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Knejzlík Z, Doležal M, Herkommerová K, Clarova K, Klíma M, Dedola M, Zborníková E, Rejman D, Pichová I. The mycobacterial guaB1 gene encodes a guanosine 5'-monophosphate reductase with a cystathionine-β-synthase domain. FEBS J 2022; 289:5571-5598. [PMID: 35338694 PMCID: PMC9790621 DOI: 10.1111/febs.16448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 02/11/2022] [Accepted: 03/24/2022] [Indexed: 12/30/2022]
Abstract
Mycobacteria express enzymes from both the de novo and purine-salvage pathways. However, the regulation of these processes and the roles of individual metabolic enzymes have not been sufficiently detailed. Both Mycobacterium tuberculosis (Mtb) and Mycobacterium smegmatis (Msm) possess three guaB genes, but information is only available on guaB2, which encodes an essential inosine 5'-monophosphate dehydrogenase (IMPDH) involved in de novo purine biosynthesis. This study shows that guaB1, annotated in databases as a putative IMPDH, encodes a guanosine 5'-monophosphate reductase (GMPR), which recycles guanosine monophosphate to inosine monophosphate within the purine-salvage pathway and contains a cystathionine-β-synthase domain (CBS), which is essential for enzyme activity. GMPR activity is allosterically regulated by the ATP/GTP ratio in a pH-dependent manner. Bioinformatic analysis has indicated the presence of GMPRs containing CBS domains across the entire Actinobacteria phylum.
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Affiliation(s)
- Zdeněk Knejzlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Michal Doležal
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Klára Herkommerová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Kamila Clarova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Martin Klíma
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Matteo Dedola
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Eva Zborníková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Dominik Rejman
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Iva Pichová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
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Methane from microbial hydrogenolysis of sediment organic matter before the Great Oxidation Event. Nat Commun 2021; 12:5032. [PMID: 34413314 PMCID: PMC8376905 DOI: 10.1038/s41467-021-25336-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 08/04/2021] [Indexed: 11/24/2022] Open
Abstract
Methane, along with other short-chain alkanes from some Archean metasedimentary rocks, has unique isotopic signatures that possibly reflect the generation of atmospheric greenhouse gas on early Earth. We find that alkane gases from the Kidd Creek mines in the Canadian Shield are microbial products in a Neoarchean ecosystem. The widely varied hydrogen and relatively uniform carbon isotopic compositions in the alkanes infer that the alkanes result from the biodegradation of sediment organic matter with serpentinization-derived hydrogen gas. This proposed process is supported by published geochemical data on the Kidd Creek gas, including the distribution of alkane abundances, stable isotope variations in alkanes, and CH2D2 signatures in methane. The recognition of Archean microbial methane in this work reveals a biochemical process of greenhouse gas generation before the Great Oxidation Event and improves the understanding of the carbon and hydrogen geochemical cycles. Microbial CH4 kept the early Earth warm under the faint young sun, but clear records are lacking. Here the authors present isotopic evidence that CH4 seepage in the Canadian shield is from hydrogen biodegradation in a Neoarchean ecosystem rather than an abiotic synthesis product.
