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Mabood F, Hadi F, Jan AU, Ditta A, Islam Z, Siddiqui MH, Ali HM, Sabagh AEL. Assessment of Pb and Ni and potential health risks associated with the consumption of vegetables grown on the roadside soils in District Swat, Khyber Pakhtunkhwa, Pakistan. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 194:906. [PMID: 36253629 DOI: 10.1007/s10661-022-10627-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Vegetables cultivated near roads absorb toxic metals from polluted soil, which enter the human body through the food chain and cause serious health problems to humans. The present study investigated the concentration of lead (Pb) and nickel (Ni) in soils and vegetables grown along the roadside of District Swat, Pakistan, and the health risks associated with the consumption of the tested vegetables. In results, Pb concentration was higher in plants located at the distance between 0-10 m away from the roadside than the WHO permissible limit. In such plants, Pb concentration was higher than Ni. Rumex dentatus contained the highest concentration of Pb (75.63 mg kg-1 DW) among the tested vegetables while Ni concentration (27.57 mg kg-1 DW) was highest in Trachyspermum ammi as compared to other plants. Concentration and accumulation of both the metals decreased in soil and plants with increasing distance from the road. Similarly, target hazard quotient values noted for Pb (up to 3.37) were greater than unity, which shows that there is a potential risk associated with the consumption of tested vegetables near the road. Moreover, the values of target cancer risk (up to 0.8413) were greater than 0.0001, which shows that there is a risk of cancer with the consumption of tested vegetables. In conclusion, the consumption of tested vegetables was very dangerous as it may lead to higher risks of cancer. Strict regulatory control is recommended on the cultivation of these vegetables along the roadside to avoid any contamination due to roadside exhaust.
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Affiliation(s)
- Fazal Mabood
- Department of Botany, Faculty of Science, University of Malakand, KPK, Pakistan
| | - Fazal Hadi
- Department of Biotechnology, Faculty of Science, University of Malakand, KPK, Pakistan
| | - Amin Ullah Jan
- Department of Biotechnology, Faculty of Science, Shaheed Benazir Bhutto University, Sheringal Dir (U), 18000, Pakistan
| | - Allah Ditta
- Department of Environmental Sciences, Faculty of Sciences, Shaheed Benazir Bhutto University, Sheringal Dir (U), 18000, Pakistan.
- School of Biological Sciences, the University of Western Australia, Perth, WA, 6009, Australia.
| | - Ziaul Islam
- Department of Animal Sciences, Shaheed Benazir Bhutto University Sheringal Dir Upper, KPK, Pakistan
| | - Manzer H Siddiqui
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Hayssam M Ali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Ayman E L Sabagh
- Department of Agronomy, Faculty of Agriculture, University of Kafrelsheikh, Kafrelsheikh, 33516, Egypt
- Department of Field Crops, Faculty of Agriculture, Cukurova University, Adana, 01330, Turkey
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Elemo GN, Erukainure OL, Okafor JNC, Banerjee P, Preissner R, Nwachukwu Nicholas-Okpara VA, Atolani O, Omowunmi O, Ezeanyanaso CS, Awosika A, Shode F. Underutilized legumes, Cajanus cajan and Glycine max may bring about antisickling effect in sickle cell disease by modulation of redox homeostasis in sickled erythrocytes and alteration of its functional chemistry. J Food Biochem 2022; 46:e14322. [PMID: 35894096 DOI: 10.1111/jfbc.14322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 06/20/2022] [Accepted: 06/23/2022] [Indexed: 11/28/2022]
Abstract
The antisickling and anti-oxidative effect of the Cajanus cajan, Glycine max, and their blends were investigated in sickled erythrocytes. The powdered samples were analyzed for their nutritional and anti-nutritional constituents. Their aqueous extracts were analyzed for in vitro antioxidant activities. The extracts were incubated with sickled erythrocytes at 37°C for 6 hours and the antisickling effect examined via microscopic analysis. The blend was the most active and its incubated cells were subjected to anti-oxidative analysis which covers for GSH, SOD, catalase, and lipid peroxidation (LPO). Chemical functional group of the treated cells was analyzed with FTIR spectroscopy. The in silico binding of the predominant amino acid to hemoglobin