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Stepanova V, Moczulska KE, Vacano GN, Kurochkin I, Ju X, Riesenberg S, Macak D, Maricic T, Dombrowski L, Schörnig M, Anastassiadis K, Baker O, Naumann R, Khrameeva E, Vanushkina A, Stekolshchikova E, Egorova A, Tkachev A, Mazzarino R, Duval N, Zubkov D, Giavalisco P, Wilkinson TG, Patterson D, Khaitovich P, Pääbo S. Reduced purine biosynthesis in humans after their divergence from Neandertals. eLife 2021; 10:58741. [PMID: 33942714 PMCID: PMC8133780 DOI: 10.7554/elife.58741] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 05/02/2021] [Indexed: 12/02/2022] Open
Abstract
We analyze the metabolomes of humans, chimpanzees, and macaques in muscle, kidney and three different regions of the brain. Although several compounds in amino acid metabolism occur at either higher or lower concentrations in humans than in the other primates, metabolites downstream of adenylosuccinate lyase, which catalyzes two reactions in purine synthesis, occur at lower concentrations in humans. This enzyme carries an amino acid substitution that is present in all humans today but absent in Neandertals. By introducing the modern human substitution into the genomes of mice, as well as the ancestral, Neandertal-like substitution into the genomes of human cells, we show that this amino acid substitution contributes to much or all of the reduction of de novo synthesis of purines in humans.
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Affiliation(s)
- Vita Stepanova
- Skolkovo Institute for Science and Technology, Skolkovo, Russian Federation.,Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | | | - Guido N Vacano
- The Eleanor Roosevelt Institute and Knoebel Institute for Healthy Aging, University of Denver, Denver, United States
| | - Ilia Kurochkin
- Skolkovo Institute for Science and Technology, Skolkovo, Russian Federation
| | - Xiangchun Ju
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Okinawa Institute of Science and Technology, Onna-son, Japan
| | | | - Dominik Macak
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tomislav Maricic
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Linda Dombrowski
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Maria Schörnig
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Konstantinos Anastassiadis
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technical University Dresden, Dresden, Germany
| | - Oliver Baker
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technical University Dresden, Dresden, Germany
| | - Ronald Naumann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Anna Vanushkina
- Skolkovo Institute for Science and Technology, Skolkovo, Russian Federation
| | | | - Alina Egorova
- Skolkovo Institute for Science and Technology, Skolkovo, Russian Federation
| | - Anna Tkachev
- Skolkovo Institute for Science and Technology, Skolkovo, Russian Federation
| | - Randall Mazzarino
- The Eleanor Roosevelt Institute and Knoebel Institute for Healthy Aging, University of Denver, Denver, United States
| | - Nathan Duval
- The Eleanor Roosevelt Institute and Knoebel Institute for Healthy Aging, University of Denver, Denver, United States
| | - Dmitri Zubkov
- Skolkovo Institute for Science and Technology, Skolkovo, Russian Federation
| | | | - Terry G Wilkinson
- The Eleanor Roosevelt Institute and Knoebel Institute for Healthy Aging, University of Denver, Denver, United States
| | - David Patterson
- The Eleanor Roosevelt Institute and Knoebel Institute for Healthy Aging, University of Denver, Denver, United States
| | - Philipp Khaitovich
- Skolkovo Institute for Science and Technology, Skolkovo, Russian Federation
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Okinawa Institute of Science and Technology, Onna-son, Japan
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2
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Van Laer B, Kapp U, Soler-Lopez M, Moczulska K, Pääbo S, Leonard G, Mueller-Dieckmann C. Molecular comparison of Neanderthal and Modern Human adenylosuccinate lyase. Sci Rep 2018; 8:18008. [PMID: 30573755 PMCID: PMC6301967 DOI: 10.1038/s41598-018-36195-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/16/2018] [Indexed: 12/04/2022] Open
Abstract
The availability of genomic data from extinct homini such as Neanderthals has caused a revolution in palaeontology allowing the identification of modern human-specific protein substitutions. Currently, little is known as to how these substitutions alter the proteins on a molecular level. Here, we investigate adenylosuccinate lyase, a conserved enzyme involved in purine metabolism for which several substitutions in the modern human protein (hADSL) have been described to affect intelligence and behaviour. During evolution, modern humans acquired a specific substitution (Ala429Val) in ADSL distinguishing it from the ancestral variant present in Neanderthals (nADSL). We show here that despite this conservative substitution being solvent exposed and located distant from the active site, there is a difference in thermal stability, but not enzymology or ligand binding between nADSL and hADSL. Substitutions near residue 429 which do not profoundly affect enzymology were previously reported to cause neurological symptoms in humans. This study also reveals that ADSL undergoes conformational changes during catalysis which, together with the crystal structure of a hitherto undetermined product bound conformation, explains the molecular origin of disease for several modern human ADSL mutants.
