101
|
Abstract
AbstractSix allozymes of aspartate aminotransferase (AAT, EC 2.6.1.1): three plastidial (AAT-2 zone) and three cytosolic (AAT-3 zone) were isolated from common wheat (Triticum aestivum) seedlings and highly purified by a five-step purification procedure. The identity of the studied proteins was confirmed by mass spectrometry. The molecular weight of AAT allozymes determined by gel filtration was 72.4±3.6 kDa. The molecular weights of plastidial and cytosolic allozymes estimated by SDS-PAGE were 45.3 and 43.7 kDa, respectively. The apparent Michaelis constant (K
m) values determined for four substrates appeared to be very similar for each allozyme. The values of the turnover number (k
cat) and the k
cat/K
m ratio calculated for allozymes with L-aspartate as a leading substrate were in the range of 88.5–103.8 s−1/10,412–10,795 s−1 M−1 for AAT-2 zone and 4.6–7.0 s−1/527–700 s−1 M−1 for AAT-3 zone. These results clearly demonstrated much higher catalytic efficiency of AAT-2 allozymes. Therefore, partial sequences of cDNA encoding AATs from different zones were obtained using the RT-PCR technique. Comparison of the AAT-2 and AAT-3 amino acid sequences from active site regions revealed five non-conservative substitutions, which impact on the observed differences in the isozymes catalytic efficiency is discussed.
Collapse
|
102
|
Tibhe JD, Fu H, Noël T, Wang Q, Meuldijk J, Hessel V. Flow synthesis of phenylserine using threonine aldolase immobilized on Eupergit support. Beilstein J Org Chem 2013; 9:2168-79. [PMID: 24204429 PMCID: PMC3817483 DOI: 10.3762/bjoc.9.254] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 09/24/2013] [Indexed: 11/23/2022] Open
Abstract
Threonine aldolase (TA) from Thermotoga maritima was immobilized on an Eupergit support by both a direct and an indirect method. The incubation time for the direct immobilization method was optimized for the highest amount of enzyme on the support. By introducing the immobilized TA in a packed-bed microreactor, a flow synthesis of phenylserine was developed, and the effects of temperature and residence time were studied in particular. Calculations of the Damköhler number revealed that no mass transfer limitations are given in the micro-interstices of the packed bed. The yield does not exceed 40% and can be rationalized by the natural equilibrium as well as product inhibition which was experimentally proven. The flow synthesis with the immobilized enzyme was compared with the corresponding transformation conducted with the free enzyme. The product yield was further improved by operating under slug flow conditions which is related to the very short residence time distribution. In all cases 20% diastereomeric excess (de) and 99% enantiomeric excess (ee) were observed. A continuous run of the reactant solution was carried out for 10 hours in order to check enzyme stability at higher temperature. Stable operation was achieved at 20 minute residence time. Finally, the productivity of the reactor was calculated, extrapolated to parallel run units, and compared with data collected previously.
Collapse
Affiliation(s)
- Jagdish D Tibhe
- Micro Flow Chemistry and Process Technology, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, the Netherlands
| | | | | | | | | | | |
Collapse
|
103
|
Jordan F, Patel H. Catalysis in Enzymatic Decarboxylations: Comparison of Selected Cofactor-dependent and Cofactor-independent Examples. ACS Catal 2013; 3:1601-1617. [PMID: 23914308 DOI: 10.1021/cs400272x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
This review is focused on three types of enzymes decarboxylating very different substrates: (1) Thiamin diphosphate (ThDP)-dependent enzymes reacting with 2-oxo acids; (2) Pyridoxal phosphate (PLP)-dependent enzymes reacting with α-amino acids; and (3) An enzyme with no known co-factors, orotidine 5'-monophosphate decarboxylase (OMPDC). While the first two classes have been much studied for many years, during the past decade studies of both classes have revealed novel mechanistic insight challenging accepted understanding. The enzyme OMPDC has posed a challenge to the enzymologist attempting to explain a 1017-fold rate acceleration in the absence of cofactors or even metal ions. A comparison of the available evidence on the three types of decarboxylases underlines some common features and more differences. The field of decarboxylases remains an interesting and challenging one for the mechanistic enzymologist notwithstanding the large amount of information already available.
Collapse
Affiliation(s)
- Frank Jordan
- Department of Chemistry, Rutgers, The State University of New Jersey, 73 Warren Street, Newark,
New Jersey 07102, United States
| | - Hetalben Patel
- Department of Chemistry, Rutgers, The State University of New Jersey, 73 Warren Street, Newark,
New Jersey 07102, United States
| |
Collapse
|
104
|
Kim S, Kim KJ. Cloning, expression, purification, crystallization and X-ray crystallographic analysis of Rv2606c from Mycobacterium tuberculosis H37Rv. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:578-80. [PMID: 23695582 PMCID: PMC3660906 DOI: 10.1107/s1744309113010683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 04/19/2013] [Indexed: 11/10/2022]
Abstract
Tuberculosis is a widespread and deadly infectious disease, and one third of the human population is already infected. Vitamin B6 is known to be synthesized through consecutive reactions mediated by pyridoxal biosynthesis lyase (PdxS) and glutamine amidotransferase (PdxT). The gene product Rv2606c, the PdxS pyridoxal biosynthesis lyase from Mycobacterium tuberculosis, was crystallized using the hanging-drop vapour-diffusion method in the presence of 8%(w/v) PEG 8000, 0.1 M 3-(cyclohexylamino)-1-propanesulfonic acid pH 10.5 and 0.2 M sodium chloride at 295 K. X-ray diffraction data were collected to a maximum resolution of 1.7 Å on a synchrotron beamline. The crystal belonged to space group I222 or I212121, with unit-cell parameters a = 110.75, b = 126.08, c = 180.82 Å, α = β = γ = 90°. With three molecules per asymmetric unit, the crystal volume per unit protein weight (VM) was 3.79 Å(3) Da(-1).
Collapse
Affiliation(s)
- Sangwoo Kim
- School of Life Science and Biotechnology, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Science and Biotechnology, Kyungpook National University, Daegu 702-701, Republic of Korea
| |
Collapse
|
105
|
Crystal structure of Mycobacterium tuberculosis Rv2606c: a pyridoxal biosynthesis lyase. Biochem Biophys Res Commun 2013; 435:255-9. [PMID: 23643787 DOI: 10.1016/j.bbrc.2013.04.068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 04/23/2013] [Indexed: 11/24/2022]
Abstract
Tuberculosis is a lethal infectious disease caused by Mycobacterium tuberculosis. We determined the crystal structure of Rv2606c, a potential pyridoxal biosynthesis lyase (PdxS), from M. tuberculosis H37Rv at 1.8 Å resolution. The overall structure of the protein, composed of a (β/α)8-barrel and two small 310-helices, was quite similar to those of other PdxS proteins. A glycerol molecule was observed to be bound at the active site of the Rv2606c structure through interactions with the conserved residues of Asp29 and Lys86, providing information regarding the potential active site and the substrate-binding environment of the protein. The interface for Rv2606c dodecamerization, which is primarily mediated by salt bridges and hydrophobic interactions, was quite different from those of other PdxS proteins. Furthermore, we observed that the Rv2606c and Rv2604c form a stable complex, suggesting that these proteins might function as PdxS and PdxT in M. tuberculosis.