was also investigated. An increased concentration of leucine was observed in the blend compared to that of C. cajan and G. max, respectively. Vitamins C, B6, and B9 were the only vitamins observed in the blend. Phytate and oxalate were present in all samples. All extracts displayed significant (p < .05) scavenging activities. Treatment with the blend exacerbated SOD and catalase activities as well as the GSH level, while suppressing LPO. FTIR analysis of the treated cells showed the presence of hydrophobic functional groups. Leucine was the predominant amino acid, and it showed a potent molecular interaction with HIS-87 residue of the alpha chain of 1HCO. C. cajan and G. max blend inhibited sickling activities of sickle erythrocytes, while concomitantly exacerbating their endogenous antioxidant enzymes activity and modification of the functional chemistry. PRACTICAL APPLICATIONS: Cajanus cajan and Glycine max are among the common underutilized legumes in Nigeria. Aside their nutritional properties, these legumes have been used from time immemorial for the treatment and management of various ailments. Sickle cell anemia is a class of hemoglobinopathy common in Sub-Saharan Africa. There have been concerns about its treatment owing to the increasing scourge of the disease coupled to the financial burden of its management. This study reports the ability of the potentials of the legumes to prevent sickling activities of sickled erythrocytes and the possible biochemical mechanism involved.
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Affiliation(s)
- Gloria N Elemo
- Nutraceutical Laboratories, Nutrition and Toxicology Division, Federal Institute of Industrial Research, Lagos, Nigeria.,Department of Chemical Sciences, Ajayi Crowther University, Oyo, Nigeria
| | - Ochuko L Erukainure
- Department of Pharmacology, University of the Free State, Bloemfontein, South Africa
| | - Jane N C Okafor
- Nutraceutical Laboratories, Nutrition and Toxicology Division, Federal Institute of Industrial Research, Lagos, Nigeria
| | - Priyanka Banerjee
- Structural Bioinformatics Group, Institute for Physiology, Charité-University Medicine Berlin, Berlin, Germany
| | - Robert Preissner
- Structural Bioinformatics Group, Institute for Physiology, Charité-University Medicine Berlin, Berlin, Germany
| | | | | | - Olusola Omowunmi
- Laboratory Management & Services, Federal Institute of Industrial Research, Lagos, Nigeria
| | - Chika S Ezeanyanaso
- Polymer & Textile Division, Federal Institute of Industrial Research, Lagos, Nigeria
| | | | - Francis Shode
- Department of Biotechnology and Food Science, Durban University of Technology, Durban, South Africa.,Sholab Nutraceuticals (Pty) Ltd, Westville North, South Africa
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Watson DG, Pomeroy PP, Al-Tannak NF, Kennedy MW. Stockpiling by pups and self-sacrifice by their fasting mothers observed in birth to weaning serum metabolomes of Atlantic grey seals. Sci Rep 2020; 10:7465. [PMID: 32366923 PMCID: PMC7198541 DOI: 10.1038/s41598-020-64488-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 04/15/2020] [Indexed: 12/23/2022] Open
Abstract
During the uniquely short lactations of true seals, pups acquire a greater proportion of maternal body resources, at a greater rate, than in any other group of mammals. Mothers in many species enter a period of anorexia but must preserve sufficient reserves to fuel hunting and thermoregulation for return to cold seas. Moreover, pups may undergo a period of development after weaning during which they have no maternal care or nutrition. This nutritionally closed system presents a potentially extreme case of conflict between maternal survival and adequate provisioning of offspring, likely presenting strains on their metabolisms. We examined the serum metabolomes of five mother and pup pairs of Atlantic grey seals, Halichoerus grypus, from birth to weaning. Changes with time were particularly evident in pups, with indications of strain in the fat and energy metabolisms of both. Crucially, pups accumulate certain compounds to levels that are dramatically greater than in mothers. These include compounds that pups cannot synthesise themselves, such as pyridoxine/vitamin B6, taurine, some essential amino acids, and a conditionally essential amino acid and its precursor. Fasting mothers therefore appear to mediate stockpiling of critical metabolites in their pups, potentially depleting their own reserves and prompting cessation of lactation.