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Affiliation(s)
- Bart Van Laer
- Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, F-38043, Grenoble, France
| | - Ulrike Kapp
- Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, F-38043, Grenoble, France
| | - Montserrat Soler-Lopez
- Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, F-38043, Grenoble, France
| | - Kaja Moczulska
- Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany.,The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany
| | - Gordon Leonard
- Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, F-38043, Grenoble, France
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3
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Yeast Cell Wall Chitin Reduces Wine Haze Formation. Appl Environ Microbiol 2018; 84:AEM.00668-18. [PMID: 29703738 DOI: 10.1128/aem.00668-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 04/24/2018] [Indexed: 11/20/2022] Open
Abstract
Protein haze formation in bottled wines is a significant concern for the global wine industry, and wine clarification before bottling is therefore a common but expensive practice. Previous studies have shown that wine yeast strains can reduce haze formation through the secretion of certain mannoproteins, but it has been suggested that other yeast-dependent haze protective mechanisms exist. On the other hand, the addition of chitin has been shown to reduce haze formation, likely because grape chitinases have been shown to be the major contributors to haze. In this study, Chardonnay grape must fermented by various yeast strains resulted in wines with different protein haze levels, indicating differences in haze-protective capacities of the strains. The cell wall chitin levels of these strains were determined, and a strong correlation between cell wall chitin levels and haze protection capability was observed. To further evaluate the mechanism of haze protection, Escherichia coli-produced green fluorescent protein (GFP)-tagged grape chitinase was shown to bind efficiently to yeast cell walls in a cell wall chitin concentration-dependent manner, while commercial chitinase was removed from synthetic wine in quantities that also correlated with the cell wall chitin levels of the strains. Our findings suggest a new mechanism of reducing wine haze, and we propose a strategy for optimizing wine yeast strains to improve wine clarification.IMPORTANCE In this study, we establish a new mechanism by which wine yeast strains can impact the protein haze formation of wines, and we demonstrate that yeast cell wall chitin binds grape chitinase in a chitin concentration-dependent manner. We also show that yeast can remove this haze-forming protein from wine. Chitin has in the past been shown to efficiently reduce wine haze formation when added to the wine in high concentration as a clarifying agent. Our data suggest that the selection of yeast strains with high levels of cell wall chitin can reduce protein haze. We also investigate how yeast cell wall chitin levels are affected by environmental conditions.
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4
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Galina L, Dalberto PF, Borges Martinelli LK, Roth CD, Michel Pinto AF, Villela AD, Bizarro CV, Machado P, Saraiva Macedo Timmers LF, Norberto de Souza O, Marcelino de Carvalho Filho E, Basso LA, Santos DS. Biochemical, thermodynamic and structural studies of recombinant homotetrameric adenylosuccinate lyase fromLeishmania braziliensis. RSC Adv 2017. [DOI: 10.1039/c7ra10526f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Functional and structural data suggested that His197and Ser322residues play a role inLbASL catalysis.
