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Enzyme Superfamily (enzyme + superfamily)
Selected AbstractsNew ways to break an old bond: the bacterial carbon,phosphorus hydrolases and their role in biogeochemical phosphorus cyclingENVIRONMENTAL MICROBIOLOGY, Issue 10 2007John P. Quinn Summary Phosphonates are organophosphorus molecules that contain the highly stable C,P bond, rather than the more common, and more labile, C,O,P phosphate ester bond. They have ancient origins but their biosynthesis is widespread among more primitive organisms and their importance in the contemporary biosphere is increasingly recognized; for example phosphonate-P is believed to play a particularly significant role in the productivity of the oceans. The microbial degradation of phosphonates was originally thought to occur only under conditions of phosphate limitation, mediated exclusively by the poorly characterized C,P lyase multienzyme system, under Pho regulon control. However, more recent studies have demonstrated the Pho-independent mineralization by environmental bacteria of three of the most widely distributed biogenic phosphonates: 2-aminoethylphosphonic acid (ciliatine), phosphonoacetic acid, and 2-amino-3-phosphonopropionic acid (phosphonoalanine). The three phosphonohydrolases responsible have unique specificities and are members of separate enzyme superfamilies; their expression is regulated by distinct members of the LysR family of bacterial transcriptional regulators, for each of which the phosphonate substrate of the respective degradative operon serves as coinducer. Previously no organophosphorus compound was known to induce the enzymes required for its own degradation. Whole-genome and metagenome sequence analysis indicates that the genes encoding these newly described C,P hydrolases are distributed widely among prokaryotes. As they are able to function under conditions in which C,P lyases are inactive, the three enzymes may play a hitherto-unrecognized role in phosphonate breakdown in the environment and hence make a significant contribution to global biogeochemical P-cycling. [source] The putative l -lactate dehydrogenase from Methanococcus jannaschii is an NADPH-dependent l -malate dehydrogenaseMOLECULAR MICROBIOLOGY, Issue 6 2000Dominique Madern The enyme encoded by Methanococcus jannaschii open reading frame (ORF) 0490 was purified and characterized. It was shown to be an NADPH-dependent [lactate dehydrogenase (LDH)-like]l -malate dehydrogenase (MalDH) and not an l -lactate dehydrogenase, as had been suggested previously on the basis of amino acid sequence similarity. The results show the importance of biochemical data in the assignment of ORF function in genomic sequences and have implications for the phylogenetic distribution of members of the MalDH/LDH enzyme superfamilies within the prokaryotic kingdom. [source] Potential active-site residues in polyneuridine aldehyde esterase, a central enzyme of indole alkaloid biosynthesis, by modelling and site-directed mutagenesisFEBS JOURNAL, Issue 12 2002Emine Mattern-Dogru In the biosynthesis of the antiarrhythmic alkaloid ajmaline, polyneuridine aldehyde esterase (PNAE) catalyses a central reaction by transforming polyneuridine aldehyde into epi-vellosimine, which is the immediate precursor for the synthesis of the ajmalane skeleton. The PNAE cDNA was previously heterologously expressed in E. coli. Sequence alignments indicated that PNAE has a 43% identity to a hydroxynitrile lyase from Hevea brasiliensis, which is a member of the ,/, hydrolase superfamily. The catalytic triad, which is typical for this family, is conserved. By site-directed mutagenesis, the members of the catalytic triad were identified. For further detection of the active residues, a model of PNAE was constructed based on the X-ray crystallographic structure of hydroxynitrile lyase. The potential active site residues were selected on this model, and were mutated in order to better understand the relationship of PNAE with the ,/, hydrolases, and as well its mechanism of action. The results showed that PNAE is a novel member of the ,/, hydrolase enzyme superfamily. [source] Mala s 12 is a major allergen in patients with atopic eczema and has sequence similarities to the GMC oxidoreductase family,ALLERGY, Issue 6 2007A. Zargari Background:, Atopic eczema (AE) is a chronic inflammatory skin disorder, characterized by impaired skin barrier and itch. The yeast Malassezia belongs to the normal human skin microflora and can induce IgE- and T-cell-mediated allergic reactions in AE patients. Previously, we have identified several IgE-binding components in Malassezia sympodialis extract. Methods:, Here, we report cloning, production and characterization of a M. sympodialis 67-kDa allergen. Results:, The sequence of the 67-kDa protein, termed Mala s 12, showed sequence similarity to the glucose,methanol,choline (GMC) oxidoreductase enzyme superfamily and was expressed as a recombinant protein in Escherichia coli. The purified protein bound flavin adenine dinucleotide with 1:1 stoichiometry per monomer of protein. The protein-bound flavin showed an extinction coefficient at 451 nm of 11.3 mM,1cm,1. The recombinant 67-kDa protein did not show any enzymatic activity when tested as oxidase or dehydrogenase using choline, glucose, myo-inositol, methanol, ethanol, 1-pentanol, benzyl alcohol, 2-phenylethanol, cholesterol or lauryl alcohol as possible substrates. Recombinant Mala s 12 was recognized by serum IgE from 13 of 21 (62%) M. sympodialis -sensitized AE patients indicating that the 67-kDa component is a major allergen. Conclusions:, The data show that Mala s 12 has sequence similarity to the GMC oxidoreductase family and is a major allergen in AE patients. [source] Structures of apo and GTP-bound molybdenum cofactor biosynthesis protein MoaC from Thermus thermophilus HB8ACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2010Shankar Prasad Kanaujia The first step in the molybdenum cofactor (Moco) biosynthesis pathway involves the conversion of guanosine triphosphate (GTP) to precursor Z by two proteins (MoaA and MoaC). MoaA belongs to the S -adenosylmethionine-dependent radical enzyme superfamily and is believed to generate protein and/or substrate radicals by reductive cleavage of S -adenosylmethionine using an Fe,S cluster. MoaC has been suggested to catalyze the release of pyrophosphate and the formation of the cyclic phosphate of precursor Z. However, structural evidence showing the binding of a substrate-like molecule to MoaC is not available. Here, apo and GTP-bound crystal structures of MoaC from Thermus thermophilus HB8 are reported. Furthermore, isothermal titration calorimetry experiments have been carried out in order to obtain thermodynamic parameters for the protein,ligand interactions. In addition, molecular-dynamics (MD) simulations have been carried out on the protein,ligand complex of known structure and on models of relevant complexes for which X-ray structures are not available. The biophysical, structural and MD results reveal the residues that are involved in substrate binding and help in speculating upon a possible mechanism. [source] Crystallization and initial crystallographic analysis of phosphoglucosamine mutase from Bacillus anthracisACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2009Ritcha Mehra-Chaudhary The enzyme phosphoglucosamine mutase catalyzes the conversion of glucosamine 6-phosphate to glucosamine 1-phosphate, an early step in the formation of the nucleotide sugar UDP- N -acetylglucosamine, which is involved in peptidoglycan biosynthesis. These enzymes are part of the large ,- d -phosphohexomutase enzyme superfamily, but no proteins from the phosphoglucosamine mutase subgroup have been structurally characterized to date. Here, the crystallization of phosphoglucosamine mutase from Bacillus anthracis in space group P3221 by hanging-drop vapor diffusion is reported. The crystals diffracted to 2.7,Å resolution under cryocooling conditions. Structure determination by molecular replacement was successful and refinement is under way. The crystal structure of B. anthracis phosphoglucosamine mutase should shed light on the substrate-specificity of these enzymes and will also serve as a template for inhibitor design. [source] The quaternary structure of the amidase from Geobacillus pallidus RAPc8 is revealed by its crystal packingACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2006Vinod B. Agarkar The amidase from Geobacillus pallidus RAPc8, a moderate thermophile, is a member of the nitrilase enzyme superfamily. It converts amides to the corresponding acids and ammonia and has application as an industrial catalyst. RAPc8 amidase has been cloned and functionally expressed in Escherichia coli and has been purified by heat treatment and a number of chromatographic steps. The enzyme was crystallized using the hanging-drop vapour-diffusion method. Crystals produced in the presence of 1.2,M sodium citrate, 400,mM NaCl, 100,mM sodium acetate pH 5.6 were selected for X-ray diffraction studies. A data set having acceptable statistics to 1.96,Å resolution was collected under cryoconditions using an in-house X-ray source. The space group was determined to be primitive cubic P4232, with unit-cell parameter a = 130.49 (±0.05) Å. The structure was solved by molecular replacement using the backbone of the hypothetical protein PH0642 from Pyrococcus horikoshii (PDB code 1j31) with all non-identical side chains substituted with alanine as a probe. There is one subunit per asymmetric unit. The subunits are packed as trimers of dimers with D3 point-group symmetry around the threefold axis in such a way that the dimer interface seen in the homologues is preserved. [source] Ethylene Biosynthesis by 1-Aminocyclopropane-1-Carboxylic Acid Oxidase: A DFT StudyCHEMISTRY - A EUROPEAN JOURNAL, Issue 34 2006Arianna Bassan Dr. Abstract The reaction catalyzed by the plant enzyme 1-aminocyclopropane-1-carboxylic acid oxidase (ACCO) was investigated by using hybrid density functional theory. ACCO belongs to the non-heme iron(II) enzyme superfamily and carries out the bicarbonate-dependent two-electron oxidation of its substrate ACC (1-aminocyclopropane-1-carboxylic acid) concomitant with the reduction of dioxygen and oxidation of a reducing agent probably ascorbate. The reaction gives ethylene, CO2, cyanide and two water molecules. A model including the mononuclear iron complex with ACC in the first coordination sphere was used to study the details of OO bond cleavage and cyclopropane ring opening. Calculations imply that this unusual and complex reaction is triggered by a hydrogen atom abstraction step generating a radical on the amino nitrogen of ACC. Subsequently, cyclopropane ring opening followed by OO bond heterolysis leads to a very reactive iron(IV),oxo intermediate, which decomposes to ethylene and cyanoformate with very low energy barriers. The reaction is assisted by bicarbonate located in the second coordination sphere of the metal. [source] | |||||||||||||