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Ott F, Rabe KS, Niemeyer CM, Gygli G. Toward Reproducible Enzyme Modeling with Isothermal Titration Calorimetry. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Felix Ott
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Kersten S. Rabe
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Gudrun Gygli
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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Sarwono AEY, Suganuma K, Mitsuhashi S, Okada T, Musinguzi SP, Shigetomi K, Inoue N, Ubukata M. Identification and characterization of guanosine 5'-monophosphate reductase of Trypanosoma congolense as a drug target. Parasitol Int 2017; 66:537-544. [PMID: 28366788 DOI: 10.1016/j.parint.2017.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/17/2017] [Accepted: 03/27/2017] [Indexed: 10/19/2022]
Abstract
Trypanosoma congolense is one of the most prevalent pathogens which causes trypanosomosis in African animals, resulting in a significant economic loss. In its life cycle, T. congolense is incapable of synthesizing purine nucleotides via a de novo pathway, and thus relies on a salvage pathway to survive. In this study, we identified a gene from T. congolense, TcIL3000_5_1940, as a guanosine 5'-monophosphate reductase (GMPR), an enzyme that modulates the concentration of intracellular guanosine in the pathogen. The recombinant protein was expressed in Escherichia coli, and the gene product was enzymatically confirmed as a unique GMPR, designated as rTcGMPR. This enzyme was constitutively expressed in glycosomes at all of the parasite's developmental stages similar to other purine nucleotide metabolic enzymes. Mycophenolic acid (MPA) was found to inhibit rTcGMPR activity. Hence, it is a potential lead compound for the design of trypanocidal agents, specifically GMPR inhibitor.
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Affiliation(s)
- Albertus Eka Yudistira Sarwono
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Keisuke Suganuma
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, Hokkaido 080-8555, Japan; Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Shinya Mitsuhashi
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Tadashi Okada
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, Hokkaido 080-8555, Japan; Division of Neurology, Respirology, Endocrinology and Metabolism, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Simon Peter Musinguzi
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Kengo Shigetomi
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo, Hokkaido 060-8589, Japan
| | - Noboru Inoue
- Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Makoto Ubukata
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo, Hokkaido 060-8589, Japan.
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Smith S, Boitz J, Chidambaram ES, Chatterjee A, Ait-Tihyaty M, Ullman B, Jardim A. The cystathionine-β-synthase domains on the guanosine 5''-monophosphate reductase and inosine 5'-monophosphate dehydrogenase enzymes from Leishmania regulate enzymatic activity in response to guanylate and adenylate nucleotide levels. Mol Microbiol 2016; 100:824-40. [PMID: 26853689 DOI: 10.1111/mmi.13352] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2016] [Indexed: 01/24/2023]
Abstract
The Leishmania guanosine 5'-monophosphate reductase (GMPR) and inosine 5'-monophosphate dehydrogenase (IMPDH) are purine metabolic enzymes that function maintaining the cellular adenylate and guanylate nucleotide. Interestingly, both enzymes contain a cystathionine-β-synthase domain (CBS). To investigate this metabolic regulation, the Leishmania GMPR was cloned and shown to be sufficient to complement the guaC (GMPR), but not the guaB (IMPDH), mutation in Escherichia coli. Kinetic studies confirmed that the Leishmania GMPR catalyzed a strict NADPH-dependent reductive deamination of GMP to produce IMP. Addition of GTP or high levels of GMP induced a marked increase in activity without altering the Km values for the substrates. In contrast, the binding of ATP decreased the GMPR activity and increased the GMP Km value 10-fold. These kinetic changes were correlated with changes in the GMPR quaternary structure, induced by the binding of GMP, GTP, or ATP to the GMPR CBS domain. The capacity of these CBS domains to mediate the catalytic activity of the IMPDH and GMPR provides a regulatory mechanism for balancing the intracellular adenylate and guanylate pools.
