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Biochimica et biophysica acta
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pyridoxal phosphate
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- Author:
- Emily J. Fogle; Michael D. Toney
- Source:
- Biochimica et biophysica acta 2011 v.1814 no.9 pp. 1113-1119
- ISSN:
- 1570-9639
- Subject:
- African trypanosomiasis; active sites; alanine; decarboxylation; drugs; microbial growth; ornithine; ornithine decarboxylase; pathogenicity; pyridoxal phosphate
- Abstract:
- ... Diaminopimelate decarboxylase (DAPDC) and ornithine decarboxylase (ODC) are pyridoxal 5'-phosphate dependent enzymes that are critical to microbial growth and pathogenicity. The latter is the target of drugs that cure African sleeping sickness, while the former is an attractive target for antibacterials. These two enzymes share the (β/α)₈ (i.e., TIM barrel) fold with alanine racemase, another pyri ...
- DOI:
- 10.1016/j.bbapap.2011.05.014
- PubMed:
- 21640851
- PubMed Central:
- PMC3124589
- https://doi.org/10.1016/j.bbapap.2011.05.014
- Author:
- Michael D. Toney
- Source:
- Biochimica et biophysica acta 2011 v.1814 no.11 pp. 1407-1418
- ISSN:
- 1878-1454
- Subject:
- nitrogen metabolism; organisms; transamination; pyridoxal phosphate; enzymes; acids; decarboxylation; amino acids; active sites; pyridoxal; enzymology
- Abstract:
- ... Pyridoxal 5′-phosphate enzymes are ubiquitous in the nitrogen metabolism of all organisms. They catalyze a wide variety of reactions including racemization, transamination, decarboxylation, elimination, retro-aldol cleavage, Claisen condensation, and others on substrates containing an amino group, most commonly α-amino acids. The wide variety of reactions catalyzed by PLP enzymes is enabled by the ...
- DOI:
- 10.1016/j.bbapap.2011.05.019
- PubMed:
- 21664990
- PubMed Central:
- PMC3359020
- https://doi.org/10.1016/j.bbapap.2011.05.019
- Author:
- Hans-Heinrich Limbach; Monique Chan-Huot; Shasad Sharif; Peter M. Tolstoy; Ilya G. Shenderovich; Gleb S. Denisov; Michael D. Toney
- Source:
- Biochimica et biophysica acta 2011 v.1814 no.11 pp. 1426-1437
- ISSN:
- 1878-1454
- Subject:
- aqueous solutions; aspartate transaminase; aspartic acid; correlation; enzymatic reactions; enzymology; histidine; hydrogen bonding; models; nitrogen; nuclear magnetic resonance spectroscopy; proteins; pyridoxal; pyridoxal phosphate; schiff bases; solvents; stable isotopes; zwitterions
- Abstract:
- ... In this contribution we review recent NMR studies of protonation and hydrogen bond states of pyridoxal 5′-phosphate (PLP) and PLP model Schiff bases in different environments, starting from aqueous solution, the organic solid state to polar organic solution and finally to enzyme environments. We have established hydrogen bond correlations that allow one to estimate hydrogen bond geometries from ¹⁵ ...
- DOI:
- 10.1016/j.bbapap.2011.06.004
- https://doi.org/10.1016/j.bbapap.2011.06.004
- Author:
- Anthony J. Romo; Hung-wen Liu
- Source:
- Biochimica et biophysica acta 2011 v.1814 no.11 pp. 1534-1547
- ISSN:
- 1878-1454
- Subject:
- bioactive properties; biosynthesis; catalytic activity; crystal structure; deoxysugars; enzymatic reactions; enzymology; pyridoxal phosphate; transaminases; transamination
- Abstract:
- ... PLP is well-regarded for its role as a coenzyme in a number of diverse enzymatic reactions. Transamination, deoxygenation, and aldol reactions mediated by PLP-dependent enzymes enliven and enrich deoxy sugar biosynthesis, endowing these compounds with unique structures and contributing to their roles as determinants of biological activity in many natural products. The importance of deoxy aminosuga ...