Collapse
|
106
|
Mandal S, Modak R, Goswami S. Synthesis and characterization of a copper(II) complex of a ONN donor Schiff base ligand derived from pyridoxal and 2-(pyrid-2-yl)ethylamine – A novel pyridoxal based fluorescent probe. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.01.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
107
|
A 1-step microplate method for assessing the substrate range of l-α-amino acid aminotransferase. Enzyme Microb Technol 2013; 52:218-25. [DOI: 10.1016/j.enzmictec.2013.02.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Revised: 02/13/2013] [Accepted: 02/14/2013] [Indexed: 11/20/2022]
|
108
|
Paul L, Ueland PM, Selhub J. Mechanistic perspective on the relationship between pyridoxal 5'-phosphate and inflammation. Nutr Rev 2013; 71:239-44. [PMID: 23550784 DOI: 10.1111/nure.12014] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A variety of inflammatory disease conditions have been found to be associated with low levels of plasma pyridoxal 5'-phosphate (PLP), the active form of vitamin B6 , without any indication of a lower dietary intake of vitamin B6 , excessive catabolism of the vitamin, or congenital defects in its metabolism. The present review was conducted to examine the existing literature in this regard. Current evidence suggests that the inverse association between plasma PLP and inflammation may be the result of mobilization of this coenzyme to the site of inflammation, for use by the PLP-dependent enzymes of the kynurenine pathway of tryptophan degradation, metabolism of the immunomodulatory sphingolipids, ceramide and sphingosine 1-phosphate, and for serine hydroxymethylase for immune cell proliferation.
Collapse
Affiliation(s)
- Ligi Paul
- JM USDA HNRC, Tufts University, Boston, Massachusetts 02111, USA
| | | | | |
Collapse
|
109
|
Singh VP, Poon JF, Engman L. Turning Pyridoxine into a Catalytic Chain-Breaking and Hydroperoxide-Decomposing Antioxidant. J Org Chem 2013; 78:1478-87. [DOI: 10.1021/jo3024297] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Vijay P. Singh
- Department of Chemistry−BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Jia-fei Poon
- Department of Chemistry−BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Lars Engman
- Department of Chemistry−BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| |
Collapse
|
110
|
Kezuka Y, Yoshida Y, Nonaka T. Structural insights into catalysis by βC-S lyase from Streptococcus anginosus. Proteins 2012; 80:2447-58. [DOI: 10.1002/prot.24129] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 05/29/2012] [Accepted: 05/31/2012] [Indexed: 11/11/2022]
|
111
|
Gökcan H, Konuklar FAS. Theoretical study on HF elimination and aromatization mechanisms: a case of pyridoxal 5' phosphate-dependent enzyme. J Org Chem 2012; 77:5533-43. [PMID: 22646918 DOI: 10.1021/jo3005815] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyridoxal 5-phosphate (PLP), the phosphorylated and the oxidized form of vitamin B6 is an organic cofactor. PLP forms a Schiff base with the ϵ-amino group of a lysine residue of PLP-dependent enzymes. γ-Aminobutyric acid (GABA) aminotransferase is a PLP-dependent enzyme that degrades GABA to succinic semialdehyde, while reduction of GABA concentration in the brain causes convolution besides several neurological diseases. The fluorine-containing substrate analogues for the inactivation of the GABA-AT are synthesized extensively in cases where the inactivation mechanisms involve HF elimination. Although two proposed mechanisms are present for the HF elimination, the details of the base-induced HF elimination are not well identified. In this density functional theory (DFT) study, fluorine-containing substrate analogue, 5-amino-2-fluorocyclohex-3-enecarboxylic acid, is particularly chosen in order to explain the details of the HF elimination reactions. On the other hand, the experimental studies revealed that aromatization competes with Michael addition mechanism in the presence of 5-amino-2-fluorocyclohex-3-enecarboxylic acid. The results allowed us to draw a conclusion for the nature of HF elimination, besides the elucidation of the mechanism preference for the inactivation mechanism. Furthermore, the solvent phase calculations carried out in this study ensure that the proton transfer steps should be assisted either by a water molecule or a base for lower activation energy barriers.
Collapse
Affiliation(s)
- Hatice Gökcan
- Informatics Institute, Computational Science and Engineering Programme, Istanbul Technical University, Ayazağa Campus 34469, Maslak, Istanbul, Turkey
| | | |
Collapse
|
112
|
Yoon HJ, Jung H, Ahn YS, Nandhakumar R, Kim JS, Kim KM. The Chirality Conversion Reagent for Amino Acids Based on Salicyl Aldehyde. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.5.1715] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
113
|
Hawkins NA, Kearney JA. Confirmation of an epilepsy modifier locus on mouse chromosome 11 and candidate gene analysis by RNA-Seq. GENES BRAIN AND BEHAVIOR 2012; 11:452-60. [PMID: 22471526 DOI: 10.1111/j.1601-183x.2012.00790.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Epilepsy is a neurological disorder affecting approximately 1% of the worldwide population. Mutations in voltage-gated sodium channels have been identified in several monogenic epilepsy syndromes. Over 800 mutations have been identified in the voltage-gated sodium channel genes SCN1A and SCN2A in human epilepsies, including genetic epilepsy with febrile seizures plus (GEFS+) and Dravet syndrome. In GEFS+ families, affected members with the same mutation often display variability in clinical severity of the disease. This suggests that additional genes modify the effect of the primary mutation, resulting in the variable clinical presentation. The Scn2a(Q54) transgenic mouse model has an epilepsy phenotype that varies depending on the genetic strain background. Scn2a(Q54) mice congenic on the C57BL/6J strain exhibit delayed seizure onset and improved survival compared to (C57BL/6J × SJL/J)F1.Q54 mice. Two modifier loci of Scn2a(Q54) seizure susceptibility were mapped and designated Moe1 (modifier of epilepsy) on chromosome (chr) 11 and Moe2 on chr 19. To confirm Moe1 and refine its position, we generated interval-specific congenic lines carrying C57BL/6J-derived chr 11 alleles on the SJL/J strain and refined the map position to 89-104 Mb. We then used RNA-Seq for candidate analysis in the modifier region. C57BL/6J and SJL/J male and female brain RNAs were sequenced, revealing numerous significant transcriptome differences and coding single-nucleotide polymorphisms. Additional consideration of gene function and expression suggested several strong candidate modifier genes, including two voltage-gated calcium channel subunits, Cacna1g and Cacnb1, and the proline and acidic amino acid-rich basic leucine zipper transcription factor, Hlf.
Collapse
Affiliation(s)
- N A Hawkins
- Neuroscience Program Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | |
Collapse
|
114
|
Humble MS, Cassimjee KE, Håkansson M, Kimbung YR, Walse B, Abedi V, Federsel HJ, Berglund P, Logan DT. Crystal structures of the Chromobacterium violaceumω-transaminase reveal major structural rearrangements upon binding of coenzyme PLP. FEBS J 2012; 279:779-92. [PMID: 22268978 DOI: 10.1111/j.1742-4658.2012.08468.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
UNLABELLED The bacterial ω-transaminase from Chromobacterium violaceum (Cv-ωTA, EC2.6.1.18) catalyses industrially important transamination reactions by use of the coenzyme pyridoxal 5'-phosphate (PLP). Here, we present four crystal structures of Cv-ωTA: two in the apo form, one in the holo form and one in an intermediate state, at resolutions between 1.35 and 2.4 Å. The enzyme is a homodimer with a molecular mass of ∼ 100 kDa. Each monomer has an active site at the dimeric interface that involves amino acid residues from both subunits. The apo-Cv-ωTA structure reveals unique 'relaxed' conformations of three critical loops involved in structuring the active site that have not previously been seen in a transaminase. Analysis of the four crystal structures reveals major structural rearrangements involving elements of the large and small domains of both monomers that reorganize the active site in the presence of PLP. The conformational change appears to be triggered by binding of the phosphate group of PLP. Furthermore, one of the apo structures shows a disordered 'roof ' over the PLP-binding site, whereas in the other apo form and the holo form the 'roof' is ordered. Comparison with other known transaminase crystal structures suggests that ordering of the 'roof' structure may be associated with substrate binding in Cv-ωTA and some other transaminases. DATABASE The atomic coordinates and structure factors for the Chromobacterium violaceumω-transaminase crystal structures can be found in the RCSB Protein Data Bank (http://www.rcsb.org) under the accession codes 4A6U for the holoenzyme, 4A6R for the apo1 form, 4A6T for the apo2 form and 4A72 for the mixed form STRUCTURED DIGITAL ABSTRACT • -transaminases and -transaminases bind by dynamic light scattering (View interaction) • -transaminase and -transaminase bind by x-ray crystallography (View interaction) • -transaminase and -transaminase bind by x-ray crystallography (View interaction).