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Affiliation(s)
- David G Watson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, Scotland, UK.
| | - Patrick P Pomeroy
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, St Andrews, Fife, Scotland, United Kingdom
| | - Naser F Al-Tannak
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, Scotland, UK.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kuwait University, P.O. Box 23924, Safat, 13110, Kuwait City, Kuwait
| | - Malcolm W Kennedy
- Institute of Biodiversity, Animal Health & Comparative Medicine, Graham Kerr Building, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK.
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Azim N, Gardner QA, Rashid N, Akhtar M. Mechanistic studies on Pyrobaculum calidifontis porphobilinogen synthase (5-aminolevulinic acid dehydratase). Bioorg Chem 2019; 91:103117. [PMID: 31377385 DOI: 10.1016/j.bioorg.2019.103117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 10/26/2022]
Abstract
Porphobilinogen synthase (PBG synthase) gene from Pyrobaculum calidifontis was cloned and expressed in E. coli. The recombinant enzyme was purified as an octamer and was found by mass spectrometry to have a subunit Mr of 37676.59 (calculated, 37676.3). The enzyme showed high thermal stability and retained almost all of its activity after incubation at 70 °C for 16 h in the presence of β-mercaptoethanol (β-ME) and zinc chloride. However, in the absence of the latter the enzyme was inactivated after 16 h although it regained full activity in the presence of β-ME and zinc chloride. The protein contained 4 mol of tightly bound zinc per octamer. Further, 4 mol of low affinity zinc could be incorporated following incubation with exogenous zinc salts. The enzyme was inactivated by incubation with levulinic acid followed by treatment with sodium borohydride. Tryptic digest of the modified enzyme and mass spectrometric analysis showed that Lys257 was the site of modification, which has previously been shown to be the site for the binding of 5-aminolevulinic acid giving rise to the propionate-half of porphobilinogen. P. calidifontis PBG synthase was inactivated by 5-chlorolevulinic acid and the residue modified was shown to be the central cysteine (Cys127) of the zinc-binding cysteine-triad, comprising Cys125, 127, 135. The present results in conjunction with earlier findings on zinc containing PBG synthases, are discussed which advocate that the catalytic role of zinc in the activation of the 5-aminolevulinic acid molecule forming the acetate-half of PBG is possible.
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Affiliation(s)
- Naseema Azim
- School of Biological Sciences, University of the Punjab, New Campus, Lahore 54590, Pakistan
| | | | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, New Campus, Lahore 54590, Pakistan
| | - Muhammad Akhtar
- School of Biological Sciences, University of the Punjab, New Campus, Lahore 54590, Pakistan; Biological Sciences, University of Southampton SO17 1BJ, UK.
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5
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Klimaczewski CV, Nogara PA, Barbosa NV, da Rocha JBT. Interaction of metals from group 10 (Ni, Pd, and Pt) and 11 (Cu, Ag, and Au) with human blood δ-ALA-D: in vitro and in silico studies. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:30557-30566. [PMID: 30173384 DOI: 10.1007/s11356-018-3048-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/23/2018] [Indexed: 06/08/2023]
Abstract
Mammalian δ-aminolevulinate dehydratase (δ-ALA-D) is a metalloenzyme, which requires Zn(II) and reduced thiol groups for catalytic activity, and is an important molecular target for the widespread environmental toxic metals. The δ-ALA-D inhibition mechanism by metals of Group 10 (Ni, Pd, and Pt) and 11 (Cu, Ag, and Au) of the periodic table has not yet been determined. The objective of this study was to characterize the molecular mechanism of δ-ALA-D inhibition caused by the elements of groups 10 and 11 using in vitro (δ-ALA-D activity from human erythrocytes) and in silico (docking simulations) methods. Our results showed that Ni(II) and Pd(II) caused a small inhibition (~ 10%) of the δ-ALA-D. Pt(II) and Pt(IV) significantly inhibited the enzyme (75% and 44%, respectively), but this inhibition was attenuated by Zn(II) and dithiothreitol (DTT). In group 11, all metals inhibited δ-ALA-D with great potency (~ 70-90%). In the presence of Zn(II) and DTT, the enzyme activity was restored to the control levels. The in silico molecular docking data suggest that the coordination of the ions Pt(II), Pt(IV), Cu(II), Ag(I), and Au(III) with thiolates groups from C135 and C143 residues from the δ-ALA-D active site are crucial to the enzyme inhibition. The results indicate that a possible mechanism of inhibition of δ-ALA-D by these metals may involve the replacement of the Zn(II) from the active site and/or the cysteinyl residue oxidation.