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Affiliation(s)
- Sabrina Smith
- Institute of Parasitology and Centre for Host-Parasite Interactions, Macdonald Campus of McGill University, 21 111 Lakeshore Road, Ste-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Jan Boitz
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Ehzilan Subramanian Chidambaram
- Institute of Parasitology and Centre for Host-Parasite Interactions, Macdonald Campus of McGill University, 21 111 Lakeshore Road, Ste-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Abhishek Chatterjee
- Institute of Parasitology and Centre for Host-Parasite Interactions, Macdonald Campus of McGill University, 21 111 Lakeshore Road, Ste-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Maria Ait-Tihyaty
- Institute of Parasitology and Centre for Host-Parasite Interactions, Macdonald Campus of McGill University, 21 111 Lakeshore Road, Ste-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Buddy Ullman
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Armando Jardim
- Institute of Parasitology and Centre for Host-Parasite Interactions, Macdonald Campus of McGill University, 21 111 Lakeshore Road, Ste-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
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Bessho T, Okada T, Kimura C, Shinohara T, Tomiyama A, Imamura A, Kuwamura M, Nishimura K, Fujimori K, Shuto S, Ishibashi O, Kubata BK, Inui T. Novel Characteristics of Trypanosoma brucei Guanosine 5'-monophosphate Reductase Distinct from Host Animals. PLoS Negl Trop Dis 2016; 10:e0004339. [PMID: 26731263 PMCID: PMC4701174 DOI: 10.1371/journal.pntd.0004339] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 12/08/2015] [Indexed: 12/02/2022] Open
Abstract
The metabolic pathway of purine nucleotides in parasitic protozoa is a potent drug target for treatment of parasitemia. Guanosine 5’-monophosphate reductase (GMPR), which catalyzes the deamination of guanosine 5’-monophosphate (GMP) to inosine 5’-monophosphate (IMP), plays an important role in the interconversion of purine nucleotides to maintain the intracellular balance of their concentration. However, only a few studies on protozoan GMPR have been reported at present. Herein, we identified the GMPR in Trypanosoma brucei, a causative protozoan parasite of African trypanosomiasis, and found that the GMPR proteins were consistently localized to glycosomes in T. brucei bloodstream forms. We characterized its recombinant protein to investigate the enzymatic differences between GMPRs of T. brucei and its host animals. T. brucei GMPR was distinct in having an insertion of a tandem repeat of the cystathionine β-synthase (CBS) domain, which was absent in mammalian and bacterial GMPRs. The recombinant protein of T. brucei GMPR catalyzed the conversion of GMP to IMP in the presence of NADPH, and showed apparent affinities for both GMP and NADPH different from those of its mammalian counterparts. Interestingly, the addition of monovalent cations such as K+ and NH4+ to the enzymatic reaction increased the GMPR activity of T. brucei, whereas none of the mammalian GMPR’s was affected by these cations. The monophosphate form of the purine nucleoside analog ribavirin inhibited T. brucei GMPR activity, though mammalian GMPRs showed no or only a little inhibition by it. These results suggest that the mechanism of the GMPR reaction in T. brucei is distinct from that in the host organisms. Finally, we demonstrated the inhibitory effect of ribavirin on the proliferation of trypanosomes in a dose-dependent manner, suggesting the availability of ribavirin to develop a new therapeutic agent against African trypanosomiasis. Only a limited number of therapeutics for human African trypanosomiasis also known as African sleeping sickness is available today, and it narrows the choice of the drugs to escape from the side effects and the emergence of drug-resistant pathogens. The parasitic protozoa Trypanosoma brucei is the causative reagent of African trypanosomiasis, and is infective to various mammalian species. T. brucei and its mammalian hosts share almost the same metabolic machinery, and therefore it is important to understand the differences in biochemical properties of the metabolic enzymes between T. brucei and its hosts. Here we report that guanosine 5’-monophosphate reductase (GMPR) of T. brucei showed apparent differences in its primary structure and biochemical properties from those of its host counterparts, and was more sensitive to purine nucleotide analogs such as monophosphate forms of ribavirin and mizoribine than were the host GMPRs. Furthermore, ribavirin prevented the proliferation of trypanosomes in vitro. Our present findings may imply the availability of ribavirin and/or its derivatives in a treatment of African trypanosomiasis.
