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Paul F. Cook - One of the best experts on this subject based on the ideXlab platform.
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A Lysine-Tyrosine Pair Carries Out Acid−Base Chemistry in the Metal Ion-Dependent Pyridine Dinucleotide-Linked β-Hydroxyacid Oxidative Decarboxylases†
Biochemistry, 2009Co-Authors: Deniz F. Aktas, Paul F. CookAbstract:This work reviews published structural and kinetic data on the pyridine nucleotide-linked beta-Hydroxyacid oxidative decarboxylases. The family of metal ion-dependent pyridine nucleotide-linked beta-Hydroxyacid oxidative decarboxylases can be divided into two structural families with the malic enzyme, which has an (S)-Hydroxyacid substrate, comprising one subfamily and isocitrate dehydrogenase, isopropylmalate dehydrogenase, homoisocitrate dehydrogenase, and tartrate dehydrogenase, which have an (R)-Hydroxyacid substrate, comprising the second subclass. Multiple-sequence alignment of the members of the (R)-Hydroxyacid family indicates a high degree of sequence identity with most of the active site residues conserved. The three-dimensional structures of the members of the (R)-Hydroxyacid family with structures available superimpose on one another, and the active site structures of the enzymes have a similar overall geometry of residues in the substrate and metal ion binding sites. In addition, a number of residues in the malic enzyme active site are also conserved, and the arrangement of these residues has a similar geometry, although the (R)-Hydroxyacid and (S)-Hydroxyacid family sites are geometrically mirror images of one another. The active sites of the (R)-Hydroxyacid family have a higher positive charge density when compared to those of the (S)-Hydroxyacid family, largely due to the number of arginine residues in the vicinity of the substrate alpha-carboxylate and one fewer carboxylate ligand to the divalent metal ion. Data available for all of the enzymes in the family have been considered, and a general mechanism that makes use of a lysine (general base)-tyrosine (general acid) pair is proposed. Differences exist in the mechanism for generating the neutral form of lysine so that it can act as a base.
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a lysine tyrosine pair carries out acid base chemistry in the metal ion dependent pyridine dinucleotide linked beta Hydroxyacid oxidative decarboxylases
Biochemistry, 2009Co-Authors: Deniz F. Aktas, Paul F. CookAbstract:This work reviews published structural and kinetic data on the pyridine nucleotide-linked β-Hydroxyacid oxidative decarboxylases. The family of metal ion-dependent pyridine nucleotide-linked β-Hydroxyacid oxidative decarboxylases can be divided into two structural families with the malic enzyme, which has an (S)-Hydroxyacid substrate, comprising one subfamily and isocitrate dehydrogenase, isopropylmalate dehydrogenase, homoisocitrate dehydrogenase, and tartrate dehydrogenase, which have an (R)-Hydroxyacid substrate, comprising the second subclass. Multiple-sequence alignment of the members of the (R)-Hydroxyacid family indicates a high degree of sequence identity with most of the active site residues conserved. The three-dimensional structures of the members of the (R)-Hydroxyacid family with structures available superimpose on one another, and the active site structures of the enzymes have a similar overall geometry of residues in the substrate and metal ion binding sites. In addition, a number of residu...
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a lysine tyrosine pair carries out acid base chemistry in the metal ion dependent pyridine dinucleotide linked β Hydroxyacid oxidative decarboxylases
Biochemistry, 2009Co-Authors: Deniz F. Aktas, Paul F. CookAbstract:This work reviews published structural and kinetic data on the pyridine nucleotide-linked beta-Hydroxyacid oxidative decarboxylases. The family of metal ion-dependent pyridine nucleotide-linked beta-Hydroxyacid oxidative decarboxylases can be divided into two structural families with the malic enzyme, which has an (S)-Hydroxyacid substrate, comprising one subfamily and isocitrate dehydrogenase, isopropylmalate dehydrogenase, homoisocitrate dehydrogenase, and tartrate dehydrogenase, which have an (R)-Hydroxyacid substrate, comprising the second subclass. Multiple-sequence alignment of the members of the (R)-Hydroxyacid family indicates a high degree of sequence identity with most of the active site residues conserved. The three-dimensional structures of the members of the (R)-Hydroxyacid family with structures available superimpose on one another, and the active site structures of the enzymes have a similar overall geometry of residues in the substrate and metal ion binding sites. In addition, a number of residues in the malic enzyme active site are also conserved, and the arrangement of these residues has a similar geometry, although the (R)-Hydroxyacid and (S)-Hydroxyacid family sites are geometrically mirror images of one another. The active sites of the (R)-Hydroxyacid family have a higher positive charge density when compared to those of the (S)-Hydroxyacid family, largely due to the number of arginine residues in the vicinity of the substrate alpha-carboxylate and one fewer carboxylate ligand to the divalent metal ion. Data available for all of the enzymes in the family have been considered, and a general mechanism that makes use of a lysine (general base)-tyrosine (general acid) pair is proposed. Differences exist in the mechanism for generating the neutral form of lysine so that it can act as a base.
