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1. Controlling reaction specificity in pyridoxal phosphate enzymes

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

2. Critical hydrogen bonds and protonation states of pyridoxal 5′-phosphate revealed by NMR Proteins and proteomics

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

3. Human liver peroxisomal alanine:glyoxylate aminotransferase: Characterization of the two allelic forms and their pathogenic variants Proteins and proteomics

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

4. Mechanisms and structures of vitamin B₆-dependent enzymes involved in deoxy sugar biosynthesis

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

5. Mechanistic enzymology of serine palmitoyltransferase

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

6. Molecular dynamics simulations of the intramolecular proton transfer and carbanion stabilization in the pyridoxal 5′-phosphate dependent enzymes l-dopa decarboxylase and alanine racemase

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

7. Molecular enzymology of 5-Aminolevulinate synthase, the gatekeeper of heme biosynthesis

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

8. PLP-dependent enzymes as potential drug targets for protozoan diseases Proteins and proteomics

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

9. PLP-dependent H₂S biogenesis

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

10. ³¹P NMR spectroscopy senses the microenvironment of the 5′-phosphate group of enzyme-bound pyridoxal 5′-phosphate Proteins and proteomics

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

11. Pyridoxal-5′-phosphate as the catalyst for radical isomerization in reactions of PLP-dependent aminomutases Proteins and proteomics

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

12. Pyridoxal phosphate: Biosynthesis and catabolism Proteins and proteomics

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

13. Pyridoxal-5′-phosphate-dependent enzymes involved in biotin biosynthesis: Structure, reaction mechanism and inhibition Proteins and proteomics

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

14. Serine hydroxymethyltransferase: A model enzyme for mechanistic, structural, and evolutionary studies Proteins and proteomics

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

15. Serine racemase and the serine shuttle between neurons and astrocytes Proteins and proteomics

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

16. Structural insights for the substrate recognition mechanism of LL-diaminopimelate aminotransferase Proteins and proteomics

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

17. Structure, mechanism, and substrate specificity of kynureninase

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

18. The enzymes of the transsulfuration pathways: Active-site characterizations Proteins and proteomics

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

19. The multifaceted pyridoxal 5′-phosphate-dependent O-acetylserine sulfhydrylase Proteins and proteomics

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

20. The PLP cofactor: Lessons from studies on model reactions

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