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Jabłońska J, Tawfik DS. Innovation and tinkering in the evolution of oxidases. Protein Sci 2022; 31:e4310. [PMID: 35481655 PMCID: PMC9040561 DOI: 10.1002/pro.4310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/25/2022] [Accepted: 04/01/2022] [Indexed: 12/19/2022]
Abstract
Although molecular oxygen is a relative newcomer to the biosphere, it has had a profound impact on metabolism. About 700 oxygen‐dependent enzymatic reactions are known, the vast majority of which emerged only after the appearance of oxygen in the biosphere, circa 3 billion years ago. Oxygen was a major driving force for evolutionary innovation—~60% of all known oxygen‐dependent enzyme families emerged as such; that is, the founding ancestor was an O2‐dependent enzyme. The other 40% seem to have diverged by tinkering from pre‐existing proteins whose function was not related to oxygen. Here, we focus on the latter. We describe transitions from various enzyme classes, as well as from non‐enzymatic proteins, and we explore these transitions in terms of catalytic chemistry, metabolism, and protein structure. These transitions vary from subtle ones, such as simply repurposing oxidoreductases by replacing an electron acceptor such as NAD by O2, to drastic changes in reaction mechanism, such as turning carboxylases and hydrolases into oxidases. The latter is more common and can occur with strikingly minor changes, for example, only one mutation in the active site. We further suggest that engineering enzymes to harness the extraordinary reactivity of oxygen may yield higher catabolic power and versatility.
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Affiliation(s)
- Jagoda Jabłońska
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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2
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Liu H, Cui H, Huang Y, Gao S, Tao S, Hu J, Wan Y. Xenobiotics Targeting Cardiolipin Metabolism to Promote Thrombosis in Zebrafish. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:3855-3866. [PMID: 33629855 DOI: 10.1021/acs.est.0c08068] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Exposure to environmental pollutants is an important factor contributing to the development and severity of thrombosis. However, the important physiological molecules in the thrombotic processes affected by environmental exposures remain unknown. In this study, we show that exposure to environmental chemicals disrupts the equilibrium of cardiolipins (CLs), and directing CL synthesis promotes thrombosis. Using an untargeted metabolomics approach, approximately 3030 molecules were detected in zebrafish embryos exposed to 11 environmental chemicals and automatically clustered into a network. Interconnectivity among CLs and linoleates or isoxanthopterin was discovered through the highly consistent variations in the coregulated metabolites in the network. The chemical exposure resulted in significant upregulation of CLs through influencing the enzymatic activities of phospholipase A2, cardiolipin synthase, and lysocardiolipin acyltransferase. Consequently, metabolic disorders of CLs affected the levels of anticardiolipin antibodies, disrupted the homeostasis between platelet thromboxane A2 and endothelial prostacyclin, and promoted thrombotic events including heart ischemia and tachycardia. Our study thus reveals the common molecular mechanisms underlying the CL-induced thrombosis targeted by environmental exposures.
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Affiliation(s)
- Hang Liu
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Hongyang Cui
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yixuan Huang
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Shixiong Gao
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Shu Tao
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Jianying Hu
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yi Wan
- Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
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3
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Folate biosynthesis pathway: mechanisms and insights into drug design for infectious diseases. Future Med Chem 2018; 10:935-959. [PMID: 29629843 DOI: 10.4155/fmc-2017-0168] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Folate pathway is a key target for the development of new drugs against infectious diseases since the discovery of sulfa drugs and trimethoprim. The knowledge about this pathway has increased in the last years and the catalytic mechanism and structures of all enzymes of the pathway are fairly understood. In addition, differences among enzymes from prokaryotes and eukaryotes could be used for the design of specific inhibitors. In this review, we show a panorama of progress that has been achieved within the folate pathway obtained in the last years. We explored the structure and mechanism of enzymes, several genetic features, strategies, and approaches used in the design of new inhibitors that have been used as targets in pathogen chemotherapy.