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Affiliation(s)
- Cláudia Vargas Klimaczewski
- Programa de Pós Graduação em Ciências Biológicas: Bioquímica Toxicológica, Universidade Federal de Santa Maria (UFSM), Santa Maria, RS, Brazil
| | - Pablo Andrei Nogara
- Programa de Pós Graduação em Ciências Biológicas: Bioquímica Toxicológica, Universidade Federal de Santa Maria (UFSM), Santa Maria, RS, Brazil.
- Centro de Ciências Naturais e Exatas, Programa de Pós-graduação em Bioquímica Toxicológica, Santa Maria, RS, 97115-900, Brazil.
| | - Nilda Vargas Barbosa
- Programa de Pós Graduação em Ciências Biológicas: Bioquímica Toxicológica, Universidade Federal de Santa Maria (UFSM), Santa Maria, RS, Brazil
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Santa Maria, RS, Brazil
| | - João Batista Teixeira da Rocha
- Programa de Pós Graduação em Ciências Biológicas: Bioquímica Toxicológica, Universidade Federal de Santa Maria (UFSM), Santa Maria, RS, Brazil.
- Centro de Ciências Naturais e Exatas, Programa de Pós-graduação em Bioquímica Toxicológica, Santa Maria, RS, 97115-900, Brazil.
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Santa Maria, RS, Brazil.
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Interaction energy profile for diphenyl diselenide in complex with δ-aminolevulinic acid dehydratase enzyme using quantum calculations and a molecular fragmentation method. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.comtox.2018.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Mills-Davies N, Butler D, Norton E, Thompson D, Sarwar M, Guo J, Gill R, Azim N, Coker A, Wood SP, Erskine PT, Coates L, Cooper JB, Rashid N, Akhtar M, Shoolingin-Jordan PM. Structural studies of substrate and product complexes of 5-aminolaevulinic acid dehydratase from humans,Escherichia coliand the hyperthermophilePyrobaculum calidifontis. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:9-21. [DOI: 10.1107/s2059798316019525] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/06/2016] [Indexed: 11/11/2022]
Abstract
A number of X-ray analyses of an enzyme involved in a key early stage of tetrapyrrole biosynthesis are reported. Two structures of human 5-aminolaevulinate dehydratase (ALAD), native and recombinant, have been determined at 2.8 Å resolution, showing that the enzyme adopts an octameric quaternary structure in accord with previously published analyses of the enzyme from a range of other species. However, this is in contrast to the finding that a disease-related F12L mutant of the human enzyme uniquely forms hexamers [Breiniget al.(2003),Nature Struct. Biol.10, 757–763]. Monomers of all ALADs adopt the TIM-barrel fold; the subunit conformation that assembles into the octamer includes the N-terminal tail of one monomer curled around the (α/β)8barrel of a neighbouring monomer. Both crystal forms of the human enzyme possess two monomers per asymmetric unit, termedAandB. In the native enzyme there are a number of distinct structural differences between theAandBmonomers, with the latter exhibiting greater disorder in a number of loop regions and in the active site. In contrast, the second monomer of the recombinant enzyme appears to be better defined and the active site of both monomers clearly possesses a zinc ion which is bound by three conserved cysteine residues. In native human ALAD, theAmonomer also has a ligand resembling the substrate ALA which is covalently bound by a Schiff base to one of the active-site lysines (Lys252) and is held in place by an ordered active-site loop. In contrast, these features of the active-site structure are disordered or absent in theBsubunit of the native human enzyme. The octameric structure of the zinc-dependent ALAD from the hyperthermophilePyrobaculum calidifontisis also reported at a somewhat lower resolution of 3.5 Å. Finally, the details are presented of a high-resolution structure of theEscherichia coliALAD enzyme co-crystallized with a noncovalently bound moiety of the product, porphobilinogen (PBG). This structure reveals that the pyrrole side-chain amino group is datively bound to the active-site zinc ion and that the PBG carboxylates interact with the enzymeviahydrogen bonds and salt bridges with invariant residues. A number of hydrogen-bond interactions that were previously observed in the structure of yeast ALAD with a cyclic intermediate resembling the product PBG appear to be weaker in the new structure, suggesting that these interactions are only optimal in the transition state.
