The Experts below are selected from a list of 143442 Experts worldwide ranked by ideXlab platform
Barbara K Pomper - One of the best experts on this subject based on the ideXlab platform.
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generation of formate by the formyltransferase hydrolase complex fhc from methylobacterium extorquens am1
FEBS Letters, 2002Co-Authors: Olivier Saurel, Barbara K Pomper, Alain Milon, Julia A. VorholtAbstract:Methylobacterium extorquens AM1 possesses a formyltransferase (Ftr) complex that is essential for growth in the presence of methanol and involved in formaldehyde oxidation to CO2. One of the subunits of the complex carries the catalytic site for transfer of the formyl group from tetrahydromethanopterin to methanofuran (MFR). We now found via nuclear magnetic resonance-based studies that the Ftr complex also catalyzes the hydrolysis of formyl-MFR and generates formate. The enzyme was therefore renamed Ftr/hydrolase complex (Fhc). FhcA shares a Sequence Pattern with amidohydrolases and is assumed to be the catalytic site where the hydrolysis takes place.
Margarida Archer - One of the best experts on this subject based on the ideXlab platform.
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X-ray structure of a CDP-alcohol phosphatidyltransferase membrane enzyme and insights into its catalytic mechanism
Nature Communications, 2015Co-Authors: Przemyslaw Nogly, Pikyee Ma, Isabel Moraes, Ivan Yu. Gushchin, Nuno Borges, Valentin I. Gordeliy, Andrii Ishchenko, Ekaterina Round, Valentin Borshchevskiy, Sergei Grudinin, Alina Remeeva, Helena Santos, Ana Maria Esteves, Margarida ArcherAbstract:Phospholipids have major roles in the structure and function of all cell membranes. Most integral membrane proteins from the large CDP-alcohol phosphatidyltransferase family are involved in phospholipid biosynthesis across the three domains of life. They share a conserved Sequence Pattern and catalyse the displacement of CMP from a CDP-alcohol by a second alcohol. Here we report the crystal structure of a bifunctional enzyme comprising a cytoplasmic nucleotidyltransferase domain (IPCT) fused with a membrane CDP-alcohol phosphotransferase domain (DIPPS) at 2.65 Å resolution. The bifunctional protein dimerizes through the DIPPS domains, each comprising six transmembrane α-helices. The active site cavity is hydrophilic and widely open to the cytoplasm with a magnesium ion surrounded by four highly conserved aspartate residues from helices TM2 and TM3. We show that magnesium is essential for the enzymatic activity and is involved in catalysis. Substrates docking is validated by mutagenesis studies, and a structure-based catalytic mechanism is proposed.
Julia A. Vorholt - One of the best experts on this subject based on the ideXlab platform.
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generation of formate by the formyltransferase hydrolase complex fhc from methylobacterium extorquens am1
FEBS Letters, 2002Co-Authors: Olivier Saurel, Barbara K Pomper, Alain Milon, Julia A. VorholtAbstract:Methylobacterium extorquens AM1 possesses a formyltransferase (Ftr) complex that is essential for growth in the presence of methanol and involved in formaldehyde oxidation to CO2. One of the subunits of the complex carries the catalytic site for transfer of the formyl group from tetrahydromethanopterin to methanofuran (MFR). We now found via nuclear magnetic resonance-based studies that the Ftr complex also catalyzes the hydrolysis of formyl-MFR and generates formate. The enzyme was therefore renamed Ftr/hydrolase complex (Fhc). FhcA shares a Sequence Pattern with amidohydrolases and is assumed to be the catalytic site where the hydrolysis takes place.
Przemyslaw Nogly - One of the best experts on this subject based on the ideXlab platform.