Collapse
Affiliation(s)
- Maria S Humble
- Division of Biochemistry, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | | | | | | | | | | | | | | |
Collapse
|
115
|
Saenko SV, Jerónimo MA, Beldade P. Genetic basis of stage-specific melanism: a putative role for a cysteine sulfinic acid decarboxylase in insect pigmentation. Heredity (Edinb) 2012; 108:594-601. [PMID: 22234245 DOI: 10.1038/hdy.2011.127] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Melanism, the overall darkening of the body, is a widespread form of animal adaptation to particular environments, and includes bookcase examples of evolution by natural selection, such as industrial melanism in the peppered moth. The major components of the melanin biosynthesis pathway have been characterized in model insects, but little is known about the genetic basis of life-stage specific melanism such as cases described in some lepidopteran species. Here, we investigate two melanic mutations of Bicyclus anynana butterflies, called Chocolate and melanine, that exclusively affect pigmentation of the larval and adult stages, respectively. Our analysis of Mendelian segregation patterns reveals that the larval and adult melanic phenotypes are due to alleles at different, independently segregating loci. Our linkage mapping analysis excludes the pigmentation candidate gene black as the melanine locus, and implicates a gene encoding a putative pyridoxal phosphate-dependant cysteine sulfinic acid decarboxylase as the Chocolate locus. We show variation in coding sequence and in expression levels for this candidate larval melanism locus. This is the first study that suggests a biological function for this gene in insects. Our findings open up exciting opportunities to study the role of this locus in the evolution of adaptive variation in pigmentation, and the uncoupling of regulation of pigment biosynthesis across developmental stages with different ecologies and pressures on body coloration.
Collapse
Affiliation(s)
- S V Saenko
- Institute of Biology, Leiden University, Leiden, The Netherlands.
| | | | | |
Collapse
|
116
|
Serine hydroxymethyltransferase: A model enzyme for mechanistic, structural, and evolutionary studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1489-96. [DOI: 10.1016/j.bbapap.2010.10.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Revised: 10/25/2010] [Accepted: 10/29/2010] [Indexed: 11/18/2022]
|
117
|
Conti P, Tamborini L, Pinto A, Blondel A, Minoprio P, Mozzarelli A, De Micheli C. Drug Discovery Targeting Amino Acid Racemases. Chem Rev 2011; 111:6919-46. [DOI: 10.1021/cr2000702] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Paola Conti
- Dipartimento di Scienze Farmaceutiche “P. Pratesi”, via Mangiagalli 25, 20133 Milano, Italy
| | - Lucia Tamborini
- Dipartimento di Scienze Farmaceutiche “P. Pratesi”, via Mangiagalli 25, 20133 Milano, Italy
| | - Andrea Pinto
- Dipartimento di Scienze Farmaceutiche “P. Pratesi”, via Mangiagalli 25, 20133 Milano, Italy
| | - Arnaud Blondel
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS-URA 2185, Département de Biologie Structurale et Chimie, 25 rue du Dr. Roux, 75724 Paris, France
| | - Paola Minoprio
- Institut Pasteur, Laboratoire des Processus Infectieux à Trypanosoma; Département d’Infection et Epidémiologie; 25 rue du Dr. Roux, 75724 Paris, France
| | - Andrea Mozzarelli
- Dipartimento di Biochimica e Biologia Molecolare, via G. P. Usberti 23/A, 43100 Parma, Italy
- Istituto di Biostrutture e Biosistemi, viale Medaglie d’oro, Roma, Italy
| | - Carlo De Micheli
- Dipartimento di Scienze Farmaceutiche “P. Pratesi”, via Mangiagalli 25, 20133 Milano, Italy
| |
Collapse
|
118
|
McIntyre CL, Casu RE, Rattey A, Dreccer MF, Kam JW, van Herwaarden AF, Shorter R, Xue GP. Linked gene networks involved in nitrogen and carbon metabolism and levels of water-soluble carbohydrate accumulation in wheat stems. Funct Integr Genomics 2011; 11:585-97. [PMID: 21789636 DOI: 10.1007/s10142-011-0232-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 06/07/2011] [Accepted: 06/17/2011] [Indexed: 11/25/2022]
Abstract
High levels of water-soluble carbohydrates (WSC) provide an important source of stored assimilate for grain filling in wheat. To better understand the interaction between carbohydrate metabolism and other metabolic processes associated with the WSC trait, a genome-wide expression analysis was performed using eight field-grown lines from the high and low phenotypic tails of a wheat population segregating for WSC and the Affymetrix wheat genome array. The 259 differentially expressed probe sets could be assigned to 26 functional category bins, as defined using MapMan software. There were major differences in the categories to which the differentially expressed probe sets were assigned; for example, probe sets upregulated in high relative to low WSC lines were assigned to category bins such as amino acid metabolism, protein degradation and transport and to be involved in starch synthesis-related processes (carbohydrate metabolism bin), whereas downregulated probe sets were assigned to cell wall-related bins, amino acid synthesis and stress and were involved in sucrose breakdown. Using the set of differentially expressed genes as input, chemical-protein network analyses demonstrated a linkage between starch and N metabolism via pyridoxal phosphate. Twelve C and N metabolism-related genes were selected for analysis of their expression response to varying N and water treatments in the field in the four high and four low WSC progeny lines; the two nitrogen/amino acid metabolism genes demonstrated a consistent negative association between their level of expression and level of WSC. Our results suggest that the assimilation of nitrogen into amino acids is an important factor that influences the levels of WSC in the stems of field-grown wheat.
Collapse
Affiliation(s)
- C Lynne McIntyre
- CSIRO Plant Industry, 306 Carmody Road, St Lucia, QLD 4067, Australia.
| | | | | | | | | | | | | | | |
Collapse
|
119
|
Controlling reaction specificity in pyridoxal phosphate enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1407-18. [PMID: 21664990 DOI: 10.1016/j.bbapap.2011.05.019] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 05/18/2011] [Accepted: 05/25/2011] [Indexed: 11/20/2022]
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 ability of the covalent aldimine intermediate formed between substrate and PLP to stabilize carbanionic intermediates at Cα of the substrate. This review attempts to summarize the mechanisms by which reaction specificity can be achieved in PLP enzymes by focusing on three aspects of these reactions: stereoelectronic effects, protonation state of the external aldimine intermediate, and interaction of the carbanionic intermediate with the protein side chains present in the active site. This article is part of a Special Issue entitled: Pyridoxal Phosphate Enzymology.