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Falcão VCA, Villela AD, Rodrigues-Junior VS, Pissinate K, Eichler P, Pinto AFM, Basso LA, Santos DS, Bizarro CV. Validation of Mycobacterium tuberculosis dihydroneopterin aldolase as a molecular target for anti-tuberculosis drug development. Biochem Biophys Res Commun 2017; 485:814-819. [PMID: 28257847 DOI: 10.1016/j.bbrc.2017.02.137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 02/27/2017] [Indexed: 12/17/2022]
Abstract
An early step of target validation in antimicrobial drug discovery is to prove that a gene coding for a putative target is essential for pathogen's viability. However, little attention has been paid to demonstrate the causal links between gene essentiality and a particular protein function that will be the focus of a drug discovery effort. This should be considered an important step in target validation since a growing number of proteins are found to exhibit multiple and unrelated tasks. Here, we show that the Mycobacterium tuberculosis (Mtb) folB gene is essential and that this essentiality depends on the dihydroneopterin aldolase/epimerase activities of its protein product, the FolB protein from the folate biosynthesis pathway. The wild-type (WT) MtFolB and point mutants K99A and Y54F were cloned, expressed, purified and monitored for the aldolase, epimerase and oxygenase activities using HPLC. In contrast to the WT MtFolB, both mutants have neither aldolase nor epimerase activities in the conditions assayed. We then performed gene knockout experiments and showed that folB gene is essential for Mtb survival under the conditions tested. Moreover, only the WT folB sequence could be used as a rescue copy in gene complementation studies. When the sequences of mutants K99A or Y54F were used for complementation, no viable colonies were obtained, indicating that aldolase and/or epimerase activities are crucial for Mtb survival. These results provide a solid basis for further work aiming to develop new anti-TB agents acting as inhibitors of the aldolase/epimerase activities of MtFolB.
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Affiliation(s)
- V C A Falcão
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular (PUCRS), Brazil
| | - A D Villela
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Medicina e Ciências da Saúde (PUCRS), Porto Alegre, RS, Brazil
| | - V S Rodrigues-Junior
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Medicina e Ciências da Saúde (PUCRS), Porto Alegre, RS, Brazil
| | - K Pissinate
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil
| | - P Eichler
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil
| | - A F M Pinto
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil
| | - L A Basso
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular (PUCRS), Brazil; Programa de Pós-Graduação em Medicina e Ciências da Saúde (PUCRS), Porto Alegre, RS, Brazil
| | - D S Santos
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular (PUCRS), Brazil
| | - C V Bizarro
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular (PUCRS), Brazil.
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Blaszczyk J, Lu Z, Li Y, Yan H, Ji X. Crystallographic and molecular dynamics simulation analysis of Escherichia coli dihydroneopterin aldolase. Cell Biosci 2014; 4:52. [PMID: 25264482 PMCID: PMC4176595 DOI: 10.1186/2045-3701-4-52] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 08/26/2014] [Indexed: 11/26/2022] Open
Abstract
Background Dihydroneopterin aldolase (DHNA) catalyzes the conversion of 7,8-dihydroneopterin to 6-hydroxymethyl-7,8-dihydropterin and also the epimerization of DHNP to 7,8-dihydromonapterin. Previously, we determined the crystal structure of Staphylococcus aureus DHNA (SaDHNA) in complex with the substrate analogue neopterin (NP). We also showed that Escherichia coli DHNA (EcDHNA) and SaDHNA have significantly different binding and catalytic properties by biochemical analysis. On the basis of these structural and functional data, we proposed a catalytic mechanism involving two proton wires. Results To understand the structural basis for the biochemical differences and further investigate the catalytic mechanism of DHNA, we have determined the structure of EcDHNA complexed with NP at 1.07-Å resolution [PDB:2O90], built an atomic model of EcDHNA complexed with the substrate DHNP, and performed molecular dynamics (MD) simulation analysis of the substrate complex. EcDHNA has the same fold as SaDHNA and also forms an octamer that consists of two tetramers, but the packing of one tetramer with the other is significantly different between the two enzymes. Furthermore, the structures reveal significant differences in the vicinity of the active site, particularly in the loop that connects strands β3 and β4, mainly due to the substitution of nearby residues. The building of an atomic model of the complex of EcDHNA and the substrate DHNP and the MD simulation of the complex show that some of the hydrogen bonds between the substrate and the enzyme are persistent, whereas others are transient. The substrate binding model and MD simulation provide the molecular basis for the biochemical behaviors of the enzyme, including noncooperative substrate binding, indiscrimination of a pair of epimers as the substrates, proton wire switching during catalysis, and formation of epimerization product. Conclusions The EcDHNA and SaDHNA structures, each in complex with NP, reveal the basis for the biochemical differences between EcDHNA and SaDHNA. The atomic substrate binding model and MD simulation offer insights into substrate binding and catalysis by DHNA. The EcDHNA structure also affords an opportunity to develop antimicrobials specific for Gram-negative bacteria, as DHNAs from Gram-negative bacteria are highly homologous and E. coli is a representative of this class of bacteria.