Deniz F. Aktas - One of the best experts on this subject based on the ideXlab platform.
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A Lysine-Tyrosine Pair Carries Out Acid−Base Chemistry in the Metal Ion-Dependent Pyridine Dinucleotide-Linked β-Hydroxyacid Oxidative Decarboxylases†
Biochemistry, 2009Co-Authors: Deniz F. Aktas, Paul F. CookAbstract:This work reviews published structural and kinetic data on the pyridine nucleotide-linked beta-Hydroxyacid oxidative decarboxylases. The family of metal ion-dependent pyridine nucleotide-linked beta-Hydroxyacid oxidative decarboxylases can be divided into two structural families with the malic enzyme, which has an (S)-Hydroxyacid substrate, comprising one subfamily and isocitrate dehydrogenase, isopropylmalate dehydrogenase, homoisocitrate dehydrogenase, and tartrate dehydrogenase, which have an (R)-Hydroxyacid substrate, comprising the second subclass. Multiple-sequence alignment of the members of the (R)-Hydroxyacid family indicates a high degree of sequence identity with most of the active site residues conserved. The three-dimensional structures of the members of the (R)-Hydroxyacid family with structures available superimpose on one another, and the active site structures of the enzymes have a similar overall geometry of residues in the substrate and metal ion binding sites. In addition, a number of residues in the malic enzyme active site are also conserved, and the arrangement of these residues has a similar geometry, although the (R)-Hydroxyacid and (S)-Hydroxyacid family sites are geometrically mirror images of one another. The active sites of the (R)-Hydroxyacid family have a higher positive charge density when compared to those of the (S)-Hydroxyacid family, largely due to the number of arginine residues in the vicinity of the substrate alpha-carboxylate and one fewer carboxylate ligand to the divalent metal ion. Data available for all of the enzymes in the family have been considered, and a general mechanism that makes use of a lysine (general base)-tyrosine (general acid) pair is proposed. Differences exist in the mechanism for generating the neutral form of lysine so that it can act as a base.
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a lysine tyrosine pair carries out acid base chemistry in the metal ion dependent pyridine dinucleotide linked beta Hydroxyacid oxidative decarboxylases
Biochemistry, 2009Co-Authors: Deniz F. Aktas, Paul F. CookAbstract:This work reviews published structural and kinetic data on the pyridine nucleotide-linked β-Hydroxyacid oxidative decarboxylases. The family of metal ion-dependent pyridine nucleotide-linked β-Hydroxyacid oxidative decarboxylases can be divided into two structural families with the malic enzyme, which has an (S)-Hydroxyacid substrate, comprising one subfamily and isocitrate dehydrogenase, isopropylmalate dehydrogenase, homoisocitrate dehydrogenase, and tartrate dehydrogenase, which have an (R)-Hydroxyacid substrate, comprising the second subclass. Multiple-sequence alignment of the members of the (R)-Hydroxyacid family indicates a high degree of sequence identity with most of the active site residues conserved. The three-dimensional structures of the members of the (R)-Hydroxyacid family with structures available superimpose on one another, and the active site structures of the enzymes have a similar overall geometry of residues in the substrate and metal ion binding sites. In addition, a number of residu...