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5
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Davis BW, Aumiller WM, Hashemian N, An S, Armaou A, Keating CD. Colocalization and Sequential Enzyme Activity in Aqueous Biphasic Systems: Experiments and Modeling. Biophys J 2015; 109:2182-94. [PMID: 26588576 PMCID: PMC4656855 DOI: 10.1016/j.bpj.2015.09.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 09/10/2015] [Accepted: 09/21/2015] [Indexed: 12/13/2022] Open
Abstract
Subcellular compartmentalization of biomolecules and their reactions is common in biology and provides a general strategy for improving and/or controlling kinetics in metabolic pathways that contain multiple sequential enzymes. Enzymes can be colocalized in multiprotein complexes, on scaffolds or inside subcellular organelles. Liquid organelles formed by intracellular phase coexistence could provide an additional means of sequential enzyme colocalization. Here we use experiment and computation to explore the kinetic consequences of sequential enzyme compartmentalization into model liquid organelles in a crowded polymer solution. Two proteins of the de novo purine biosynthesis pathway, ASL (adenylosuccinate lyase, Step 8) and ATIC (5-aminoimidazole-4-carboxamide ribonucleotide transformylase/inosine monophosphate cyclohydrolase, Steps 9 and 10), were studied in a polyethylene glycol/dextran aqueous two-phase system. Dextran-rich phase droplets served as model liquid compartments for enzyme colocalization. In this system, which lacks any specific binding interactions between the phase-forming polymers and the enzymes, we did not observe significant rate enhancements from colocalization for the overall reaction under our experimental conditions. The experimental results were used to adapt a mathematical model to quantitatively describe the kinetics. The mathematical model was then used to explore additional, experimentally inaccessible conditions to predict when increased local concentrations of enzymes and substrates can (or cannot) be expected to yield increased rates of product formation. Our findings indicate that colocalization within these simplified model liquid organelles can lead to enhanced metabolic rates under some conditions, but that very strong partitioning into the phase that serves as the compartment is necessary. In vivo, this could be provided by specific binding affinities between components of the liquid compartment and the molecules to be localized within it.
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Affiliation(s)
- Bradley W Davis
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania
| | - William M Aumiller
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania
| | - Negar Hashemian
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania
| | - Songon An
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania
| | - Antonios Armaou
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania.
| | - Christine D Keating
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania.
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6
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Chen X, Wu J, Song W, Zhang L, Wang H, Liu L. Fumaric acid production by Torulopsis glabrata: engineering the urea cycle and the purine nucleotide cycle. Biotechnol Bioeng 2014; 112:156-67. [PMID: 25060134 DOI: 10.1002/bit.25334] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 06/01/2014] [Accepted: 07/07/2014] [Indexed: 11/09/2022]
Abstract
A multi-vitamin auxotrophic Torulopsis glabrata strain, a pyruvate producer, was further engineered to produce fumaric acid. Using the genome-scale metabolic model iNX804 of T. glabrata, four fumaric acid biosynthetic pathways, involving the four cytosolic enzymes, argininosuccinate lyase (ASL), adenylosuccinate lyase (ADSL), fumarylacetoacetase (FAA), and fumarase (FUM1), were found. Athough single overexpression of each of the four enzymes in the cytosol improved fumaric acid production, the highest fumaric acid titer (5.62 g L(-1) ) was obtained with strain T.G-ASL(H) -ADSL(L) by controlling the strength of ASL at a high level and ADSL at a low level. In order to further improve the production of fumaric acid, the SpMAE1 gene encoding the C4 -dicarboxylic acids transporter was overexpressed in strain T.G-ASL(H) -ADSL(L) -SpMAE1 and the final fumaric acid titer increased to 8.83 g L(-1) . This study provides a novel strategy for fumaric acid biosynthesis by utilizing the urea cycle and the purine nucleotide cycle to enhance the bridge between carbon metabolism and nitrogen metabolism.