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Affiliation(s)
- Tomoaki Bessho
- Laboratory of Biological Macromolecules, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Tetsuya Okada
- Laboratory of Biological Macromolecules, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Chihiro Kimura
- Laboratory of Biological Macromolecules, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Takahiro Shinohara
- Laboratory of Biological Macromolecules, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Ai Tomiyama
- Laboratory of Biological Macromolecules, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Akira Imamura
- Laboratory of Biological Macromolecules, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Mitsuru Kuwamura
- Laboratory of Veterinary Pathology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Kazuhiko Nishimura
- Laboratory of Toxicology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Ko Fujimori
- Laboratory of Biodefense and Regulation, Osaka University of Pharmaceutical Sciences, Takatsuki, Osaka, Japan
| | - Satoshi Shuto
- Laboratory of Organic Chemistry for Drug Development, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Osamu Ishibashi
- Laboratory of Biological Macromolecules, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | | | - Takashi Inui
- Laboratory of Biological Macromolecules, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
- * E-mail:
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Ran S, Liu B, Jiang W, Sun Z, Liang J. Transcriptome analysis of Enterococcus faecalis in response to alkaline stress. Front Microbiol 2015; 6:795. [PMID: 26300863 PMCID: PMC4528170 DOI: 10.3389/fmicb.2015.00795] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 07/22/2015] [Indexed: 11/13/2022] Open
Abstract
Enterococcus faecalis is the most commonly isolated species from endodontic failure root canals; its persistence in treated root canals has been attributed to its ability to resist high pH stress. The goal of this study was to characterize the E. faecalis transcriptome and to identify candidate genes for response and resistance to alkaline stress using Illumina HiSeq 2000 sequencing. We found that E. faecalis could survive and form biofilms in a pH 10 environment and that alkaline stress had a great impact on the transcription of many genes in the E. faecalis genome. The transcriptome sequencing results revealed that 613 genes were differentially expressed (DEGs) for E. faecalis grown in pH 10 medium; 211 genes were found to be differentially up-regulated and 402 genes differentially down-regulated. Many of the down-regulated genes found are involved in cell energy production and metabolism and carbohydrate and amino acid metabolism, and the up-regulated genes are mostly related to nucleotide transport and metabolism. The results presented here reveal that cultivation of E. faecalis in alkaline stress has a profound impact on its transcriptome. The observed regulation of genes and pathways revealed that E. faecalis reduced its carbohydrate and amino acid metabolism and increased nucleotide synthesis to adapt and grow in alkaline stress. A number of the regulated genes may be useful candidates for the development of new therapeutic approaches for the treatment of E. faecalis infections.
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Affiliation(s)
- Shujun Ran
- Shanghai Key Laboratory of Stomatology, Department of Endodontics and Operative Dentistry, School of Medicine, Ninth People's Hospital, Shanghai Jiao Tong University Shanghai, China
| | - Bin Liu
- Shanghai Key Laboratory of Stomatology, Department of Endodontics and Operative Dentistry, School of Medicine, Ninth People's Hospital, Shanghai Jiao Tong University Shanghai, China
| | - Wei Jiang
- Shanghai Key Laboratory of Stomatology, Department of Endodontics and Operative Dentistry, School of Medicine, Ninth People's Hospital, Shanghai Jiao Tong University Shanghai, China
| | - Zhe Sun
- Shanghai Key Laboratory of Stomatology, Department of Endodontics and Operative Dentistry, School of Medicine, Ninth People's Hospital, Shanghai Jiao Tong University Shanghai, China
| | - Jingping Liang
- Shanghai Key Laboratory of Stomatology, Department of Endodontics and Operative Dentistry, School of Medicine, Ninth People's Hospital, Shanghai Jiao Tong University Shanghai, China
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An improved method and cost effective strategy for soluble expression and purification of human N-myristoyltransferase 1 in E. coli. Mol Cell Biochem 2014; 392:175-86. [PMID: 24668448 DOI: 10.1007/s11010-014-2029-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 03/07/2014] [Indexed: 10/25/2022]
Abstract
N-myristoyltransferase (NMT) is an indispensible enzyme, which exists as two isoforms (NMT1 and NMT2) in humans and has proven roles in development of cancerous states. It is thus a target for novel anti-cancer drug design, but understanding of the biochemical and functional differences of these isozymes is not fully deciphered. A soluble expression under the T7 promoter for human NMT1 was achieved in E. coli BL21 (DE3) cells, devoid of any isopropyl β-D-1-thiogalactopyranoside-based induction. The identity of expressed protein was confirmed by matrix-assisted laser desorption ionization mass spectrometry peptide-fingerprint analysis and a two-step purification protocol yielded homogeneous enzyme. The intact mass of the purified protein was verified by electrospray ionization mass spectrometry and found to be in agreement with the theoretical mass (48.141 vs. 48.140 kDa). The fluorescence spectrophotometric analyses of the ligand binding and enzyme activity demonstrated that the recombinant form is functional. The yield of purified protein was ~8-10 mg/L culture (batch to batch variation) with a specific activity value of 18,500 ± 513 U/mg of protein under the experimental conditions used. The final verification of the myristoylation was demonstrated by mass spectrometry analysis of reaction product. The described approach could be readily adapted for production of human NMT1, with high yields of pure enzyme preparations, which should aid in downstream applications involving inhibitor design and structure-function studies of NMT's.