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Affiliation(s)
- Jaroslaw Blaszczyk
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702 USA ; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824 USA ; Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Zhenwei Lu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824 USA ; Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232 USA
| | - Yue Li
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824 USA
| | - Honggao Yan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824 USA
| | - Xinhua Ji
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702 USA
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Biochemical characterization of a dihydroneopterin aldolase used for methanopterin biosynthesis in methanogens. J Bacteriol 2014; 196:3191-8. [PMID: 24982305 DOI: 10.1128/jb.01812-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gene encoding 7,8-dihydroneopterin aldolase (DHNA) was recently identified in archaea through comparative genomics as being involved in methanopterin biosynthesis (V. Crécy-Lagard, G. Phillips, L. L. Grochowski, B. El Yacoubi, F. Jenney, M. W. Adams, A. G. Murzin, and R. H. White, ACS Chem. Biol. 7:1807-1816, 2012, doi:10.1021/cb300342u). Archaeal DHNA shows a unique secondary and quaternary structure compared with bacterial and plant DHNAs. Here, we report a detailed biochemical examination of DHNA from the methanogen Methanocaldococcus jannaschii. Kinetic studies show that M. jannaschii DHNA possesses a catalytic capability with a kcat/Km above 10(5) M(-1) s(-1) at 70°C, and at room temperature it exhibits a turnover number (0.07 s(-1)) comparable to bacterial DHNAs. We also found that this enzyme follows an acid-base catalytic mechanism similar to the bacterial DHNAs, except when using alternative catalytic residues. We propose that in the absence of lysine, which is considered to be the general base in bacterial DHNAs, an invariant water molecule likely functions as the catalytic base, and the strictly conserved His35 and Gln61 residues serve as the hydrogen bond partners to adjust the basicity of the water molecule. Indeed, substitution of either His35 or Gln61 causes a 20-fold decrease in kcat. An invariant Tyr78 is also shown to be important for catalysis, likely functioning as a general acid. Glu25 plays an important role in substrate binding, since replacing Glu25 by Gln caused a ≥25-fold increase in Km. These results provide important insights into the catalytic mechanism of archaeal DHNAs.
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Czekster CM, Blanchard JS. One substrate, five products: reactions catalyzed by the dihydroneopterin aldolase from Mycobacterium tuberculosis. J Am Chem Soc 2012; 134:19758-71. [PMID: 23150985 DOI: 10.1021/ja308350f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Tetrahydrofolate cofactors are required for one carbon transfer reaction involved in the synthesis of purines, amino acids, and thymidine. Inhibition of tetrahydrofolate biosynthesis is a powerful therapeutic strategy in the treatment of several diseases, and the possibility of using antifolates to inhibit enzymes from Mycobacterium tuberculosis has been explored. This work focuses on the study of the first enzyme in tetrahydrofolate biosynthesis that is unique to bacteria, dihydroneopterin aldolase (MtDHNA). This enzyme requires no metals or cofactors and does not form a protein-mediated Schiff base with the substrate, unlike most aldolases. Here, we were able to demonstrate that the reaction catalyzed by MtDHNA generates three different pterin products, one of which is not produced by other wild-type DHNAs. The enzyme-substrate complex partitions 51% in the first turnover to form the aldolase products, 24% to the epimerase product and 25% to the oxygenase products. The aldolase reaction is strongly pH dependent, and apparent pK(a) values were obtained for the first time for this class of enzyme. Furthermore, chemistry is rate limiting for the aldolase reaction, and the analysis of solvent kinetic isotope effects in steady-state and pre-steady-state conditions, combined with proton inventory studies, revealed that two protons and a likely solvent contribution are involved in formation and breakage of a common intermediate. This study provides information about the plasticity required from a catalyst that possesses high substrate specificity while being capable of utilizing two distinct epimers with the same efficiency to generate five distinct products.