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Affiliation(s)
- Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, Wuxi, 214122, China
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7
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Ray SP, Duval N, Wilkinson TG, Shaheen SE, Ghosh K, Patterson D. Inherent properties of adenylosuccinate lyase could explain S-Ado/SAICAr ratio due to homozygous R426H and R303C mutations. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1545-53. [PMID: 23714113 DOI: 10.1016/j.bbapap.2013.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 05/16/2013] [Accepted: 05/17/2013] [Indexed: 12/11/2022]
Abstract
Adenylosuccinate lyase (ADSL) is a homotetrameric enzyme involved in the de novo purine biosynthesis pathway and purine nucleotide cycle. Missense mutations in the protein lead to ADSL deficiency, an inborn error of purine metabolism characterized by neurological and physiological symptoms. ADSL deficiency is biochemically diagnosed by elevated levels of succinylaminoimidazolecarboxamide riboside (SAICAr) and succinyladenosine (S-Ado), the dephosphorylated derivatives of the substrates. S-Ado/SAICAr ratios have been associated with three phenotypic groups. Different hypotheses to explain these ratios have been proposed. Recent studies have focused on measuring activity on the substrates independently. However, it is important to examine mixtures of the substrates to determine if mutations affect enzyme activity on both substrates similarly in these conditions. The two substrates may experience an indirect communication due to being acted upon by the same enzyme, altering their activities from the non-competitive case. In this study, we investigate this hidden coupling between the two substrates. We chose two mutations that represent extremes of the phenotype, R426H and R303C. We describe a novel electrochemical-detection method of measuring the kinetic activity of ADSL in solution with its two substrates at varying concentration ratios. Furthermore, we develop an enzyme kinetic model to predict substrate activity from a given ratio of substrate concentrations. Our findings indicate a non-linear dependence of the activities on the substrate ratios due to competitive binding, distinct differences in the behaviors of the different mutations, and S-Ado/SAICAr ratios in patients could be explained by inherent properties of the mutant enzyme.
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Affiliation(s)
- Stephen P Ray
- Department of Physics and Astronomy, University of Denver, Denver, CO, USA.
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8
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Keller KE, Tan IS, Lee YS. SAICAR stimulates pyruvate kinase isoform M2 and promotes cancer cell survival in glucose-limited conditions. Science 2012; 338:1069-72. [PMID: 23086999 DOI: 10.1126/science.1224409] [Citation(s) in RCA: 163] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Pyruvate kinase isoform M2 (PKM2) plays an important role in the growth and metabolic reprogramming of cancer cells in stress conditions. Here, we report that SAICAR (succinylaminoimidazolecarboxamide ribose-5'-phosphate, an intermediate of the de novo purine nucleotide synthesis pathway) specifically stimulates PKM2. Upon glucose starvation, cellular SAICAR concentration increased in an oscillatory manner and stimulated PKM2 activity in cancer cells. Changes in SAICAR amounts in cancer cells altered cellular energy level, glucose uptake, and lactate production. The SAICAR-PKM2 interaction also promoted cancer cell survival in glucose-limited conditions. SAICAR accumulation was not observed in normal adult epithelial cells or lung fibroblasts, regardless of glucose conditions. This allosteric regulation may explain how cancer cells coordinate different metabolic pathways to optimize their growth in the nutrient-limited conditions commonly observed in the tumor microenvironment.
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Affiliation(s)
- Kirstie E Keller
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
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9
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Ray SP, Deaton MK, Capodagli GC, Calkins LAF, Sawle L, Ghosh K, Patterson D, Pegan SD. Structural and biochemical characterization of human adenylosuccinate lyase (ADSL) and the R303C ADSL deficiency-associated mutation. Biochemistry 2012; 51:6701-13. [PMID: 22812634 DOI: 10.1021/bi300796y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Adenylosuccinate lyase (ADSL) deficiency is a rare autosomal recessive disorder, which causes a defect in purine metabolism resulting in neurological and physiological symptoms. ADSL executes two nonsequential steps in the de novo synthesis of AMP: the conversion of phosphoribosylsuccinyl-aminoimidazole carboxamide (SAICAR) to phosphoribosylaminoimidazole carboxamide, which occurs in the de novo synthesis of IMP, and the conversion of adenylosuccinate to AMP, which occurs in the de novo synthesis of AMP and also in the purine nucleotide cycle, using the same active site. Mutation of ADSL's arginine 303 to a cysteine is known to lead to ADSL deficiency. Interestingly, unlike other mutations leading to ADSL deficiency, the R303C mutation has been suggested to more significantly affect the enzyme's ability to catalyze the conversion of succinyladenosine monophosphate than that of SAICAR to their respective products. To better understand the causation of disease due to the R303C mutation, as well as to gain insights into why the R303C mutation potentially has a disproportional decrease in activity toward its substrates, the wild type (WT) and the R303C mutant of ADSL were investigated enzymatically and thermodynamically. Additionally, the X-ray structures of ADSL in its apo form as well as with the R303C mutation were elucidated, providing insight into ADSL's cooperativity. By utilizing this information, a model for the interaction between ADSL and SAICAR is proposed.