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8
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Wang Y, Jones MK, Xu H, Ray WK, White RH. Mechanism of the Enzymatic Synthesis of 4-(Hydroxymethyl)-2-furancarboxaldehyde-phosphate (4-HFC-P) from Glyceraldehyde-3-phosphate Catalyzed by 4-HFC-P Synthase. Biochemistry 2015; 54:2997-3008. [DOI: 10.1021/acs.biochem.5b00176] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yu Wang
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Michael K. Jones
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Huimin Xu
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - W. Keith Ray
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Robert H. White
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
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9
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Tian BX, Erdtman E, Eriksson LA. Catalytic mechanism of porphobilinogen synthase: the chemical step revisited by QM/MM calculations. J Phys Chem B 2012; 116:12105-12. [PMID: 22974111 DOI: 10.1021/jp304743c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Porphobilinogen synthase (PBGS) catalyzes the asymmetric condensation and cyclization of two 5-aminolevulinic acid (5-ALA) substrate molecules to give porphobilinogen (PBG). The chemical step of PBGS is herein revisited using QM/MM (ONIOM) calculations. Two different protonation states and several different mechanisms are considered. Previous mechanisms based on DFT-only calculations are shown unlikely to occur. According to these new calculations, the deprotonation step rather than ring closure is rate-limiting. Both the C-C bond formation first mechanism and the C-N bond formation first mechanism are possible, depending on how the A-site ALA binds to the enzyme. We furthermore propose that future work should focus on the substrate binding step rather than the enzymatic mechanism.
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Affiliation(s)
- Bo-Xue Tian
- School of Chemistry, National University of Ireland-Galway, Galway, Ireland
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10
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van Severen MC, Chaudret R, Parisel O, Piquemal JP. Toward a ligand specific of Pb2+ with respect to the Zn2+ and Ca2+ cations: A track from quantum chemistry. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.02.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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11
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Erdtman E, Bushnell EAC, Gauld JW, Eriksson LA. Computational Insights into the Mechanism of Porphobilinogen Synthase. J Phys Chem B 2010; 114:16860-70. [DOI: 10.1021/jp103590d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Edvin Erdtman
- School of Science and Technology, Örebro Life Science Center and Modeling and Simulation Research Center, Örebro University, Örebro, Sweden; Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada; and School of Chemistry, NUI Galway, Galway, Ireland
| | - Eric A. C. Bushnell
- School of Science and Technology, Örebro Life Science Center and Modeling and Simulation Research Center, Örebro University, Örebro, Sweden; Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada; and School of Chemistry, NUI Galway, Galway, Ireland
| | - James W. Gauld
- School of Science and Technology, Örebro Life Science Center and Modeling and Simulation Research Center, Örebro University, Örebro, Sweden; Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada; and School of Chemistry, NUI Galway, Galway, Ireland
| | - Leif A. Eriksson
- School of Science and Technology, Örebro Life Science Center and Modeling and Simulation Research Center, Örebro University, Örebro, Sweden; Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada; and School of Chemistry, NUI Galway, Galway, Ireland
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12