Collapse
|
120
|
Hill MP, Freer LH, Vang MC, Carroll EC, Larsen DS. Multiphoton Manipulations of Enzymatic Photoactivity in Aspartate Aminotransferase. J Phys Chem B 2011; 115:4474-83. [DOI: 10.1021/jp112400g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Melissa P. Hill
- Department of Chemistry, University of California—Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - Lucy H. Freer
- Department of Chemistry, University of California—Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - Mai C. Vang
- Department of Chemistry, University of California—Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - Elizabeth C. Carroll
- Department of Chemistry, University of California—Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - Delmar S. Larsen
- Department of Chemistry, University of California—Davis, 1 Shields Avenue, Davis, California 95616, United States
| |
Collapse
|
121
|
Crugeiras J, Rios A, Riveiros E, Richard JP. Substituent effects on electrophilic catalysis by the carbonyl group: anatomy of the rate acceleration for PLP-catalyzed deprotonation of glycine. J Am Chem Soc 2011; 133:3173-83. [PMID: 21323335 DOI: 10.1021/ja110795m] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
First-order rate constants, determined by (1)H NMR, are reported for deuterium exchange between solvent D(2)O and the α-amino carbon of glycine in the presence of increasing concentrations of carbonyl compounds (acetone, benzaldehyde, and salicylaldehyde) and at different pD and buffer concentrations. These rate data were combined with (1)H NMR data that define the position of the equilibrium for formation of imines/iminium ions from addition of glycine to the respective carbonyl compounds, to give second-order rate constants k(DO) for deprotonation of α-imino carbon by DO(-). The assumption that these second-order rate constants lie on linear structure-reactivity correlations between log k(OL) and pK(a) was made in estimating the following pK(a)'s for deprotonation of α-imino carbon: pK(a) = 22, glycine-acetone iminium ion; pK(a) = 27, glycine-benzaldehyde imine; pK(a) ≈ 23, glycine-benzaldehyde iminium ion; and, pK(a) = 25, glycine-salicylaldehyde iminium ion. The much lower pK(a) of 17 [Toth, K.; Richard, J. P. J. Am. Chem. Soc. 2007, 129, 3013-3021] for carbon deprotonation of the adduct between 5'-deoxypyridoxal (DPL) and glycine shows that the strongly electron-withdrawing pyridinium ion is unique in driving the extended delocalization of negative charge from the α-iminium to the α-pyridinium carbon. This favors carbanion protonation at the α-pyridinium carbon, and catalysis of the 1,3-aza-allylic isomerization reaction that is a step in enzyme-catalyzed transamination reactions. An analysis of the effect of incremental changes in structure on the activity of benzaldehyde in catalysis of deprotonation of glycine shows the carbonyl group electrophile, the 2-O(-) ring substituent and the cation pyridinium nitrogen of DPL each make a significant contribution to the catalytic activity of this cofactor analogue. The extraordinary activity of DPL in catalysis of deprotonation of α-amino carbon results from the summation of these three smaller effects.
Collapse
Affiliation(s)
- Juan Crugeiras
- Departamento de Química Física, Facultad de Química, Universidad de Santiago, 15782 Santiago de Compostela, Spain
| | | | | | | |
Collapse
|
122
|
Kanjee U, Gutsche I, Alexopoulos E, Zhao B, El Bakkouri M, Thibault G, Liu K, Ramachandran S, Snider J, Pai EF, Houry WA. Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase. EMBO J 2011; 30:931-44. [PMID: 21278708 DOI: 10.1038/emboj.2011.5] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Accepted: 12/21/2010] [Indexed: 11/09/2022] Open
Abstract
The Escherichia coli inducible lysine decarboxylase, LdcI/CadA, together with the inner-membrane lysine-cadaverine antiporter, CadB, provide cells with protection against mild acidic conditions (pH∼5). To gain a better understanding of the molecular processes underlying the acid stress response, the X-ray crystal structure of LdcI was determined. The structure revealed that the protein is an oligomer of five dimers that associate to form a decamer. Surprisingly, LdcI was found to co-crystallize with the stringent response effector molecule ppGpp, also known as the alarmone, with 10 ppGpp molecules in the decamer. ppGpp is known to mediate the stringent response, which occurs in response to nutrient deprivation. The alarmone strongly inhibited LdcI enzymatic activity. This inhibition is important for modulating the consumption of lysine in cells during acid stress under nutrient limiting conditions. Hence, our data provide direct evidence for a link between the bacterial acid stress and stringent responses.
Collapse
Affiliation(s)
- Usheer Kanjee
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
123
|
Moccand C, Kaufmann M, Fitzpatrick TB. It takes two to tango: defining an essential second active site in pyridoxal 5'-phosphate synthase. PLoS One 2011; 6:e16042. [PMID: 21283685 PMCID: PMC3024981 DOI: 10.1371/journal.pone.0016042] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 12/09/2010] [Indexed: 11/24/2022] Open
Abstract
The prevalent de novo biosynthetic pathway of vitamin B6 involves only two enzymes (Pdx1 and Pdx2) that form an ornate multisubunit complex functioning as a glutamine amidotransferase. The synthase subunit, Pdx1, utilizes ribose 5-phosphate and glyceraldehyde 3-phosphate, as well as ammonia derived from the glutaminase activity of Pdx2 to directly form the cofactor vitamer, pyridoxal 5′-phosphate. Given the fact that a single enzyme performs the majority of the chemistry behind this reaction, a complicated mechanism is anticipated. Recently, the individual steps along the reaction co-ordinate are beginning to be unraveled. In particular, the binding of the pentose substrate and the first steps of the reaction have been elucidated but it is not known if the latter part of the chemistry, involving the triose sugar, takes place in the same or a disparate site. Here, we demonstrate through the use of enzyme assays, enzyme kinetics, and mutagenesis studies that indeed a second site is involved in binding the triose sugar and moreover, is the location of the final vitamin product, pyridoxal 5′-phosphate. Furthermore, we show that product release is triggered by the presence of a PLP-dependent enzyme. Finally, we provide evidence that a single arginine residue of the C terminus of Pdx1 is responsible for coordinating co-operativity in this elaborate protein machinery.
Collapse
Affiliation(s)
- Cyril Moccand
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Markus Kaufmann
- Bio-Molecular Analysis Platform, University of Geneva, Geneva, Switzerland
| | - Teresa B. Fitzpatrick
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
- * E-mail:
| |
Collapse
|
124
|
Structural insights into the catalytic mechanism of the yeast pyridoxal 5-phosphate synthase Snz1. Biochem J 2011; 432:445-50. [PMID: 20919991 DOI: 10.1042/bj20101241] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In most eubacteria, fungi, apicomplexa, plants and some metazoans, the active form of vitamin B6, PLP (pyridoxal 5-phosphate), is de novo synthesized from three substrates, R5P (ribose 5-phosphate), DHAP (dihydroxyacetone phosphate) and ammonia hydrolysed from glutamine by a complexed glutaminase. Of the three active sites of DXP (deoxyxylulose 5-phosphate)independent PLP synthase (Pdx1), the R5P isomerization site has been assigned, but the sites for DHAP isomerization and PLP formation remain unknown. In the present study, we present the crystal structures of yeast Pdx1/Snz1, in apo-, G3P (glyceraldehyde 3-phosphate)- and PLP-bound forms, at 2.3, 1.8 and 2.2 Å (1 Å=0.1 nm) respectively. Structural and biochemical analysis enabled us to assign the PLP-formation site, a G3P-binding site and a G3P-transfer site. We propose a putative catalytic mechanism for Pdx1/Snz1 in which R5P and DHAP are isomerized at two distinct sites and transferred along well-defined routes to a final destination for PLP synthesis.
