genetic model for G protein signaling in a multicellular context. Additionally, because there is high similarity between the ...

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One Protein, Two Enzymes Revisited: A Structural Entropy Switch Interconverts the Two Isoforms of Acireductone Dioxygenase

Cited by 58 publications

References 32 publications

Nickel Ions Inhibit Histone Demethylase JMJD1A and DNA Repair Enzyme ABH2 by Replacing the Ferrous Iron in the Catalytic Centers

Nickel Ions Inhibit Histone Demethylase JMJD1A and DNA Repair Enzyme ABH2 by Replacing the Ferrous Iron in the Catalytic Centers

Characterization of Metal Binding in the Active Sites of Acireductone Dioxygenase Isoforms from Klebsiella ATCC 8724

Acireductone Dioxygenase 1 (ARD1) Is an Effector of the Heterotrimeric G Protein β Subunit in Arabidopsis

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