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Affiliation(s)
- Clarissa M Czekster
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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8
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Cofactor-independent oxidases and oxygenases. Appl Microbiol Biotechnol 2010; 86:791-804. [DOI: 10.1007/s00253-010-2455-0] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 01/14/2010] [Accepted: 01/14/2010] [Indexed: 10/19/2022]
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Toscano MD, Woycechowsky KJ, Hilvert D. Minimalist active-site redesign: teaching old enzymes new tricks. Angew Chem Int Ed Engl 2007; 46:3212-36. [PMID: 17450624 DOI: 10.1002/anie.200604205] [Citation(s) in RCA: 212] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Although nature evolves its catalysts over millions of years, enzyme engineers try to do it a bit faster. Enzyme active sites provide highly optimized microenvironments for the catalysis of biologically useful chemical transformations. Consequently, changes at these centers can have large effects on enzyme activity. The prediction and control of these effects provides a promising way to access new functions. The development of methods and strategies to explore the untapped catalytic potential of natural enzyme scaffolds has been pushed by the increasing demand for industrial biocatalysts. This Review describes the use of minimal modifications at enzyme active sites to expand their catalytic repertoires, including targeted mutagenesis and the addition of new reactive functionalities. Often, a novel activity can be obtained with only a single point mutation. The many successful examples of active-site engineering through minimal mutations give useful insights into enzyme evolution and open new avenues in biocatalyst research.
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Affiliation(s)
- Miguel D Toscano
- Laboratory of Organic Chemistry, ETH Zürich, Hönggerberg, Switzerland
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Toscano M, Woycechowsky K, Hilvert D. Minimale Umgestaltung aktiver Enzymtaschen – wie man alten Enzymen neue Kunststücke beibringt. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200604205] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Abstract
Dihydroneopterin aldolase (DHNA) catalyzes both the cleavage of 7,8-dihydro-D-neopterin (DHNP) to form 6-hydroxymethyl-7,8-dihydropterin (HP) and glycolaldehyde and the epimerization of DHNP to form 7,8-dihydro-L-monapterin (DHMP). Whether the epimerization reaction uses the same reaction intermediate as the aldol reaction or the deprotonation and reprotonation of C2' of DHNP has been investigated by NMR analysis of the reaction products in a D2O solvent. No deuteration of C2' was observed for the newly formed DHMP. This result strongly suggests that the epimerization reaction uses the same reaction intermediate as the aldol reaction. In contrast with an earlier observation, the DHNA-catalyzed reaction is reversible, which also supports a nonstereospecific retroaldol/aldol mechanism for the epimerization reaction. The binding and catalytic properties of DHNAs from both Staphylococcus aureus (SaDHNA) and Escherichia coli (EcDHNA) were determined by equilibrium binding and transient kinetic studies. A complete set of kinetic constants for both the aldol and epimerization reactions according to a unified kinetic mechanism was determined for both SaDHNA and EcDHNA. The results show that the two enzymes have significantly different binding and catalytic properties, in accordance with the significant sequence differences between them.