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Deves C, Rostirolla DC, Martinelli LKB, Bizarro CV, Santos DS, Basso LA. The kinetic mechanism of Human Thymidine Phosphorylase - a molecular target for cancer drug development. MOLECULAR BIOSYSTEMS 2014; 10:592-604. [PMID: 24407036 DOI: 10.1039/c3mb70453j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Human Thymidine Phosphorylase (HTP), also known as the platelet-derived endothelial cell growth factor (PD-ECGF) or gliostatin, catalyzes the reversible phosphorolysis of thymidine (dThd) to thymine and 2-deoxy-α-d-ribose-1-phosphate (2dR1P). HTP is a key enzyme in the pyrimidine salvage pathway involved in dThd homeostasis in cells. HTP is a target for anticancer drug development as its enzymatic activity promotes angiogenesis. Here, we describe cloning, expression, and purification to homogeneity of recombinant TYMP-encoded HTP. Peptide fingerprinting and the molecular mass value of the homogenous protein confirmed its identity as HTP assessed by mass spectrometry. Size exclusion chromatography showed that HTP is a dimer in solution. Kinetic studies revealed that HTP displayed substrate inhibition for dThd. Initial velocity and isothermal titration calorimetry (ITC) studies suggest that HTP catalysis follows a rapid-equilibrium random bi-bi kinetic mechanism. ITC measurements also showed that dThd and Pi binding are favorable processes. The pH-rate profiles indicated that maximal enzyme activity was achieved at low pH values. Functional groups with apparent pK values of 5.2 and 9.0 are involved in dThd binding and groups with pK values of 6.1 and 7.8 are involved in phosphate binding.
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Affiliation(s)
- Candida Deves
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), 6681/92-A Av. Ipiranga, 90619-900, Porto Alegre, RS, Brazil.
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Villela AD, Ducati RG, Rosado LA, Bloch CJ, Prates MV, Gonçalves DC, Ramos CHI, Basso LA, Santos DS. Biochemical characterization of uracil phosphoribosyltransferase from Mycobacterium tuberculosis. PLoS One 2013; 8:e56445. [PMID: 23424660 PMCID: PMC3570474 DOI: 10.1371/journal.pone.0056445] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 01/14/2013] [Indexed: 11/18/2022] Open
Abstract
Uracil phosphoribosyltransferase (UPRT) catalyzes the conversion of uracil and 5-phosphoribosyl-α-1-pyrophosphate (PRPP) to uridine 5′-monophosphate (UMP) and pyrophosphate (PPi). UPRT plays an important role in the pyrimidine salvage pathway since UMP is a common precursor of all pyrimidine nucleotides. Here we describe cloning, expression and purification to homogeneity of upp-encoded UPRT from Mycobacterium tuberculosis (MtUPRT). Mass spectrometry and N-terminal amino acid sequencing unambiguously identified the homogeneous protein as MtUPRT. Analytical ultracentrifugation showed that native MtUPRT follows a monomer-tetramer association model. MtUPRT is specific for uracil. GTP is not a modulator of MtUPRT ativity. MtUPRT was not significantly activated or inhibited by ATP, UTP, and CTP. Initial velocity and isothermal titration calorimetry studies suggest that catalysis follows a sequential ordered mechanism, in which PRPP binding is followed by uracil, and PPi product is released first followed by UMP. The pH-rate profiles indicated that groups with pK values of 5.7 and 8.1 are important for catalysis, and a group with a pK value of 9.5 is involved in PRPP binding. The results here described provide a solid foundation on which to base upp gene knockout aiming at the development of strategies to prevent tuberculosis.