Collapse
|
125
|
Sang Y, Locy RD, Goertzen LR, Rashotte AM, Si Y, Kang K, Singh NK. Expression, in vivo localization and phylogenetic analysis of a pyridoxine 5'-phosphate oxidase in Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2011; 49:88-95. [PMID: 21051239 DOI: 10.1016/j.plaphy.2010.10.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Revised: 09/29/2010] [Accepted: 10/08/2010] [Indexed: 05/30/2023]
Abstract
Pyridoxal phosphate (PLP), a vitamin B(6) vitamer, is an essential cofactor for numerous enzymes. Pyridoxine/pyridoxamine phosphate oxidase (PPOX) catalyzes the synthesis of pyridoxal phosphate from pyridoxine phosphate (PNP) and/or pyridoxamine phosphate (PMP). The At5g49970 locus in Arabidopsis thaliana encodes an AtPPOX, a PNP/PMP oxidase. The expression of the AtPPOX gene varied in different tissues of Arabidopsis examined, being up-regulated by light, heat shock, ABA, and ethylene treatments, and down-regulated by exposure to drought and NaCl. Monoclonal antibodies raised against two different domains of AtPPOX recognized different sizes of AtPPOX, suggesting that AtPPOX proteins are produced as splice variants of the AtPPOX gene in Arabidopsis. Phylogenetic analysis of AtPPOX across all domains of life demonstrated that plant AtPPOX homologs have an additional Yjef_N domain preceding the Pyridox_Oxidase domain at the C-terminal end of the protein, while AtPPOX homologs from bacteria, fungi and animals have only Pyridox_Oxidase domain. The presence of the Yjef_N domain in plant AtPPOX homologs suggests that acquisition of this domain, and its fusion with the pyridox_oxidase domain began with the endosymbiotic acquisition of the chloroplast. Bioinformatic analysis suggested that AtPPOX is localized in chloroplast, but the monoclonal antibody could not be used for subcellular localization of this protein. A GFP-AtPPOX fusion construct introduced into the Arabidopsis protoplast confirmed localization of AtPPOX into the chloroplast. An RNAi mutant of AtPPOX showed sensitivity to high light suggesting a role for PPOX in resistance to photooxidative damage, and alteration in root growth in the presence of sucrose suggests a role for PPOX in root development.
Collapse
Affiliation(s)
- Yuying Sang
- Department of Biological Sciences, 101 Rouse Life Sciences Building, Auburn University, AL 36849, USA
| | | | | | | | | | | | | |
Collapse
|
126
|
Asensi-Fabado MA, Munné-Bosch S. Vitamins in plants: occurrence, biosynthesis and antioxidant function. TRENDS IN PLANT SCIENCE 2010; 15:582-92. [PMID: 20729129 DOI: 10.1016/j.tplants.2010.07.003] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 07/13/2010] [Accepted: 07/22/2010] [Indexed: 05/03/2023]
Abstract
Plant-derived vitamins are of great interest because of their impact on human health. They are essential for metabolism because of their redox chemistry and role as enzymatic cofactors, not only in animals but also in plants. Several vitamins have strong antioxidant potential, including both water-soluble (vitamins B and C) and lipid-soluble (vitamins A, E and K) compounds. Here, we review recent advances in the understanding of antioxidant roles of vitamins and present an overview of their occurrence within the plant kingdom, different organs and subcellular location; their major biosynthetic pathways, including common precursors and competitive pathways; and their antioxidant function. In particular, we discuss novel evidence for, as well as evidence against, a role of B vitamins as important antioxidants.
Collapse
Affiliation(s)
- M Amparo Asensi-Fabado
- Departament de Biologia Vegetal, Universitat de Barcelona, Facultat de Biologia, Avinguda Diagonal 645, E-08028 Barcelona, Spain
| | | |
Collapse
|
127
|
Larkin A, Olivier NB, Imperiali B. Structural analysis of WbpE from Pseudomonas aeruginosa PAO1: a nucleotide sugar aminotransferase involved in O-antigen assembly. Biochemistry 2010; 49:7227-37. [PMID: 20604544 DOI: 10.1021/bi100805b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In recent years, the opportunistic pathogen Pseudomonas aeruginosa has emerged as a major source of hospital-acquired infections. Effective treatment has proven increasingly difficult due to the spread of multidrug resistant strains and thus requires a deeper understanding of the biochemical mechanisms of pathogenicity. The central carbohydrate of the P. aeruginosa PAO1 (O5) B-band O-antigen, ManNAc(3NAc)A, has been shown to be critical for virulence and is produced in a stepwise manner by five enzymes in the Wbp pathway (WbpA, WbpB, WbpE, WbpD, and WbpI). Herein, we present the crystal structure of the aminotransferase WbpE from P. aeruginosa PAO1 in complex with the cofactor pyridoxal 5'-phosphate (PLP) and product UDP-GlcNAc(3NH(2))A as the external aldimine at 1.9 A resolution. We also report the structures of WbpE in complex with PMP alone as well as the PLP internal aldimine and show that the dimeric structure of WbpE observed in the crystal structure is confirmed by analytical ultracentrifugation. Analysis of these structures reveals that the active site of the enzyme is composed of residues from both subunits. In particular, we show that a key residue (Arg229), which has previously been implicated in direct interactions with the alpha-carboxylate moiety of alpha-ketoglutarate, is also uniquely positioned to bestow specificity for the 6''-carboxyl group of GlcNAc(3NH(2))A through a salt bridge. This finding is intriguing because while an analogous basic residue is present in WbpE homologues that do not process 6''-carboxyl-modified saccharides, recent structural studies reveal that this side chain is retracted to accommodate a neutral C6'' atom. This work represents the first structural analysis of a nucleotide sugar aminotransferase with a bound product modified at the C2'', C3'', and C6'' positions and provides insight into a novel target for treatment of P. aeruginosa infection.
Collapse
Affiliation(s)
- Angelyn Larkin
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | | | | |
Collapse
|
128
|
Coumans JVF, Moens PDJ, Poljak A, Al-Jaaidi S, Pereg L, Raftery MJ. Plant-extract-induced changes in the proteome of the soil-borne pathogenic fungus Thielaviopsis basicola. Proteomics 2010; 10:1573-91. [PMID: 20186748 DOI: 10.1002/pmic.200900301] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Thielaviopsis basicola is a hemibiotroph fungus that causes black root rot disease in diverse plants with significant impact on cotton production in Australia. To elucidate how T. basicola growth and proteome are influenced by interactions with natural sources, this fungus was cultured in the presence of root extracts from non-host (wheat, hairy vetch) and susceptible host (cotton, lupin) plants. We found that T. basicola growth was significantly favored in the presence of host extracts, while hierarchical clustering analysis of 2-DE protein profiles of T. basicola showed plant species had a larger effect on the proteome than host/non-host status. Analysis by LC-MS/MS of unique and differentially expressed spots and identification using cross-species similarity searching and de novo sequencing allowed successful identification of 41 spots. These proteins were principally involved in primary metabolism with smaller numbers implicated in other diverse functions. Identification of several "morpho" proteins suggested morphological differences that were further microscopically investigated. Identification of several highly expressed spots suggested that vitamin B(6) is important in the T. basicola response to components present in hairy vetch extract, and finally, three spots, induced in the presence of lupin extract, may correspond to malic enzyme and be involved in lipid accumulation.
Collapse
Affiliation(s)
- Joëlle V F Coumans
- Molecular and Cellular Biology, School of Science and Technology, University of New England, Armidale, NSW, Australia.
| | | | | | | | | | | |
Collapse
|
129
|
Identification and Partial Characterization of an L-Tyrosine Aminotransferase (TAT) from Arabidopsis thaliana. Biochem Res Int 2010; 2010:549572. [PMID: 21188077 PMCID: PMC3005984 DOI: 10.1155/2010/549572] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 06/17/2010] [Indexed: 11/17/2022] Open
Abstract
The aminotransferase gene family in the model plant Arabidopsis thaliana consists of 44 genes. Twenty six of these enzymes are classified as characterized meaning that the reaction(s) that the enzyme catalyzes are documented using experimental means. The remaining 18 enzymes are uncharacterized and are therefore deemed putative. Our laboratory is interested in elucidating the function(s) of the remaining putative aminotransferase enzymes. To this end, we have identified and partially characterized an aminotransferase (TAT) enzyme from Arabidopsis annotated by the locus tag At5g36160. The full-length cDNA was cloned and the purified recombinant enzyme was characterized using in vitro and in vivo experiments. In vitro analysis showed that the enzyme is capable of interconverting L-Tyrosine and 4-hydroxyphenylpyruvate, and L-Phenylalanine and phenylpyruvate. In vivo analysis by functional complementation showed that the gene was able to complement an E. coli with a background of aminotransferase mutations that confers auxotrophy for L-Tyrosine and L-Phenylalanine.