- DOI:
- 10.1016/j.bbapap.2011.02.003
- PubMed:
- 21315852
- PubMed Central:
- PMC3115481
- https://doi.org/10.1016/j.bbapap.2011.02.003
- Author:
- Hiroko Ikushiro; Hideyuki Hayashi
- Source:
- Biochimica et biophysica acta 2011 v.1814 no.11 pp. 1474-1480
- ISSN:
- 1878-1454
- Subject:
- biosynthesis; pyridoxal phosphate; sphingolipids; spectroscopy; enzymology; serine C-palmitoyltransferase
- Abstract:
- ... Serine palmitoyltransferase, which is one of the α-oxamine synthase family enzymes, catalyzes the condensation reaction of L-serine and palmitoyl-CoA to form 3-ketodihydrosphingosine, the first and rate-determining step of the sphingolipid biosynthesis. As with other α-oxamine synthase family enzymes, the catalytic reaction is composed of multiple elementary steps, and the mechanism to control the ...
- DOI:
- 10.1016/j.bbapap.2011.02.005
- https://doi.org/10.1016/j.bbapap.2011.02.005
- Author:
- Yen-Lin Lin; Jiali Gao; Amir Rubinstein; Dan Thomas Major
- Source:
- Biochimica et biophysica acta 2011 v.1814 no.11 pp. 1438-1446
- ISSN:
- 1878-1454
- Subject:
- L-dopa; active sites; alanine; aqueous solutions; carbon; decarboxylation; deuterium; energy; enzymes; enzymology; gases; molecular dynamics; pyridoxal; pyridoxal phosphate; schiff bases; solvents; stable isotopes
- Abstract:
- ... Molecular dynamics simulations using a combined quantum mechanical and molecular mechanical (QM/MM) potential have been carried out to investigate the internal proton transfer equilibrium of the external aldimine species in l-dopa decarboxylase, and carbanion stabilization by the enzyme cofactor in the active site of alanine racemase. Solvent effects lower the free energy of the O-protonated PLP t ...
- DOI:
- 10.1016/j.bbapap.2011.05.002
- PubMed:
- 21600315
- PubMed Central:
- PMC3780614
- https://doi.org/10.1016/j.bbapap.2011.05.002
- Author:
- Gregory A. Hunter; Gloria C. Ferreira
- Source:
- Biochimica et biophysica acta 2011 v.1814 no.11 pp. 1467-1473
- ISSN:
- 1878-1454
- Subject:
- 5-aminolevulinate synthase; active sites; amino acids; anemia; biochemical pathways; biosynthesis; catalytic activity; dissociation; energy; enzymology; fungi; gene expression regulation; heme; humans; mitochondria; mutation; pyridoxal phosphate
- Abstract:
- ... Pyridoxal-5'-phosphate (PLP) is an obligatory cofactor for the homodimeric mitochondrial enzyme 5-aminolevulinate synthase (ALAS), which controls metabolic flux into the porphyrin biosynthetic pathway in animals, fungi, and the α-subclass of proteobacteria. Recent work has provided an explanation for how this enzyme can utilize PLP to catalyze the mechanistically unusual cleavage of not one but tw ...
- DOI:
- 10.1016/j.bbapap.2010.12.015
- PubMed:
- 21215825
- PubMed Central:
- PMC3090494
- https://doi.org/10.1016/j.bbapap.2010.12.015
- Author:
- Barbara Kappes; Ivo Tews; Alexandra Binter; Peter Macheroux
- Source:
- Biochimica et biophysica acta 2011 v.1814 no.11 pp. 1567-1576
- ISSN:
- 1878-1454
- Subject:
- Protozoa; drugs; enzymatic reactions; enzymes; enzymology; parasites; physicochemical properties; pyridoxal phosphate; pyridoxine
- Abstract:
- ... The chemical properties of the B₆ vitamers are uniquely suited for wide use as cofactors in essential reactions, such as decarboxylations and transaminations. This review addresses current efforts to explore vitamin B₆ dependent enzymatic reactions as drug targets. Several current targets are described that are found amongst these enzymes. The focus is set on diseases caused by protozoan parasites ...