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a lysine tyrosine pair carries out acid base chemistry in the metal ion dependent pyridine dinucleotide linked β Hydroxyacid oxidative decarboxylases
Biochemistry, 2009Co-Authors: Deniz F. Aktas, Paul F. CookAbstract:This work reviews published structural and kinetic data on the pyridine nucleotide-linked beta-Hydroxyacid oxidative decarboxylases. The family of metal ion-dependent pyridine nucleotide-linked beta-Hydroxyacid oxidative decarboxylases can be divided into two structural families with the malic enzyme, which has an (S)-Hydroxyacid substrate, comprising one subfamily and isocitrate dehydrogenase, isopropylmalate dehydrogenase, homoisocitrate dehydrogenase, and tartrate dehydrogenase, which have an (R)-Hydroxyacid substrate, comprising the second subclass. Multiple-sequence alignment of the members of the (R)-Hydroxyacid family indicates a high degree of sequence identity with most of the active site residues conserved. The three-dimensional structures of the members of the (R)-Hydroxyacid family with structures available superimpose on one another, and the active site structures of the enzymes have a similar overall geometry of residues in the substrate and metal ion binding sites. In addition, a number of residues in the malic enzyme active site are also conserved, and the arrangement of these residues has a similar geometry, although the (R)-Hydroxyacid and (S)-Hydroxyacid family sites are geometrically mirror images of one another. The active sites of the (R)-Hydroxyacid family have a higher positive charge density when compared to those of the (S)-Hydroxyacid family, largely due to the number of arginine residues in the vicinity of the substrate alpha-carboxylate and one fewer carboxylate ligand to the divalent metal ion. Data available for all of the enzymes in the family have been considered, and a general mechanism that makes use of a lysine (general base)-tyrosine (general acid) pair is proposed. Differences exist in the mechanism for generating the neutral form of lysine so that it can act as a base.
Veronica G Maurino - One of the best experts on this subject based on the ideXlab platform.
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A rticle Plant and Animal Glycolate Oxidases Have a Common Eukaryotic Ancestor and Convergently Duplicated to Evolve Long-Chain 2-Hydroxy Acid Oxidases
2016Co-Authors: Christian Esser, Anke Kuhn, Martin J Lercher, Georg Groth, Veronica G Maurino, Associate John TrueAbstract:Glycolate oxidase (GOX) is a crucial enzyme of plant photorespiration. The encoding gene is thought to have originated from endosymbiotic gene transfer between the eukaryotic host and the cyanobacterial endosymbiont at the base of plantae. However, animals also possess GOX activities. Plant and animal GOX belong to the gene family of (L)-2-Hydroxyacid-oxidases ((L)-2-HAOX). We find that all (L)-2-HAOX proteins in animals and archaeplastida go back to one ancestral eukaryotic sequence; the sole exceptions are green algae of the chlorophyta lineage. Chlorophyta replaced the ancestral eukaryotic (L)-2-HAOX with a bacterial ortholog, a lactate oxidase that may have been obtained through the primary endosymbiosis at the base of plantae; independent losses of this gene may explain its absence in other algal lineages (glaucophyta, rhodophyta, and charophyta). We also show that in addition to GOX, plants possess (L)-2-HAOX proteins with different specificities for medium- and long-chain Hydroxyacids (lHAOX), likely involved in fatty acid and protein catabolism. Vertebrates possess lHAOX proteins acting on similar substrates as plant lHAOX; however, the existence of GOX and lHAOX subfamilies in both plants and animals is not due to shared ancestry but is the result of convergent evolution in the two most complex eukaryotic lineages. On the basis of targeting sequences and predicted substrate specificities, we conclude that the biological role of plantae (L)-2-HAOX in photorespiration evolved by co
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plant and animal glycolate oxidases have a common eukaryotic ancestor and convergently duplicated to evolve long chain 2 hydroxy acid oxidases
Molecular Biology and Evolution, 2014Co-Authors: Christian Esser, Anke Kuhn, Martin J Lercher, Georg Groth, Veronica G MaurinoAbstract:Glycolate oxidase (GOX) is a crucial enzyme of plant photorespiration. The encoding gene is thought to have originated from endosymbiotic gene transfer between the eukaryotic host and the cyanobacterial endosymbiont at the base of plantae. However, animals also possess GOX activities. Plant and animal GOX belong to the gene family of (L)-2Hydroxyacid-oxidases ((L)-2-HAOX). We find that all (L)-2-HAOX proteins in animals and archaeplastida go back to one ancestral eukaryotic sequence; the sole exceptions are green algae of the chlorophyta lineage. Chlorophyta replaced the ancestral eukaryotic (L)-2-HAOX with a bacterial ortholog, a lactate oxidase that may have been obtained through the primary endosymbiosis at the base of plantae; independent losses of this gene may explain its absence in other algal lineages (glaucophyta, rhodophyta, and charophyta). We also show that in addition to GOX, plants possess (L)-2-HAOX proteins with different specificities for medium- and long-chain Hydroxyacids (lHAOX), likely involved in fatty acid and protein catabolism. Vertebrates possess lHAOX proteins acting on similar substrates as plant lHAOX; however, the existence of GOX and lHAOX subfamilies in both plants and animals is not due to shared ancestry but is the result of convergent evolution in the two most complex eukaryotic lineages. On the basis of targeting sequences and predicted substrate specificities, we conclude that the biological role of plantae (L)-2-HAOX in photorespiration evolved by coopting an existing peroxisomal protein.