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Layer G, Reichelt J, Jahn D, Heinz DW. Structure and function of enzymes in heme biosynthesis. Protein Sci 2010; 19:1137-61. [PMID: 20506125 DOI: 10.1002/pro.405] [Citation(s) in RCA: 213] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Tetrapyrroles like hemes, chlorophylls, and cobalamin are complex macrocycles which play essential roles in almost all living organisms. Heme serves as prosthetic group of many proteins involved in fundamental biological processes like respiration, photosynthesis, and the metabolism and transport of oxygen. Further, enzymes such as catalases, peroxidases, or cytochromes P450 rely on heme as essential cofactors. Heme is synthesized in most organisms via a highly conserved biosynthetic route. In humans, defects in heme biosynthesis lead to severe metabolic disorders called porphyrias. The elucidation of the 3D structures for all heme biosynthetic enzymes over the last decade provided new insights into their function and elucidated the structural basis of many known diseases. In terms of structure and function several rather unique proteins were revealed such as the V-shaped glutamyl-tRNA reductase, the dipyrromethane cofactor containing porphobilinogen deaminase, or the "Radical SAM enzyme" coproporphyrinogen III dehydrogenase. This review summarizes the current understanding of the structure-function relationship for all heme biosynthetic enzymes and their potential interactions in the cell.
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Affiliation(s)
- Gunhild Layer
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig D-38106, Germany
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13
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Li N, Chu X, Liu X, Li D. Probing the active site of rat porphobilinogen synthase using newly developed inhibitors. Bioorg Chem 2008; 37:33-40. [PMID: 19095280 DOI: 10.1016/j.bioorg.2008.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Revised: 10/31/2008] [Accepted: 11/05/2008] [Indexed: 11/24/2022]
Abstract
The structurally related tetrapyrrolic pigments are a group of natural products that participate in many of the fundamental biosynthetic and catabolic processes of living organisms. Porphobilinogen synthase catalyzes a rate-limiting step for the biosyntheses of tetrapyrrolic natural products. In the present study, a variety of new substrate analogs and reaction intermediate analogs were synthesized, which were used as probes for studying the active site of rat porphobilinogen synthase. The compounds 1, 3, 6, 9, 14, 16, and 28 were found to be competitive inhibitors of rat porphobilinogen synthase with inhibition constants ranging from 0.96 to 73.04mM. Compounds 7, 10, 12, 13, 15, 17, 18, and 26 were found to be irreversible enzyme inhibitors. For irreversible inhibitors, loose-binding inhibitors were found to give stronger inactivation. The amino group and carboxyl group of the analogs were found to be important for their binding to the enzyme. This study increased our understanding of the active site of porphobilinogen synthase.
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Affiliation(s)
- Nan Li
- Department of Biology and Chemistry, City University of Hong Kong, Kowloon, SAR, PR China
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14
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Selwood T, Tang L, Lawrence SH, Anokhina Y, Jaffe EK. Kinetics and Thermodynamics of the Interchange of the Morpheein Forms of Human Porphobilinogen Synthase. Biochemistry 2008; 47:3245-57. [DOI: 10.1021/bi702113z] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Trevor Selwood
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111
| | - Lei Tang
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111
| | - Sarah H. Lawrence
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111
| | - Yana Anokhina
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111
| | - Eileen K. Jaffe
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111
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15
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Gumm A, Hammershøi A, Kofod-Hansen M, Mønsted O, Osholm Sørensen H. First aminoacetone chelate: [Co(tren){NH2CH2C(O)CH3}]3+-a substrate binding and activation model for zinc(II)-dependent 5-aminolaevulinic acid dehydratase. Dalton Trans 2007:3227-31. [PMID: 17893767 DOI: 10.1039/b707186h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The complex p-[Co(tren){NH(2)CH(2)C(O)CH(3)}](ClO(4))(3).H(2)O was produced stereoselectively from [Co(tren)(O(3)SCF(3))(2)]O(3)SCF(3) () and 2-(aminomethyl)-2-methyl-1,3-dioxolane. The structure of was determined by X-ray crystallography. The complex is the first aminoacetone chelate to be reported and the first structurally characterized example of a non-conjugated ketone moiety coordinated to cobalt(iii). The robust complex was stable to aquation in strong acid and behaved as an acid with pK(a) = 4.99(1) indicative of a strong activation of the aminoacetone ligand towards deprotonation. The complex constitutes a structural model for a proposed substrate binding mode relevant for substrate activation of the zinc(ii)-dependent enzyme 5-aminolaevulinic acid dehydratase.