Collapse
|
130
|
Allen GFG, Neergheen V, Oppenheim M, Fitzgerald JC, Footitt E, Hyland K, Clayton PT, Land JM, Heales SJR. Pyridoxal 5'-phosphate deficiency causes a loss of aromatic L-amino acid decarboxylase in patients and human neuroblastoma cells, implications for aromatic L-amino acid decarboxylase and vitamin B(6) deficiency states. J Neurochem 2010; 114:87-96. [PMID: 20403077 DOI: 10.1111/j.1471-4159.2010.06742.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyridoxal 5'-phosphate, the active form of vitamin B(6), is an essential cofactor for multiple enzymes, including aromatic l-amino acid decarboxylase that catalyses the final stage in the production of the neurotransmitters dopamine and serotonin. In two patients with inherited disorders of vitamin B(6) metabolism, we observed reductions in plasma aromatic l-amino acid decarboxylase activity. In one patient, this change was related to an increase in K(m) for pyridoxal 5'-phosphate. Furthermore, pyridoxal 5'-phosphate-deficient human SH-SY5Y neuroblastoma cells were found to exhibit reduced levels of aromatic l-amino acid decarboxylase activity and protein but with no alteration in expression. Further reductions in activity and protein were observed with the addition of the vitamin B(6) antagonist 4-deoxypyridoxine, which also reduced aromatic l-amino acid decarboxylase mRNA levels. Neither pyridoxal 5'-phosphate deficiency nor the addition of 4-deoxypyridoxine affected aromatic l-amino acid decarboxylase stability over 8 h with protein synthesis inhibited. Increasing extracellular availability of pyridoxal 5'-phosphate was not found to have any significant effect on intracellular pyridoxal 5'-phosphate concentrations or on aromatic l-amino acid decarboxylase. These findings suggest that maintaining adequate pyridoxal 5'-phosphate availability may be important for optimal treatment of aromatic l-amino acid decarboxylase deficiency and l-dopa-responsive conditions.
Collapse
Affiliation(s)
- George F G Allen
- Department of Molecular Neuroscience, UCL Institute of Neurology, London WC1N 3BG, UK.
| | | | | | | | | | | | | | | | | |
Collapse
|
131
|
Ortega-Castro J, Adrover M, Frau J, Salvà A, Donoso J, Muñoz F. DFT Studies on Schiff Base Formation of Vitamin B6 Analogues. Reaction between a Pyridoxamine-Analogue and Carbonyl Compounds. J Phys Chem A 2010; 114:4634-40. [DOI: 10.1021/jp909156m] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. Ortega-Castro
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, Cra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - M. Adrover
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, Cra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - J. Frau
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, Cra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - A. Salvà
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, Cra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - J. Donoso
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, Cra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| | - F. Muñoz
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, Cra. Valldemossa km 7.5, E-07122 Palma de Mallorca, Spain
| |
Collapse
|
132
|
Mishra V, Ali V, Nozaki T, Bhakuni V. Entamoeba histolytica Phosphoserine aminotransferase (EhPSAT): insights into the structure-function relationship. BMC Res Notes 2010; 3:52. [PMID: 20199659 PMCID: PMC2850911 DOI: 10.1186/1756-0500-3-52] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 03/03/2010] [Indexed: 11/29/2022] Open
Abstract
Background Presence of phosphorylated Serine biosynthesis pathway upstream to the de novo cysteine biosynthesis pathway makes PSAT a crucial enzyme. Besides this, phoshoserine produced by the enzyme can also be taken up directly by cysteine synthase as a substrate. PSAT is a PLP dependent enzyme where the cofactor serves as an epicenter for functional catalysis with the active site architecture playing crucial role in optimum function of the enzyme. Findings EhPSAT is a homodimer of molecular mass 86 kDa. To understand the structural modulations associated with pH dependent changes in functional activity of EhPSAT detailed biophysical studies were carried out. pH alterations had no significant effect on the secondary structure, cofactor orientation and oligomeric configuration of the enzyme however, pH dependent compaction in molecular dimensions was observed. Most interestingly, a direct correlation between pH induced modulation of functional activity and orientation of Trp 101 present in the active site of the enzyme was observed. Sodium halides nullified the pH induced global changes in the enzyme, however differential effect of these salts on the active site microenvironment and functional activity of the enzyme was observed. Conclusions The study unequivocally demonstrates that pH induced selective modification of active site microenvironment and not global change in structure or oligomeric status of the enzyme is responsible for the pH dependent change in enzymatic activity of PSAT.
Collapse
Affiliation(s)
- Vibhor Mishra
- Division of Molecular and Structural Biology, Central Drug Research Institute, Chattar Manzil Palace, Council of scientific and industrial research (CSIR), Lucknow 226001, India.
| | | | | | | |
Collapse
|
133
|
Quantum mechanics/molecular mechanics (QM/MM) modeling of the irreversible transamination of l-kynurenine to kynurenic acid: The round dance of kynurenine aminotransferase II. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1802-12. [DOI: 10.1016/j.bbapap.2009.08.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Revised: 08/12/2009] [Accepted: 08/18/2009] [Indexed: 11/21/2022]
|
134
|
Crugeiras J, Rios A, Riveiros E, Richard JP. Substituent effects on the thermodynamic stability of imines formed from glycine and aromatic aldehydes: implications for the catalytic activity of pyridoxal-5'-phosphate. J Am Chem Soc 2009; 131:15815-24. [PMID: 19807092 PMCID: PMC2788968 DOI: 10.1021/ja906230n] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Equilibrium constants for addition of glycine to substituted benzaldehydes to form the corresponding imines and pK(a)'s for ionization of the iminium ions were determined by (1)H NMR analysis in D(2)O. The introduction of a phenoxide anion substituent into the aromatic ring of benzaldehyde leads to a substantial increase in the pK(a) of the iminium ion from 6.3 to 10.2 for p-hydroxybenzaldehyde and to 12.1 for salicylaldehyde. An analysis of the differential effect of ortho- versus para-substitution shows that the iminium ion to salicylaldehyde is stabilized by an intramolecular hydrogen bond in aqueous solution, with an estimated energy ca. 3 kcal/mol larger than can be accounted for by a simple electrostatic interaction. A comparison of the o-O(-) substituent effect on the acidity of the iminium ions of glycine to benzaldehyde and 4-pyridine-carboxaldehyde provides evidence for the existence of an internal hydrogen bond of similar strength in pyridoxal 5'-phosphate (PLP) iminium ions in water. The effects of other ring substituents on the stability of PLP iminium ions are discussed.