Christian Esser - One of the best experts on this subject based on the ideXlab platform.
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A rticle Plant and Animal Glycolate Oxidases Have a Common Eukaryotic Ancestor and Convergently Duplicated to Evolve Long-Chain 2-Hydroxy Acid Oxidases
2016Co-Authors: Christian Esser, Anke Kuhn, Martin J Lercher, Georg Groth, Veronica G Maurino, Associate John TrueAbstract:Glycolate oxidase (GOX) is a crucial enzyme of plant photorespiration. The encoding gene is thought to have originated from endosymbiotic gene transfer between the eukaryotic host and the cyanobacterial endosymbiont at the base of plantae. However, animals also possess GOX activities. Plant and animal GOX belong to the gene family of (L)-2-Hydroxyacid-oxidases ((L)-2-HAOX). We find that all (L)-2-HAOX proteins in animals and archaeplastida go back to one ancestral eukaryotic sequence; the sole exceptions are green algae of the chlorophyta lineage. Chlorophyta replaced the ancestral eukaryotic (L)-2-HAOX with a bacterial ortholog, a lactate oxidase that may have been obtained through the primary endosymbiosis at the base of plantae; independent losses of this gene may explain its absence in other algal lineages (glaucophyta, rhodophyta, and charophyta). We also show that in addition to GOX, plants possess (L)-2-HAOX proteins with different specificities for medium- and long-chain Hydroxyacids (lHAOX), likely involved in fatty acid and protein catabolism. Vertebrates possess lHAOX proteins acting on similar substrates as plant lHAOX; however, the existence of GOX and lHAOX subfamilies in both plants and animals is not due to shared ancestry but is the result of convergent evolution in the two most complex eukaryotic lineages. On the basis of targeting sequences and predicted substrate specificities, we conclude that the biological role of plantae (L)-2-HAOX in photorespiration evolved by co
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plant and animal glycolate oxidases have a common eukaryotic ancestor and convergently duplicated to evolve long chain 2 hydroxy acid oxidases
Molecular Biology and Evolution, 2014Co-Authors: Christian Esser, Anke Kuhn, Martin J Lercher, Georg Groth, Veronica G MaurinoAbstract:Glycolate oxidase (GOX) is a crucial enzyme of plant photorespiration. The encoding gene is thought to have originated from endosymbiotic gene transfer between the eukaryotic host and the cyanobacterial endosymbiont at the base of plantae. However, animals also possess GOX activities. Plant and animal GOX belong to the gene family of (L)-2Hydroxyacid-oxidases ((L)-2-HAOX). We find that all (L)-2-HAOX proteins in animals and archaeplastida go back to one ancestral eukaryotic sequence; the sole exceptions are green algae of the chlorophyta lineage. Chlorophyta replaced the ancestral eukaryotic (L)-2-HAOX with a bacterial ortholog, a lactate oxidase that may have been obtained through the primary endosymbiosis at the base of plantae; independent losses of this gene may explain its absence in other algal lineages (glaucophyta, rhodophyta, and charophyta). We also show that in addition to GOX, plants possess (L)-2-HAOX proteins with different specificities for medium- and long-chain Hydroxyacids (lHAOX), likely involved in fatty acid and protein catabolism. Vertebrates possess lHAOX proteins acting on similar substrates as plant lHAOX; however, the existence of GOX and lHAOX subfamilies in both plants and animals is not due to shared ancestry but is the result of convergent evolution in the two most complex eukaryotic lineages. On the basis of targeting sequences and predicted substrate specificities, we conclude that the biological role of plantae (L)-2-HAOX in photorespiration evolved by coopting an existing peroxisomal protein.