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Affiliation(s)
- Andreas Gumm
- Department of Chemistry, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark
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Frère F, Nentwich M, Gacond S, Heinz DW, Neier R, Frankenberg-Dinkel N. Probing the active site of Pseudomonas aeruginosa porphobilinogen synthase using newly developed inhibitors. Biochemistry 2006; 45:8243-53. [PMID: 16819823 DOI: 10.1021/bi052611f] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Porphobilinogen synthase catalyzes the first committed step of the tetrapyrrole biosynthesis pathway. In an aldol-like condensation, two molecules of 5-aminolevulinic acid (ALA) form the first pyrrole, porphobilinogen. Newly synthesized analogues of a reaction intermediate of porphobilinogen synthase have been employed in studying the active site and the catalytic mechanism of this early enzyme of tetrapyrrole biosynthesis. This study combines structural and kinetic evaluation of the inhibition potency of these inhibitors. In addition, one of the determined protein structures provides for the first time structural evidence of a magnesium ion in the active site. From these results, we can corroborate an earlier postulated enzymatic mechanism that starts with formation of a C-C bond, linking C3 of the A-side ALA to C4 of the P-side ALA through an aldole addition. The obtained data are discussed with respect to the current literature.
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Affiliation(s)
- Frederic Frère
- Institute for Microbiology, Technical University Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany
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17
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Tang L, Stith L, Jaffe EK. Substrate-induced interconversion of protein quaternary structure isoforms. J Biol Chem 2005; 280:15786-93. [PMID: 15710608 DOI: 10.1074/jbc.m500218200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human porphobilinogen synthase (PBGS) can exist in two dramatically different quaternary structure isoforms, which have been proposed to be in dynamic equilibrium. The quaternary structure isoforms of PBGS result from two alternative conformations of the monomer; one monomer structure assembles into a high activity octamer, whereas the other monomer structure assembles into a low activity hexamer. The kinetic behavior of these oligomers led to the hypothesis that turnover facilitates the interconversion of the oligomeric structures. The current work demonstrates that the interactions of ligands at the enzyme active site promote the structural interconversion between human PBGS quaternary structure isoforms, favoring formation of the octamer. This observation illustrates that the assembly and disassembly of oligomeric proteins can be facilitated by the protein motions that accompany enzymatic catalysis.