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Affiliation(s)
- Yi Wang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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Blaszczyk J, Li Y, Gan J, Yan H, Ji X. Structural basis for the aldolase and epimerase activities of Staphylococcus aureus dihydroneopterin aldolase. J Mol Biol 2007; 368:161-9. [PMID: 17331536 PMCID: PMC1885205 DOI: 10.1016/j.jmb.2007.02.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Revised: 02/01/2007] [Accepted: 02/05/2007] [Indexed: 11/16/2022]
Abstract
Dihydroneopterin aldolase (DHNA) catalyzes the conversion of 7,8-dihydroneopterin (DHNP) to 6-hydroxymethyl-7,8-dihydropterin (HP) and the epimerization of DHNP to 7,8-dihydromonopterin (DHMP). Although crystal structures of the enzyme from several microorganisms have been reported, no structural information is available about the critical interactions between DHNA and the trihydroxypropyl moiety of the substrate, which undergoes bond cleavage and formation. Here, we present the structures of Staphylococcus aureus DHNA (SaDHNA) in complex with neopterin (NP, an analog of DHNP) and with monapterin (MP, an analog of DHMP), filling the gap in the structural analysis of the enzyme. In combination with previously reported SaDHNA structures in its ligand-free form (PDB entry 1DHN) and in complex with HP (PDB entry 2DHN), four snapshots for the catalytic center assembly along the reaction pathway can be derived, advancing our knowledge about the molecular mechanism of SaDHNA-catalyzed reactions. An additional step appears to be necessary for the epimerization of DHMP to DHNP. Three active site residues (E22, K100, and Y54) function coordinately during catalysis: together, they organize the catalytic center assembly, and individually, each plays a central role at different stages of the catalytic cycle.
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Affiliation(s)
- Jaroslaw Blaszczyk
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Yue Li
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jianhua Gan
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Honggao Yan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Correspondence authors: Honggao Yan, Phone: (517) 353-5282; Fax: (517) 353-9334; E-mail: , Xinhua Ji, Phone: 301-846-5035; Fax: 301-846-6073; E-mail:
| | - Xinhua Ji
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
- Correspondence authors: Honggao Yan, Phone: (517) 353-5282; Fax: (517) 353-9334; E-mail: , Xinhua Ji, Phone: 301-846-5035; Fax: 301-846-6073; E-mail:
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Wang Y, Li Y, Yan H. Mechanism of dihydroneopterin aldolase: functional roles of the conserved active site glutamate and lysine residues. Biochemistry 2006; 45:15232-9. [PMID: 17176045 PMCID: PMC3018710 DOI: 10.1021/bi060949j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dihydroneopterin aldolase (DHNA) catalyzes the conversion of 7,8-dihydroneopterin (DHNP) to 6-hydroxymethyl-7,8-dihydropterin (HP) in the folate biosynthetic pathway. There are four conserved active site residues at the active site, E22, Y54, E74, and K100 in Staphylococcus aureus DHNA (SaDHNA), corresponding to E21, Y53, E73, and K98, respectively, in Escherichia coli DHNA (EcDHNA). The functional roles of the conserved glutamate and lysine residues have been investigated by site-directed mutagenesis in this work. E22 and E74 of SaDHNA and E21, E73, and K98 of EcDHNA were replaced with alanine. K100 of SaDHNA was replaced with alanine and glutamine. The mutant proteins were characterized by equilibrium binding, stopped-flow binding, and steady-state kinetic analyses. For SaDHNA, none of the mutations except E74A caused dramatic changes in the affinities of the enzyme for the substrate or product analogues or the rate constants. The Kd values for SaE74A were estimated to be >3000 microM, suggesting that the Kd values of the mutant are at least 100 times those of the wild-type enzyme. For EcDHNA, the E73A mutation increased the Kd values for the substrate or product analogues neopterin (MP), monapterin (NP), and 6-hydroxypterin (HPO) by factors of 340, 160, and 5600, respectively, relative to those of the wild-type enzyme. The K98A mutation increased the Kd values for NP, MP, and HPO by factors of 14, 3.6, and 230, respectively. The E21A mutation increased the Kd values for NP and HPO by factors of 2.2 and 42, respectively, but decreased the Kd value for MP by a factor of 3.3. The E22 (E21) and K100 (K98) mutations decreased the kcat values by factors of 1.3-2 x 10(4). The E74 (E73) mutation decreased in the kcat values by factors of approximately 10. The results suggested that E74 of SaDHNA and E73 of EcDHNA are important for substrate binding, but their roles in catalysis are minor. In contrast, E22 and K100 of SaDHNA are important for catalysis, but their roles in substrate binding are minor. On the other hand, E21 and K98 of EcDHNA are important for both substrate binding and catalysis.
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Affiliation(s)
| | | | - Honggao Yan
- To whom correspondence should be addressed. Tel.: 517-353-5282; Fax: 517-353-9334;
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