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X-ray structure of a CDP-alcohol phosphatidyltransferase membrane enzyme and insights into its catalytic mechanism
Nature Communications, 2015Co-Authors: Przemyslaw Nogly, Pikyee Ma, Isabel Moraes, Ivan Yu. Gushchin, Nuno Borges, Valentin I. Gordeliy, Andrii Ishchenko, Ekaterina Round, Valentin Borshchevskiy, Sergei Grudinin, Alina Remeeva, Helena Santos, Ana Maria Esteves, Margarida ArcherAbstract:Phospholipids have major roles in the structure and function of all cell membranes. Most integral membrane proteins from the large CDP-alcohol phosphatidyltransferase family are involved in phospholipid biosynthesis across the three domains of life. They share a conserved Sequence Pattern and catalyse the displacement of CMP from a CDP-alcohol by a second alcohol. Here we report the crystal structure of a bifunctional enzyme comprising a cytoplasmic nucleotidyltransferase domain (IPCT) fused with a membrane CDP-alcohol phosphotransferase domain (DIPPS) at 2.65 Å resolution. The bifunctional protein dimerizes through the DIPPS domains, each comprising six transmembrane α-helices. The active site cavity is hydrophilic and widely open to the cytoplasm with a magnesium ion surrounded by four highly conserved aspartate residues from helices TM2 and TM3. We show that magnesium is essential for the enzymatic activity and is involved in catalysis. Substrates docking is validated by mutagenesis studies, and a structure-based catalytic mechanism is proposed.
Masaru Tomita - One of the best experts on this subject based on the ideXlab platform.
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characteristic Sequence Pattern in the 5 to 20 bp upstream region of primate alu elements
Journal of Molecular Evolution, 2000Co-Authors: Yoshimi Toda, Rintaro Saito, Masaru TomitaAbstract:We conducted comprehensive Sequence analysis of 5′ flanking regions of primate Alu elements. Information contents were computed and frequencies of 1024 pentanucleotides were measured to approximate the location of a characteristic Sequence and to specify its Pattern(s), which may be involved in the integration of Alu elements into their host genomes. A large number of samples was used, the wide region of the 5′ end of Alu elements was analyzed, and comparisons were made among different subfamilies. Through our analyses, ``TTTTAAAAA'' or ``(T) m (A) n '' can be stated as a candidate for the characteristic Sequence Pattern, which resides around the region 5 to 20 base pairs upstream of the 5′ end of Alu elements. This characteristic Sequence Pattern was more prominent in the Sequences of younger Alus, which is a strong indication that the Sequence Pattern has a role at the time of Alu integration.
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comprehensive Sequence analyses of 5 flanking regions of primate alu elements
Genome Informatics, 1998Co-Authors: Yoshimi Toda, Rintaro Saito, Masaru TomitaAbstract:Retrotransposons have been generally known to integrate randomly into host genomes. Jurka (Proc. Natl. Acad. Sci. USA 94: 1872-1877, 1977), however, showed consensus Sequence Patterns at integration sites of certain mammalian retrotransposons, and suggested involvement of Sequence specific enzymes that mediate integration. We have conducted comprehensive Sequence analyses of 5' flanking regions of primate Alu elements. In contrast to the small but clean data set Jurka (1977) used, (1) larger number of samples were used, (2) wider region of 5' end of Alu elements was analyzed, and (3) comparisons were made among different subfamilies for comprehensive analyses in order to identify characteristic Sequence Pattern(s) preceding 5' end of Alu elements. The nucleotide occurrences at each position within 500 bases of 5' end of Alus were counted to obtain profiles. Information content at each nucleotide position in the same region was, then, computed. Distinctive difference in the nucleotide composition and information content values that divides the region into two was observed. The region between -20 and 5' end of Alu elements is found to be highly adenine-rich and shows significantly higher information content values compared to the rest of the region, implying the existence of certain characteristic Sequence Pattern in this region. Also, younger subfamilies of Alu elements show higher information content values than older subfamilies. This implies that certain characteristic Sequence Pattern already existed in the region between -20 and 5' end of Alu elements at the time of Alu integration, and accumulation of mutation in the course of time resulted in the less distinctive Sequence Pattern in older Sequences. Frequencies of all possible triplets (total of 64) were measured in the same region in order to identify characteristic Sequence Pattern(s). Observation that frequencies of triplets aaa, taa and tta in the 5' flanking Sequences were high is consistent with Jurka (1977). Frequencies of some other triplets such as gaa, caa, aac, ctt, gtt, atg, etc. which do not comprise the primary candidates for the nick site in Jurka (1977) also show significantly high frequencies.