- DOI:
- 10.1016/j.bbapap.2011.07.018
- https://doi.org/10.1016/j.bbapap.2011.07.018
- Author:
- Tathagata Mukherjee; Jeremiah Hanes; Ivo Tews; Steven E. Ealick; Tadhg P. Begley
- Source:
- Biochimica et biophysica acta 2011 v.1814 no.11 pp. 1585-1596
- ISSN:
- 1878-1454
- Subject:
- biosynthesis; chemical reactions; enzymes; enzymology; fungi; oxidative stress; protective effect; pyridoxal phosphate; pyridoxine; singlet oxygen
- Abstract:
- ... Vitamin B₆ is an essential cofactor that participates in a large number of biochemical reactions. Pyridoxal phosphate is biosynthesized de novo by two different pathways (the DXP dependent pathway and the R5P pathway) and can also be salvaged from the environment. It is one of the few cofactors whose catabolic pathway has been comprehensively characterized. It is also known to function as a single ...
- DOI:
- 10.1016/j.bbapap.2011.06.018
- https://doi.org/10.1016/j.bbapap.2011.06.018
- Author:
- Rita Florio; Martino Luigi di Salvo; Mirella Vivoli; Roberto Contestabile
- Source:
- Biochimica et biophysica acta 2011 v.1814 no.11 pp. 1489-1496
- ISSN:
- 1878-1454
- Subject:
- enzymology; glycine hydroxymethyltransferase; metabolism; mutants; pyridoxal; pyridoxal phosphate; serine
- Abstract:
- ... Serine hydroxymethyltransferase is a ubiquitous representative of the family of fold type I, pyridoxal 5′-phosphate-dependent enzymes. The reaction catalyzed by this enzyme, the reversible transfer of the Cβ of serine to tetrahydropteroylglutamate, represents a link between amino acid and folates metabolism and operates as a major source of one-carbon units for several essential biosynthetic proce ...
- DOI:
- 10.1016/j.bbapap.2010.10.010
- https://doi.org/10.1016/j.bbapap.2010.10.010
- Author:
- Robert S. Phillips
- Source:
- Biochimica et biophysica acta 2011 v.1814 no.11 pp. 1481-1488
- ISSN:
- 1878-1454
- Subject:
- Pseudomonas fluorescens; active sites; bacteria; crystallography; fungi; humans; kynurenine; kynurenine pathway; metabolism; mixing; mutants; pyridoxal phosphate; site-directed mutagenesis; substrate specificity; tryptophan
- Abstract:
- ... The kynurenine pathway is the major route for tryptophan catabolism in animals and some fungi and bacteria. The procaryotic enzyme preferentially reacts with l-kynurenine, while eucaryotic kynureninases exhibit higher activity with 3-hydroxy-l-kynurenine. Crystallography of kynureninases from Pseudomonas fluorescens (PfKyn) and Homo sapiens (HsKyn) shows that the active sites are nearly identical, ...
- DOI:
- 10.1016/j.bbapap.2010.12.003
- PubMed:
- 21167323
- PubMed Central:
- PMC3102132
- https://doi.org/10.1016/j.bbapap.2010.12.003
- Author:
- Susan M. Aitken; Pratik H. Lodha; Dominique J.K. Morneau
- Source:
- Biochimica et biophysica acta 2011 v.1814 no.11 pp. 1511-1517
- ISSN:
- 1878-1454
- Subject:
- active sites; animals; anti-infective agents; bacteria; cystathionine; cystathionine beta-synthase; cystathionine gamma-lyase; cysteine; engineering; enzymology; pyridoxal; pyridoxal phosphate; therapeutics; yeasts
- Abstract:
- ... The diversity of reactions catalyzed by enzymes reliant on pyridoxal 5′-phosphate (PLP) demonstrates the catalytic versatility of this cofactor and the plasticity of the protein scaffolds of the major fold types of PLP-dependent enzymes. The enzymes of the transsulfuration (cystathionine γ-synthase and cystathionine β-lyase) and reverse transsulfuration (cystathionine β-synthase and cystathionine ...