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Affiliation(s)
- Lei Tang
- Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
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18
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Frère F, Reents H, Schubert WD, Heinz DW, Jahn D. Tracking the Evolution of Porphobilinogen Synthase Metal Dependence in Vitro. J Mol Biol 2005; 345:1059-70. [PMID: 15644204 DOI: 10.1016/j.jmb.2004.10.053] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2004] [Revised: 10/15/2004] [Accepted: 10/17/2004] [Indexed: 11/28/2022]
Abstract
Metal ions are indispensable cofactors for chemical catalysis by a plethora of enzymes. Porphobilinogen synthases (PBGSs), which catalyse the second step of tetrapyrrole biosynthesis, are grouped according to their dependence on Zn(2+). Using site-directed mutagenesis, we embarked on transforming Zn(2+)-independent Pseudomonas aeruginosa PBGS into a Zn(2+)-dependent enzyme. Nine PBGS variants were generated by permutationally introducing three cysteine residues and a further two residues into the active site of the enzyme to match the homologous Zn(2+)-containing PBGS from Escherichia coli. Crystal structures of seven enzyme variants were solved to elucidate the nature of Zn(2+) coordination at high resolution. The three single-cysteine variants were invariably found to be enzymatically inactive and only one (D139C) was found to bind detectable amounts of Zn(2+). The double mutant A129C/D139C is enzymatically active and binds Zn(2+) in a tetrahedral coordination. Structurally and functionally it mimics mycobacterial PBGS, which bears an equivalent Zn(2+)-coordination site. The remaining two double mutants, without known natural equivalents, reveal strongly distorted tetrahedral Zn(2+)-binding sites. Variant A129C/D131C possesses weak PBGS activity while D131C/D139C is inactive. The triple mutant A129C/D131C/D139C, finally, displays an almost ideal tetrahedral Zn(2+)-binding geometry and a significant Zn(2+)-dependent enzymatic activity. Two additional amino acid exchanges further optimize the active site architecture towards the E.coli enzyme with an additional increase in activity. Our study delineates the potential evolutionary path between Zn(2+)-free and Zn(2+)-dependent PBGS enyzmes showing that the rigid backbone of PBGS enzymes is an ideal framework to create or eliminate metal dependence through a limited number of amino acid exchanges.
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Affiliation(s)
- Frederic Frère
- Institute of Microbiology, Technical University Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany
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19
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Coates L, Beaven G, Erskine PT, Beale SI, Avissar YJ, Gill R, Mohammed F, Wood SP, Shoolingin-Jordan P, Cooper JB. The X-ray structure of the plant like 5-aminolaevulinic acid dehydratase from Chlorobium vibrioforme complexed with the inhibitor laevulinic acid at 2.6 A resolution. J Mol Biol 2004; 342:563-70. [PMID: 15327955 DOI: 10.1016/j.jmb.2004.07.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Revised: 06/28/2004] [Accepted: 07/09/2004] [Indexed: 11/29/2022]
Abstract
5-Aminolaevulinic acid dehydratase (ALAD), an early enzyme of the tetrapyrrole biosynthesis pathway, catalyses the dimerisation of 5-aminolaevulinic acid to form the pyrrole, porphobilinogen. ALAD from Chlorobium vibrioforme is shown to form a homo-octameric structure with 422 symmetry in which each subunit adopts a TIM-barrel fold with a 30 residue N-terminal arm extension. Pairs of monomers associate with their arms wrapped around each other. Four of these dimers interact principally via their arm regions to form octamers in which each active site is located on the surface. The active site contains two invariant lysine residues (200 and 253), one of which (Lys253) forms a Schiff base link with the bound substrate analogue, laevulinic acid. The carboxyl group of the laevulinic acid forms hydrogen bonds with the side-chains of Ser279 and Tyr318. The structure was examined to determine the location of the putative active-site magnesium ion, however, no evidence for the metal ion was found in the electron density map. This is in agreement with previous kinetic studies that have shown that magnesium stimulates but is not required for activity. A different site close to the active site flap, in which a putative magnesium ion is coordinated by a glutamate carboxyl and five solvent molecules may account for the stimulatory properties of magnesium ions on the enzyme.
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Affiliation(s)
- Leighton Coates
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK.
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Abstract
Porphobilinogen synthase (PBGS) catalyzes the first common reaction in the biosynthesis of the tetrapyrroles, the asymmetric condensation of two molecules of delta-aminolevulinic acid to form porphobilinogen. There is a variable requirement for an essential active site zinc that necessitates consideration of PBGS as an enzyme that may exhibit phylogenetic diversity in its chemical reaction mechanism. Recent crystal structures suggest reaction mechanisms that involve two covalent Schiff base linkages between adjacent active site lysine residues and each of the two substrate molecules. The reaction appears to stall at a covalently bound almost-product intermediate that is poised for breakdown to product upon binding of a substrate molecule to an adjacent active site and a subsequent conformational change.
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Affiliation(s)
- Eileen K Jaffe
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.
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