Collapse
Affiliation(s)
- Juan Crugeiras
- Departamento de Química Física, Facultad de Química, Universidad de Santiago, 15782
| | - Ana Rios
- Departamento de Química Física, Facultad de Química, Universidad de Santiago, 15782
| | - Enrique Riveiros
- Departamento de Química Física, Facultad de Química, Universidad de Santiago, 15782
| | - John P. Richard
- Santiago de Compostela, Spain and Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260, USA
| |
Collapse
|
135
|
Simon ES, Allison J. Determination of pyridoxal-5'-phosphate (PLP)-bonding sites in proteins: a peptide mass fingerprinting approach based on diagnostic tandem mass spectral features of PLP-modified peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:3401-3408. [PMID: 19810014 DOI: 10.1002/rcm.4270] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Peptides modified by pyridoxal-5'-phosphate (PLP), linked to a lysine residue via reductive amination, exhibit distinct spectral characteristics in the collision-induced dissociation (CID) tandem mass (MS/MS) spectra that are described here. The MS/MS spectra typically display two dominant peaks whose m/z values correspond to neutral losses of [H3PO4] (-98 Da) and the PLP moiety as [C8H10NO5P] (-231 Da) from the precursor peptide ion, respectively. Few other peaks are observed. Recognition of this distinct fragmentation behavior is imperative since determining sequences and sites of modifications relies on the formation of amide backbone cleavage products for subsequent interpretation via proteome database searching. Additionally, PLP-modified peptides exhibit suppressed precursor ionization efficiency which diminishes their detection in complex mixtures. Presented here is a protocol which describes an enrichment strategy for PLP-modified peptides combined with neutral loss screening and peptide mass fingerprinting to map the PLP-bonding site in a known PLP-dependent protein. This approach represents an efficient alternative to site-directed mutagenesis which has been the traditional method used for PLP-bonding site localization in proteins.
Collapse
Affiliation(s)
- Eric S Simon
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| | | |
Collapse
|
136
|
Musayev FN, Di Salvo ML, Saavedra MA, Contestabile R, Ghatge MS, Haynes A, Schirch V, Safo MK. Molecular basis of reduced pyridoxine 5'-phosphate oxidase catalytic activity in neonatal epileptic encephalopathy disorder. J Biol Chem 2009; 284:30949-56. [PMID: 19759001 DOI: 10.1074/jbc.m109.038372] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mutations in pyridoxine 5'-phosphate oxidase are known to cause neonatal epileptic encephalopathy. This disorder has no cure or effective treatment and is often fatal. Pyridoxine 5'-phosphate oxidase catalyzes the oxidation of pyridoxine 5'-phosphate to pyridoxal 5'-phosphate, the active cofactor form of vitamin B(6) required by more than 140 different catalytic activities, including enzymes involved in amino acid metabolism and biosynthesis of neurotransmitters. Our aim is to elucidate the mechanism by which a homozygous missense mutation (R229W) in the oxidase, linked to neonatal epileptic encephalopathy, leads to reduced oxidase activity. The R229W variant is approximately 850-fold less efficient than the wild-type enzyme due to an approximately 192-fold decrease in pyridoxine 5'-phosphate affinity and an approximately 4.5-fold decrease in catalytic activity. There is also an approximately 50-fold reduction in the affinity of the R229W variant for the FMN cofactor. A 2.5 A crystal structure of the R229W variant shows that the substitution of Arg-229 at the FMN binding site has led to a loss of hydrogen-bond and/or salt-bridge interactions between FMN and Arg-229 and Ser-175. Additionally, the mutation has led to an alteration of the configuration of a beta-strand-loop-beta-strand structure at the active site, resulting in loss of two critical hydrogen-bond interactions involving residues His-227 and Arg-225, which are important for substrate binding and orientation for catalysis. These results provide a molecular basis for the phenotype associated with the R229W mutation, as well as providing a foundation for understanding the pathophysiological consequences of pyridoxine 5'-phosphate oxidase mutations.
Collapse
Affiliation(s)
- Faik N Musayev
- Department of Medicinal Chemistry, School of Pharmacy, and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia 23219, USA
| | | | | | | | | | | | | | | |
Collapse
|
137
|
Percudani R, Peracchi A. The B6 database: a tool for the description and classification of vitamin B6-dependent enzymatic activities and of the corresponding protein families. BMC Bioinformatics 2009; 10:273. [PMID: 19723314 PMCID: PMC2748086 DOI: 10.1186/1471-2105-10-273] [Citation(s) in RCA: 209] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Accepted: 09/01/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Enzymes that depend on vitamin B6 (and in particular on its metabolically active form, pyridoxal 5'-phosphate, PLP) are of great relevance to biology and medicine, as they catalyze a wide variety of biochemical reactions mainly involving amino acid substrates. Although PLP-dependent enzymes belong to a small number of independent evolutionary lineages, they encompass more than 160 distinct catalytic functions, thus representing a striking example of divergent evolution. The importance and remarkable versatility of these enzymes, as well as the difficulties in their functional classification, create a need for an integrated source of information about them. DESCRIPTION The B6 database http://bioinformatics.unipr.it/B6db contains documented B6-dependent activities and the relevant protein families, defined as monophyletic groups of sequences possessing the same enzymatic function. One or more families were associated to each of 121 PLP-dependent activities with known sequences. Hidden Markov models (HMMs) were built from family alignments and incorporated in the database. These HMMs can be used for the functional classification of PLP-dependent enzymes in genomic sets of predicted protein sequences. An example of such analyses (a census of human genes coding for PLP-dependent enzymes) is provided here, whereas many more are accessible through the database itself. CONCLUSION The B6 database is a curated repository of biochemical and molecular information about an important group of enzymes. This information is logically organized and available for computational analyses, providing a key resource for the identification, classification and comparative analysis of B6-dependent enzymes.
Collapse
Affiliation(s)
- Riccardo Percudani
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy.
| | | |
Collapse
|
138
|
Rubinstein A, Major DT. Catalyzing Racemizations in the Absence of a Cofactor: The Reaction Mechanism in Proline Racemase. J Am Chem Soc 2009; 131:8513-21. [DOI: 10.1021/ja900716y] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amir Rubinstein
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| |
Collapse
|
139
|
Andréll J, Hicks MG, Palmer T, Carpenter EP, Iwata S, Maher MJ. Crystal Structure of the Acid-Induced Arginine Decarboxylase from Escherichia coli: Reversible Decamer Assembly Controls Enzyme Activity. Biochemistry 2009; 48:3915-27. [DOI: 10.1021/bi900075d] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Juni Andréll
- Division of Molecular Biosciences, Imperial College, London SW7 2AZ, U.K
| | | | | | | | - So Iwata
- Division of Molecular Biosciences, Imperial College, London SW7 2AZ, U.K
| | - Megan J. Maher
- Division of Molecular Biosciences, Imperial College, London SW7 2AZ, U.K
| |
Collapse
|
140
|
Carroll EC, Hill MP, Madsen D, Malley KR, Larsen DS. A single source femtosecond-millisecond broadband spectrometer. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2009; 80:026102. [PMID: 19256678 DOI: 10.1063/1.3070516] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Time-resolved measurement of population dynamics extending over femtosecond to millisecond time scales typically requires a combination of transient absorption techniques involving different laser systems and detection schemes. The spectrometer design presented here facilitates transient absorption measurements over 12 decades with a single ultrafast laser system by picking pump and probe pulses independently from the laser oscillator pulse train. Unamplified pulses seed a photonic crystal fiber to a supercontinuum probe source for spectrally resolved measurements. The utility of the system is demonstrated by measuring triplet state dynamics following photoexcitation of vitamin B(6) in aqueous solution.
Collapse
Affiliation(s)
- E C Carroll
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
| | | | | | | | | |
Collapse
|
141
|
Casasnovas R, Salvà A, Frau J, Donoso J, Muñoz F. Theoretical study on the distribution of atomic charges in the Schiff bases of 3-hydroxypyridine-4-aldehyde and alanine. The effect of the protonation state of the pyridine and imine nitrogen atoms. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2008.12.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
142
|
Abstract
Cofactors are organic molecules, most of them originating from vitamins, that bind to enzymes making them able to catalyze defined reactions. A cofactor-based chemogenomics approach exploits the presence of a cofactor-binding domain to develop compound scaffolds tailored to mimic the cofactor and to replace it within target enzyme classes. As a result, a loss of function is observed. An expansion of the cofactor scaffold to include structural/chemical features derived from the substrate, that usually binds at cofactor adjacent sites, increases the specificity of the enzyme fishing. This approach has been so far applied only to NAD(P)(+)-dependent enzymes. However, it is suitable for all other cofactors, with difficulties, for some of them, originated by very tight binding. In the case of cofactors covalently bound to the enzyme, the competition between the natural cofactor and the cofactor scaffold mimic can only occur during enzyme folding.