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Affiliation(s)
- Stephen P Ray
- Department of Physics and Astronomy, University of Denver, Denver, CO 80208-0183, USA
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10
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De Zoysa Ariyananda L, Antonopoulos C, Currier J, Colman RF. In vitro hybridization and separation of hybrids of human adenylosuccinate lyase from wild-type and disease-associated mutant enzymes. Biochemistry 2011; 50:1336-46. [PMID: 21210713 DOI: 10.1021/bi101734q] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human adenylosuccinate lyase (ASL) deficiency is an inherited metabolic disease in which the majority of the patients are compound heterozygotes for the mutations that occur in the ASL gene. Starting with purified wild-type (WT) and single-mutant human ASL, we generated in vitro hybrids that mimic compound heterozygote ASL. For this study, we used His-tagged WT/non-His-tagged WT, His-tagged WT/non-His-tagged R396C, His-tagged WT/non-His-tagged R396H, His-tagged R194C/non-His-tagged R396C, and His-tagged L311V/non-His-tagged R396H enzyme pairs. We generated various hybrids by denaturing pairs of enzymes in 1 M guanidinium chloride and renaturing them by removing the denaturant. The hybrids were separated on a nickel-nitrilotriacetic acid-agarose column based on the number of His tags present in the enzyme tetramer. Analytical ultracentrifuge data indicate that the hybrids have predominant amounts of heterotetramers. Analysis of the V(max) values of the hybrids indicates that most of the subunits behave independently; however, the hybrid tetramers retain weak positive cooperativity, indicating that there is some interaction between the different subunit types. The interactions between WT and mutant subunits may be advantageous to the parents of ASL deficient patients, while the interactions between some mutant subunits may assist heterozygote ASL deficient patients.
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Ariyananda LDZ, Lee P, Antonopoulos C, Colman RF. Biochemical and biophysical analysis of five disease-associated human adenylosuccinate lyase mutants. Biochemistry 2009; 48:5291-302. [PMID: 19405474 DOI: 10.1021/bi802321m] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Adenylosuccinate lyase (ASL), a catalyst of key reactions in purine biosynthesis, is normally a homotetramer in which three subunits contribute to each of four active sites. Human ASL deficiency is an inherited metabolic disease associated with autism and mental retardation. We have characterized five disease-associated ASL mutants: R194C and K246E are located at subunit interfaces, L311V is in the central helical region away from the active site, and R396C and R396H are at the entrance to the active site. The V(max) (at 25 degrees C) for R194C is comparable to that of WT, while those of L311V, R396C, R396H, and K246E are considerably reduced and affinity for adenylosuccinate is retained. The mutant enzymes have decreased positive cooperativity as compared to WT. K246E exists mainly as dimer or monomer, accounting for its negligible activity, whereas the other mutant enzymes are similar to WT in the predominance of tetramer. At 37 degrees C, the specific activity of WT and these mutant enzymes slowly decreases 30-40% with time and reaches a limiting specific activity without changing significantly the amount of tetramer. Mutant R194C is unique in being rapidly inactivated at the harsher temperature of 60 degrees C, indicating that it is the least stable enzyme in vitro. Conformational changes in the mutant enzymes are evident from protein fluorescence intensity at 25 degrees C and after incubation at 37 degrees C, which correlates with the loss of enzymatic activity. Thus, these disease-associated single mutations can yield enzyme with reduced activity either by affecting the active site or by perturbing the enzyme's structure and/or native conformation which are required for catalytic function.
