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- Author:
- Toney, Michael D.
- 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
-
http://dx.doi.org/10.1016/j.bbapap.2011.05.019
- Author:
- Limbach, Hans-Heinrich; Chan-Huot, Monique; Sharif, Shasad; Tolstoy, Peter M.; Shenderovich, Ilya G.; Denisov, Gleb S.; Toney, Michael D.
- 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
-
http://dx.doi.org/10.1016/j.bbapap.2011.06.004
- Author:
- Cellini, Barbara; Montioli, Riccardo; Voltattorni, Carla Borri
- Source:
- Biochimica et biophysica acta 2011 v.1814 no.11 pp. 1577-1584
- ISSN:
- 1878-1454
- Subject:
- alleles; binding capacity; bioinformatics; cell biology; enzymology; genotype; humans; liver; mutants; mutation; pathogenesis; patients; phenotype; pyridoxal; pyridoxine; spectral analysis
- Abstract:
- ... The hepatic peroxisomal alanine:glyoxylate aminotransferase (AGT) is a pyridoxal 5′-phosphate (PLP)-enzyme whose deficiency is responsible for Primary Hyperoxaluria Type 1 (PH1), an autosomal recessive disorder. In the last few years the knowledge of the characteristics of AGT and the transfer of this information into some pathogenic variants have significantly contributed to the improvement of th ...
- DOI:
- 10.1016/j.bbapap.2010.12.005
-
http://dx.doi.org/10.1016/j.bbapap.2010.12.005
- Author:
- Romo, Anthony J.; Liu, Hung-wen
- 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
-
http://dx.doi.org/10.1016/j.bbapap.2011.02.003
- Author:
- Ikushiro, Hiroko; Hayashi, Hideyuki
- 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
-
http://dx.doi.org/10.1016/j.bbapap.2011.02.005
- Author:
- Lin, Yen-Lin; Gao, Jiali; Rubinstein, Amir; Major, Dan Thomas
- 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
-
http://dx.doi.org/10.1016/j.bbapap.2011.05.002
- Author:
- Hunter, Gregory A.; Ferreira, Gloria C.
- 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
-
http://dx.doi.org/10.1016/j.bbapap.2010.12.015
- Author:
- Kappes, Barbara; Tews, Ivo; Binter, Alexandra; Macheroux, Peter
- 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
-
http://dx.doi.org/10.1016/j.bbapap.2011.07.018
- Author:
- Singh, Sangita; Banerjee, Ruma
- Source:
- Biochimica et biophysica acta 2011 v.1814 no.11 pp. 1518-1527
- ISSN:
- 1878-1454
- Subject:
- biochemical pathways; biogenesis; cystathionine; cystathionine beta-synthase; cystathionine gamma-lyase; cysteine; enzymology; homocysteine; hydrogen sulfide; mammals; mechanism of action; pyridoxal; sulfur
- Abstract:
- ... The role of endogenously produced H₂S in mediating varied physiological effects in mammals has spurred enormous recent interest in understanding its biology and in exploiting its pharmacological potential. In these early days in the field of H₂S signaling, large gaps exist in our understanding of its biological targets, its mechanisms of action and the regulation of its biogenesis and its clearanc ...
- DOI:
- 10.1016/j.bbapap.2011.02.004
- PubMed:
- 21315854
- PubMed Central:
- PMC3193879
-
http://dx.doi.org/10.1016/j.bbapap.2011.02.004
- Author:
- Schnackerz, Klaus D.; Andi, Babak; Cook, Paul F.
- Source:
- Biochimica et biophysica acta 2011 v.1814 no.11 pp. 1447-1458
- ISSN:
- 1878-1454
- Subject:
- enzymes; enzymology; lysine; mutation; nuclear magnetic resonance spectroscopy; pyridoxal; schiff bases; solvents
- Abstract:
- ... In this review it is demonstrated that ³¹P NMR spectroscopy can be used to elucidate information about the microenvironment around the phosphate group of enzyme-bound pyridoxal 5′-phosphate (PLP). The following information can be obtained for all PLP-dependent enzymes: 1) the protonation state of the 5′-phosphate and its exposure to solvent, and 2) tightness of binding of the 5′-phosphate. In addi ...
- DOI:
- 10.1016/j.bbapap.2011.02.001
-
http://dx.doi.org/10.1016/j.bbapap.2011.02.001
- Author:
- Frey, Perry A.; Reed, George H.
- Source:
- Biochimica et biophysica acta 2011 v.1814 no.11 pp. 1548-1557
- ISSN:
- 1878-1454
- Subject:
- active sites; catalysts; crystal structure; enzymes; enzymology; free radicals; isomerization; lysine; ornithine; pyridoxal; spectroscopy
- Abstract:
- ... PLP catalyzes the 1,2 shifts of amino groups in free radical-intermediates at the active sites of amino acid aminomutases. Free radical forms of the substrates are created upon H atom abstractions carried out by the 5′-deoxyadenosyl radical. In most of these enzymes, the 5′-deoxyadenosyl radical is generated by an iron–sulfur cluster-mediated reductive cleavage of S-adenosyl-(S)-methionine. Howeve ...
- DOI:
- 10.1016/j.bbapap.2011.03.005
-
http://dx.doi.org/10.1016/j.bbapap.2011.03.005
- Author:
- Mukherjee, Tathagata; Hanes, Jeremiah; Tews, Ivo; Ealick, Steven E.; Begley, Tadhg P.