- DOI:
- 10.1016/j.bbapap.2011.03.006
- https://doi.org/10.1016/j.bbapap.2011.03.006
- Author:
- Martino Luigi di Salvo; Roberto Contestabile; Martin K. Safo
- Source:
- Biochimica et biophysica acta 2011 v.1814 no.11 pp. 1597-1608
- ISSN:
- 1570-9639
- Subject:
- animals; enzymatic reactions; enzymes; enzymology; homeostasis; metabolism; pyridoxal; pyridoxal phosphate; pyridoxamine; pyridoxine
- Abstract:
- ... Vitamin B₆ is a generic term referring to pyridoxine, pyridoxamine, pyridoxal and their related phosphorylated forms. Pyridoxal 5′-phosphate is the catalytically active form of vitamin B₆, and acts as cofactor in more than 140 different enzyme reactions. In animals, pyridoxal 5′-phosphate is recycled from food and from degraded B₆-enzymes in a “salvage pathway”, which essentially involves two ubiq ...
- DOI:
- 10.1016/j.bbapap.2010.12.006
- https://doi.org/10.1016/j.bbapap.2010.12.006
- Author:
- Davide Schiroli; Alessio Peracchi
- Source:
- Biochimica et biophysica acta 2015 v.1854 no.9 pp. 1200-1211
- ISSN:
- 1570-9639
- Subject:
- amines; catalysts; proteins; pyridoxal phosphate; transaminases; variance
- Abstract:
- ... The present review focuses on a subfamily of pyridoxal phosphate (PLP)-dependent enzymes, belonging to the broader fold-type I structural group and whose archetypes can be considered ornithine δ-transaminase and γ-aminobutyrate transaminase. These proteins were originally christened “subgroup-II aminotransferases” (AT-II) but are very often referred to as “class-III aminotransferases”. As names su ...
- DOI:
- 10.1016/j.bbapap.2015.02.023
- https://doi.org/10.1016/j.bbapap.2015.02.023
- Author:
- Robert S. Phillips
- Source:
- Biochimica et biophysica acta 2015 v.1854 no.9 pp. 1167-1174
- ISSN:
- 1570-9639
- Subject:
- alanine; catalytic activity; decarboxylation; enzymes; kynurenine; phenol; phosphates; proteins; pyridoxal phosphate; reaction mechanisms; transamination; tyrosine
- Abstract:
- ... Pyridoxal-5′-phosphate (PLP) is a versatile cofactor that enzymes use to catalyze a wide variety of reactions of amino acids, including transamination, decarboxylation, racemization, β- and γ-eliminations and substitutions, retro-aldol and Claisen reactions. These reactions depend on the ability of PLP to stabilize, to a varying degree, α-carbanionic intermediates. Furthermore, oxidative decarboxy ...
- DOI:
- 10.1016/j.bbapap.2014.12.028
- https://doi.org/10.1016/j.bbapap.2014.12.028
- Author:
- Jared L. Taylor; Joseph E. Price; Michael D. Toney
- Source:
- Biochimica et biophysica acta 2015 v.1854 no.2 pp. 146-155
- ISSN:
- 1570-9639
- Subject:
- active sites; catalytic activity; clones; decarboxylation; denaturation; directed evolution; molecular dynamics; mutants; mutation; pyridoxal phosphate; substrate specificity; transamination
- Abstract:
- ... Dialkylglycine decarboxylase (DGD) is an unusual pyridoxal phosphate dependent enzyme that catalyzes decarboxylation in the first and transamination in the second half-reaction of its ping-pong catalytic cycle. Directed evolution was employed to alter the substrate specificity of DGD from 2-aminoisobutyrate (AIB) to 1-aminocyclohexane-1-carboxylate (AC6C). Four rounds of directed evolution led to ...
- DOI:
- 10.1016/j.bbapap.2014.12.003
- PubMed:
- 25500286
- PubMed Central:
- PMC4334570
- https://doi.org/10.1016/j.bbapap.2014.12.003
- Author:
- Magnus Monné; Daniela Valeria Miniero; Toshihiro Obata; Lucia Daddabbo; Luigi Palmieri; Angelo Vozza; M. Cristina Nicolardi; Alisdair R. Fernie; Ferdinando Palmieri
- Source:
- Biochimica et biophysica acta 2015 v.1847 no.10 pp. 1220-1230
- ISSN:
- 0005-2728
- Subject:
- Arabidopsis thaliana; EDTA (chelating agent); adenosine; adenosine diphosphate; adenosine monophosphate; adenosine triphosphate; calcium; ethylene glycol tetraacetic acid; flowers; gene expression; genes; humans; leaves; membrane proteins; mitochondria; mitochondrial membrane; phosphates; pyridoxal phosphate; seedlings; sulfates; thiosulfates; transcription (genetics)
- Abstract:
- ... The Arabidopsis thaliana genome contains 58 membrane proteins belonging to the mitochondrial carrier family. Three members of this family, here named AtAPC1, AtAPC2, and AtAPC3, exhibit high structural similarities to the human mitochondrial ATP–Mg2+/phosphate carriers. Under normal physiological conditions the AtAPC1 gene was expressed at least five times more than the other two AtAPC genes in fl ...