Anke Kuhn - One of the best experts on this subject based on the ideXlab platform.
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A rticle Plant and Animal Glycolate Oxidases Have a Common Eukaryotic Ancestor and Convergently Duplicated to Evolve Long-Chain 2-Hydroxy Acid Oxidases
2016Co-Authors: Christian Esser, Anke Kuhn, Martin J Lercher, Georg Groth, Veronica G Maurino, Associate John TrueAbstract:Glycolate oxidase (GOX) is a crucial enzyme of plant photorespiration. The encoding gene is thought to have originated from endosymbiotic gene transfer between the eukaryotic host and the cyanobacterial endosymbiont at the base of plantae. However, animals also possess GOX activities. Plant and animal GOX belong to the gene family of (L)-2-Hydroxyacid-oxidases ((L)-2-HAOX). We find that all (L)-2-HAOX proteins in animals and archaeplastida go back to one ancestral eukaryotic sequence; the sole exceptions are green algae of the chlorophyta lineage. Chlorophyta replaced the ancestral eukaryotic (L)-2-HAOX with a bacterial ortholog, a lactate oxidase that may have been obtained through the primary endosymbiosis at the base of plantae; independent losses of this gene may explain its absence in other algal lineages (glaucophyta, rhodophyta, and charophyta). We also show that in addition to GOX, plants possess (L)-2-HAOX proteins with different specificities for medium- and long-chain Hydroxyacids (lHAOX), likely involved in fatty acid and protein catabolism. Vertebrates possess lHAOX proteins acting on similar substrates as plant lHAOX; however, the existence of GOX and lHAOX subfamilies in both plants and animals is not due to shared ancestry but is the result of convergent evolution in the two most complex eukaryotic lineages. On the basis of targeting sequences and predicted substrate specificities, we conclude that the biological role of plantae (L)-2-HAOX in photorespiration evolved by co
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plant and animal glycolate oxidases have a common eukaryotic ancestor and convergently duplicated to evolve long chain 2 hydroxy acid oxidases
Molecular Biology and Evolution, 2014Co-Authors: Christian Esser, Anke Kuhn, Martin J Lercher, Georg Groth, Veronica G MaurinoAbstract:Glycolate oxidase (GOX) is a crucial enzyme of plant photorespiration. The encoding gene is thought to have originated from endosymbiotic gene transfer between the eukaryotic host and the cyanobacterial endosymbiont at the base of plantae. However, animals also possess GOX activities. Plant and animal GOX belong to the gene family of (L)-2Hydroxyacid-oxidases ((L)-2-HAOX). We find that all (L)-2-HAOX proteins in animals and archaeplastida go back to one ancestral eukaryotic sequence; the sole exceptions are green algae of the chlorophyta lineage. Chlorophyta replaced the ancestral eukaryotic (L)-2-HAOX with a bacterial ortholog, a lactate oxidase that may have been obtained through the primary endosymbiosis at the base of plantae; independent losses of this gene may explain its absence in other algal lineages (glaucophyta, rhodophyta, and charophyta). We also show that in addition to GOX, plants possess (L)-2-HAOX proteins with different specificities for medium- and long-chain Hydroxyacids (lHAOX), likely involved in fatty acid and protein catabolism. Vertebrates possess lHAOX proteins acting on similar substrates as plant lHAOX; however, the existence of GOX and lHAOX subfamilies in both plants and animals is not due to shared ancestry but is the result of convergent evolution in the two most complex eukaryotic lineages. On the basis of targeting sequences and predicted substrate specificities, we conclude that the biological role of plantae (L)-2-HAOX in photorespiration evolved by coopting an existing peroxisomal protein.