Collapse
Affiliation(s)
- Ratna Singh
- Department of Biochemistry and Molecular Biology, University of Parma, Parma, Italy
| | | |
Collapse
|
143
|
Yu S, Luo L. Expression analysis of a novel pyridoxal kinase messenger RNA splice variant, PKL, in oil rape suffering abiotic stress and phytohormones. Acta Biochim Biophys Sin (Shanghai) 2008; 40:1005-14. [PMID: 19089298 DOI: 10.1111/j.1745-7270.2008.00489.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Pyridoxal kinase is key enzyme for the biosynthesis of pyridoxal 5'-phosphate, the biologically active form of vitamin B6, in the salvage pathway. A pyridoxal kinase gene, BnPKL (GenBank accession No. DQ463962), was isolated from oilseed rape (Brassica napus L.) following water stress through rapid amplification of complementary DNA (cDNA) ends. The results showed that the gene had two splice variants: PKL and PKL2. PKL, the long cDNA, encodes a 334 amino acid protein with a complete ATP-binding site, pyridoxal kinase-binding site and dimer interface site of a pyridoxal kinase, while PKL2, the short cDNA, lacked a partial domain. Southern blot showed that there were two copies in Brassica napus. The expression of BnPKL cDNA could rescue the mutant phenotype of Escherichia coli defective in pyridoxal kinase. Real-time reverse transcription-polymerase chain reaction revealed that the relative abundance of two transcripts are modulated by development and environmental stresses. Abscisic acid and NaCl were inclined to decrease PKL expression, but H2O2 and cold temperatures induced the PKL expression. In addition, the PKL expression could be transiently induced by jasmonate acid at an early stage, abscisic acid, salicylic acid and jasmonate acid enhanced the PKL expression in roots. Our results demonstrated that BnPKL was a pyridoxal kinase involved in responses to biotic and abiotic stresses.
Collapse
Affiliation(s)
- Shunwu Yu
- Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Germsperm Resources Division (Shanghai), National Key Laboratory of Crop Genetic Improvement, Shanghai, China
| | | |
Collapse
|
144
|
Todorovic B, Glick BR. The interconversion of ACC deaminase and D-cysteine desulfhydrase by directed mutagenesis. PLANTA 2008; 229:193-205. [PMID: 18825405 DOI: 10.1007/s00425-008-0820-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Accepted: 09/08/2008] [Indexed: 05/26/2023]
Abstract
Progress in DNA sequencing of plant genomes has revealed that, in addition to microorganisms, a number of plants contain genes which share similarity to microbial 1-aminocyclopropane-1-carboxylate (ACC) deaminases. These enzymes cleave ACC, the immediate precursor of ethylene in plants, into ammonia and alpha-ketobutyrate. We therefore sought to isolate putative ACC deaminase cDNAs from tomato plants with the objective of establishing whether the product of this gene is a functional ACC deaminase. In the work reported here, it was demonstrated that the enzyme encoded by the putative ACC deaminase cDNA does not have the ability to break the cyclopropane ring of ACC, but rather it utilizes D: -cysteine as a substrate, and in fact encodes a D: -cysteine desulfhydrase. Kinetic characterization of the tomato enzyme indicates that it is similar to other, previously characterized, D: -cysteine desulfhydrases. Using site-directed mutagenesis, it was shown that altering only two amino acid residues within the predicted active site served to change the enzyme from D: -cysteine desulfhydrase to ACC deaminase. Conversely, by altering two amino acid residues at the same positions within the active site of ACC deaminase from Pseudomonas putida UW4 the enzyme was converted into D: -cysteine desulfhydrase. Therefore, it is possible that a change in these two residues may have occurred in an ancestral protein to result in two different enzymatic activities.
Collapse
Affiliation(s)
- Biljana Todorovic
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada.
| | | |
Collapse
|
145
|
Florio R, Chiaraluce R, Consalvi V, Paiardini A, Catacchio B, Bossa F, Contestabile R. The role of evolutionarily conserved hydrophobic contacts in the quaternary structure stability of Escherichia coli serine hydroxymethyltransferase. FEBS J 2008; 276:132-43. [DOI: 10.1111/j.1742-4658.2008.06761.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
146
|
Mugford P, Wagner UG, Jiang Y, Faber K, Kazlauskas R. Enantiocomplementary Enzymes: Classification, Molecular Basis for Their Enantiopreference, and Prospects for Mirror-Image Biotransformations. Angew Chem Int Ed Engl 2008; 47:8782-93. [DOI: 10.1002/anie.200705159] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
147
|
Mugford P, Wagner U, Jiang Y, Faber K, Kazlauskas R. Enantiokomplementäre Enzyme: Klassifizierung, molekulare Grundlage der Enantiopräferenz und Prognosen für spiegelbildliche Biotransformationen. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705159] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
148
|
Bertoldi M, Cellini B, Montioli R, Borri Voltattorni C. Insights into the mechanism of oxidative deamination catalyzed by DOPA decarboxylase. Biochemistry 2008; 47:7187-95. [PMID: 18547057 DOI: 10.1021/bi800478s] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The unusual oxygen-consuming oxidative deamination reaction catalyzed by the pyridoxal 5'-phosphate (PLP) enzyme DOPA decarboxylase (DDC) was here investigated. Either wild-type or Y332F DDC variant is able to perform such oxidation toward aromatic amines or aromatic l-amino acids, respectively, without the aid of any cofactor related to oxygen chemistry. Oxidative deamination produces, in equivalent amounts, a carbonyl compound and ammonia, accompanied by dioxygen consumption in a 1:2 molar ratio with respect to the products. Kinetic studies either in the pre-steady or in the steady state, together with HPLC analyses of reaction mixtures under varying experimental conditions, revealed that a ketimine accumulates during the linear phase of product formation. This species is reactive since it is converted back to PLP when the substrate is consumed. Rapid-mixing chemical quench studies provide evidence that the ketimine is indeed an intermediate formed during the first catalytic cycle. Moreover, superoxide anion and hydrogen peroxide are both generated during the catalytic cycles. On this basis, a mechanism of oxidative deamination consistent with the present data is proposed. Furthermore, the catalytic properties of the T246A DDC mutant together with those previously obtained with H192Q mutant allow us to propose that the Thr246-His192 dyad could act as a general base in promoting the first step of the oxidative deamination of aromatic amines.
Collapse
Affiliation(s)
- Mariarita Bertoldi
- Dipartimento di Scienze Morfologico-Biomediche, sezione di Chimica Biologica, Facoltà di Medicina e Chirurgia, Strada Le Grazie, 8, 37134 Verona, Italy.
| | | | | | | |
Collapse
|
149
|
Ardestani A, Yazdanparast R, Nejad AS. 2-Deoxy-d-ribose-induced oxidative stress causes apoptosis in human monocytic cells: Prevention by pyridoxal-5′-phosphate. Toxicol In Vitro 2008; 22:968-79. [DOI: 10.1016/j.tiv.2008.02.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2007] [Revised: 01/26/2008] [Accepted: 02/06/2008] [Indexed: 01/09/2023]
|
150
|
Four types of threonine aldolases: Similarities and differences in kinetics/thermodynamics. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.molcatb.2007.10.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|