- DOI:
- 10.1016/j.bbabio.2015.06.015
- https://doi.org/10.1016/j.bbabio.2015.06.015
- Author:
- Alessandra Astegno; Guido Capitani; Paola Dominici
- Source:
- Biochimica et biophysica acta 2015 v.1854 no.9 pp. 1229-1237
- ISSN:
- 1570-9639
- Subject:
- Arabidopsis thaliana; calcium; calmodulin; crystal structure; dissociation; glutamate decarboxylase; glutamic acid; mutants; oligomerization; pH; pyridoxal; pyridoxal phosphate; site-directed mutagenesis
- Abstract:
- ... Glutamate decarboxylase (GAD) is a pyridoxal 5′-phosphate (PLP)-dependent enzyme that catalyzes the α-decarboxylation of glutamate to γ-aminobutyrate. A unique feature of plant GAD is the presence of a calmodulin (CaM)-binding domain at its C-terminus. In plants, transient elevation of cytosolic Ca²⁺ in response to different types of stress is responsible for GAD activation via CaM. The crystal st ...
- DOI:
- 10.1016/j.bbapap.2015.01.001
- https://doi.org/10.1016/j.bbapap.2015.01.001
- Author:
- Riccardo Montioli; Elisa Oppici; Mirco Dindo; Alessandro Roncador; Giovanni Gotte; Barbara Cellini; Carla Borri Voltattorni
- Source:
- Biochimica et biophysica acta 2015 v.1854 no.10 pp. 1280-1289
- ISSN:
- 1570-9639
- Subject:
- Escherichia coli; alleles; binding capacity; denaturation; dissociation; dose response; haplotypes; liver; mammals; missense mutation; mitochondria; patients; peroxisomes; proteolysis; pyridoxal; pyridoxal phosphate; pyridoxine; therapeutics
- Abstract:
- ... Liver peroxisomal alanine:glyoxylate aminotransferase (AGT), a pyridoxal 5′-phosphate (PLP) enzyme, exists as two polymorphic forms, the major (AGT-Ma) and the minor (AGT-Mi) haplotype. Deficit of AGT causes Primary Hyperoxaluria Type 1 (PH1), an autosomal recessive rare disease. Although ~one-third of the 79 disease-causing missense mutations segregates on AGT-Mi, only few of them are well charac ...
- DOI:
- 10.1016/j.bbapap.2015.07.002
- https://doi.org/10.1016/j.bbapap.2015.07.002
- Author:
- Soumya G. Remesh; Mohini S. Ghatge; Mostafa H. Ahmed; Faik N. Musayev; Amit Gandhi; Nadia Chowdhury; Martino L. di Salvo; Glen E. Kellogg; Roberto Contestabile; Verne Schirch; Martin K. Safo
- Source:
- Biochimica et biophysica acta 2015 v.1854 no.4 pp. 278-283
- ISSN:
- 1570-9639
- Subject:
- Escherichia coli; acids; active sites; catalytic activity; crystal structure; drugs; fructose-bisphosphate aldolase; histidine; pH; pyridoxal; pyridoxal phosphate; serine; threonine
- Abstract:
- ... l-Threonine aldolases (TAs), a family of enzymes belonging to the fold-type I pyridoxal 5′-phosphate (PLP) dependent enzymes, play a role in catalyzing the reversible cleavage of l-3-hydroxy-α-amino acids to glycine and the corresponding aldehydes. Threonine aldolases have great biotechnological potential for the syntheses of pharmaceutically relevant drug molecules because of their stereospecific ...
- DOI:
- 10.1016/j.bbapap.2014.12.023
- PubMed:
- 25560296
- PubMed Central:
- PMC4323617
- https://doi.org/10.1016/j.bbapap.2014.12.023