- 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
-
http://dx.doi.org/10.1016/j.bbapap.2011.06.018
- Author:
- Mann, Stéphane; Ploux, Olivier
- Source:
- Biochimica et biophysica acta 2011 v.1814 no.11 pp. 1459-1466
- ISSN:
- 1570-9639
- Subject:
- 5-aminolevulinate synthase; Mycobacterium tuberculosis; acylation; antibiotics; biosynthesis; biotin; crystal structure; decarboxylation; enzyme inactivation; herbicides; microorganisms; pyridoxal; serine C-palmitoyltransferase; transamination
- Abstract:
- ... The four last steps of biotin biosynthesis, starting from pimeloyl-CoA, are conserved among all the biotin-producing microorganisms. Two enzymes of this pathway, the 8-amino-7-oxononanoate synthase (AONS) and the 7,8-diaminopelargonic acid aminotransferase (DAPA AT) are dependent on pyridoxal-5′-phosphate (PLP). This review summarizes our current understanding of the structure, reaction mechanism ...
- DOI:
- 10.1016/j.bbapap.2010.12.004
-
http://dx.doi.org/10.1016/j.bbapap.2010.12.004
- Author:
- Florio, Rita; di Salvo, Martino Luigi; Vivoli, Mirella; Contestabile, Roberto
- 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
-
http://dx.doi.org/10.1016/j.bbapap.2010.10.010
- Author:
- Wolosker, Herman
- Source:
- Biochimica et biophysica acta 2011 v.1814 no.11 pp. 1558-1566
- ISSN:
- 1878-1454
- Subject:
- ammonium compounds; astrocytes; brain; enzymology; metabolism; neurodegenerative diseases; neurons; pyridoxal; pyruvic acid; receptors; serine
- Abstract:
- ... d-Serine is a brain-enriched d-amino acid that works as a transmitter-like molecule by physiologically activating NMDA receptors. Synthesis of d-serine is carried out by serine racemase (SR), a pyridoxal 5′-phosphate-dependent enzyme. In addition to carry out racemization, SR α,β-eliminates water from l- or d-serine, generating pyruvate and NH₄ ⁺. Here I review the main mechanisms regulating SR ac ...
- DOI:
- 10.1016/j.bbapap.2011.01.001
-
http://dx.doi.org/10.1016/j.bbapap.2011.01.001
- Author:
- Watanabe, Nobuhiko; James, Michael N.G.
- Source:
- Biochimica et biophysica acta 2011 v.1814 no.11 pp. 1528-1533
- ISSN:
- 1878-1454
- Subject:
- Arabidopsis thaliana; antibiotics; biochemical pathways; crystal structure; enzymes; enzymology; glutamic acid; humans; lysine; pyridoxal
- Abstract:
- ... The enzymes involved in the lysine biosynthetic pathway have long been considered to be attractive targets for novel antibiotics due to the absence of this pathway in humans. Recently, a novel pyridoxal 5′-phosphate (PLP) dependent enzyme called ll-diaminopimelate aminotransferase (ll-DAP-AT) was identified in the lysine biosynthetic pathway of plants and Chlamydiae. Understanding its function and ...
- DOI:
- 10.1016/j.bbapap.2011.03.008
-
http://dx.doi.org/10.1016/j.bbapap.2011.03.008
- Author:
- Phillips, Robert S.
- 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
-
http://dx.doi.org/10.1016/j.bbapap.2010.12.003
- Author:
- Aitken, Susan M.; Lodha, Pratik H.; Morneau, Dominique J.K.
- 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
-
http://dx.doi.org/10.1016/j.bbapap.2011.03.006
- Author:
- Mozzarelli, Andrea; Bettati, Stefano; Campanini, Barbara; Salsi, Enea; Raboni, Samanta; Singh, Ratna; Spyrakis, Francesca; Kumar, Vidya Prasanna; Cook, Paul F.
- Source:
- Biochimica et biophysica acta 2011 v.1814 no.11 pp. 1497-1510
- ISSN:
- 1570-9639
- Subject:
- antibacterial properties; bacteria; biochemical pathways; catalytic activity; cysteine; cysteine synthase; enzyme activity; enzyme stability; glutathione; ligands; methionine; pyridoxal; reducing agents; serine O-acetyltransferase; spectral analysis
- Abstract:
- ... Cysteine is the final product of the reductive sulfate assimilation pathway in bacteria and plants and serves as the precursor for all sulfur-containing biological compounds, such as methionine, S-adenosyl methionine, iron–sulfur clusters and glutathione. Moreover, in several microorganisms cysteine plays a role as a reducing agent, eventually counteracting host oxidative defense strategies. Cyste ...
- DOI:
- 10.1016/j.bbapap.2011.04.011
-
http://dx.doi.org/10.1016/j.bbapap.2011.04.011
- Author:
- Richard, John P.; Amyes, Tina L.; Crugeiras, Juan; Rios, Ana
- Source:
- Biochimica et biophysica acta 2011 v.1814 no.11 pp. 1419-1425
- ISSN:
- 1878-1454
- Subject:
- acidity; energy; ions; acids; carbon; enzymatic reactions; active sites; pyridoxal; catalytic activity; ketones; enzymology
- Abstract:
- ... Experimental probes of the acidity of weak carbon acids have been developed and used to determine the carbon acid pKₐs of glycine, glycine derivatives and iminium ion adducts of glycine to the carbonyl group, including 5′-deoxypyridoxal (DPL). The high reactivity of the DPL-stabilized glycyl carbanion towards nucleophilic addition to both DPL and the glycine-DPL iminium ion favors the formation of ...
- DOI:
- 10.1016/j.bbapap.2010.12.007
- PubMed:
- 21182991
- PubMed Central:
- PMC3392957
-
http://dx.doi.org/10.1016/j.bbapap.2010.12.007