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12
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Sivendran S, Colman RF. Effect of a new non-cleavable substrate analog on wild-type and serine mutants in the signature sequence of adenylosuccinate lyase of Bacillus subtilis and Homo sapiens. Protein Sci 2008; 17:1162-74. [PMID: 18469177 DOI: 10.1110/ps.034777.108] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Adenylosuccinate lyase (ASL) catalyzes two beta-elimination reactions in purine biosynthesis, leading to the question of whether the two substrates occupy the same or different active sites. Kinetic studies of Bacillus subtilis and human ASL with a new substrate analog, adenosine phosphonobutyric acid, 2'(3'), 5'-diphosphate (APBADP), show that it acts as a competitive inhibitor with respect to either substrate (K(I) approximately 0.1 microM), indicating that the two substrates occupy the same active site. Binding studies show that both the B. subtilis and human ASLs bind up to 4 mol of APBADP per mole of enzyme tetramer and that both enzymes exhibit cooperativity: negative for B. subtilis ASL and positive for human ASL. Mutant B. subtilis ASLs, with replacements for residues previously identified as critical for catalysis, bind the substrate analog similarly to wild-type ASL. Two serines in a flexible loop of ASL have been proposed to play roles in catalysis because they are close to the substrate in the crystal structure of Escherichia coli ASL. We have now mutated the corresponding serines to alanines in B. subtilis and human ASL to evaluate their involvement in enzyme function. Kinetic data reveal that human Ser(289) and B. subtilis Ser(262) and Ser(263) are essential for catalysis, while the ability of these Ser mutants to bind APBADP suggests that they do not contribute to substrate affinity. Although these serines are not visible in the crystal structure of human adenylosuccinate lyase complexed with substrate or products (PDB #2VD6), they may be interacting with the active sites.
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Affiliation(s)
- Sharmila Sivendran
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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13
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Segall ML, Cashman MA, Colman RF. Important roles of hydroxylic amino acid residues in the function of Bacillus subtilis adenylosuccinate lyase. Protein Sci 2007; 16:441-8. [PMID: 17322529 PMCID: PMC2203318 DOI: 10.1110/ps.062650007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 12/06/2006] [Accepted: 12/07/2006] [Indexed: 10/23/2022]
Abstract
Thr(93), Ser(94), Thr(140), and Ser(306) are conserved in all adenylosuccinate lyases (ASL) and are close to other amino acids previously identified by mutagenesis as being in the active site. To test their involvement in the enzyme's function, each of these amino acids was replaced by alanine. All the mutants exhibit circular dichroism spectra which are similar to that of wild-type enzyme, indicating there is no appreciable change in secondary structure. T93A exhibits 0.5% of the V(max) of wild-type ASL with a 10-fold increase in K(m) for adenylosuccinate. S94A has 65% of the V(max) of wild-type ASL with little change in K(m). T140A exhibits 0.03% of the activity of wild-type enzyme with an 11-fold increase in K(m). S306A has 0.4% of the V(max) of wild-type ASL with a sevenfold increase in K(m). Measurements of the pH-V(max) profile reveal a pK(2) value for S94A of 7.83 and S306A of 7.65, in contrast to 8.24 for the wild-type enzyme and 8.42 for T93A. Thr(93) may orient adenylosuccinate optimally for catalysis, while Ser(94) stabilizes protonated His(89), a determinant of pK(2). Thr(140) may, through hydrogen bonding, interact with Asn(270), an amino acid essential for catalysis. Ser(306) may be involved in a hydrogen bond network that ultimately stabilizes protonated His(68), which is probably the general acid in the reaction of enzyme with substrate. The results of this paper demonstrate the importance in the catalytic function of ASL of hydrogen bonds and hydrogen bonding networks involving serine and threonine.
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Affiliation(s)
- Mark L Segall
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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