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Affiliation(s)
- Anne Drumond Villela
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Rodrigo Gay Ducati
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Leonardo Astolfi Rosado
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Carlos Junior Bloch
- Laboratório de Espectrometria de Massa, Empresa Brasileira de Pesquisa Agropecuária - Recursos Genéticos e Biotecnologia, Estação Parque Biológico, Brasília, Federal District, Brazil
| | - Maura Vianna Prates
- Laboratório de Espectrometria de Massa, Empresa Brasileira de Pesquisa Agropecuária - Recursos Genéticos e Biotecnologia, Estação Parque Biológico, Brasília, Federal District, Brazil
| | - Danieli Cristina Gonçalves
- Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Instituto de Química, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | | | - Luiz Augusto Basso
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail: (LAB); (DSS)
| | - Diogenes Santiago Santos
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail: (LAB); (DSS)
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Kanjee U, Ogata K, Houry WA. Direct binding targets of the stringent response alarmone (p)ppGpp. Mol Microbiol 2012; 85:1029-43. [PMID: 22812515 DOI: 10.1111/j.1365-2958.2012.08177.x] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Escherichia coli stringent response, mediated by the alarmone ppGpp, is responsible for the reorganization of cellular transcription upon nutritional starvation and other stresses. These transcriptional changes occur mainly as a result of the direct effects of ppGpp and its partner transcription factor DksA on RNA polymerase. An often overlooked feature of the stringent response is the direct targeting of other proteins by ppGpp. Here we review the literature on proteins that are known to bind ppGpp and, based on sequence homology, X-ray crystal structures and in silico docking, we propose new potential protein binding targets for ppGpp. These proteins were found to fall into five main categories: (i) cellular GTPases, (ii) proteins involved in nucleotide metabolism, (iii) proteins involved in lipid metabolism, (iv) general metabolic proteins and (v) PLP-dependent basic aliphatic amino acid decarboxylases. Bioinformatic rationale is provided for expanding the role of ppGpp in regulating the activities of the cellular GTPases. Proteins involved in nucleotide and lipid metabolism and general metabolic proteins provide an interesting set of structurally varied stringent response targets. While the inhibition of some PLP-dependent decarboxylases by ppGpp suggests the existence of cross-talk between the acid stress and stringent response systems.
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Affiliation(s)
- Usheer Kanjee
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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Breda A, Martinelli LKB, Bizarro CV, Rosado LA, Borges CB, Santos DS, Basso LA. Wild-type phosphoribosylpyrophosphate synthase (PRS) from Mycobacterium tuberculosis: a bacterial class II PRS? PLoS One 2012; 7:e39245. [PMID: 22745722 PMCID: PMC3380012 DOI: 10.1371/journal.pone.0039245] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 05/22/2012] [Indexed: 11/18/2022] Open
Abstract
The 5-phospho-α-D-ribose 1-diphosphate (PRPP) metabolite plays essential roles in several biosynthetic pathways, including histidine, tryptophan, nucleotides, and, in mycobacteria, cell wall precursors. PRPP is synthesized from α-D-ribose 5-phosphate (R5P) and ATP by the Mycobacterium tuberculosis prsA gene product, phosphoribosylpyrophosphate synthase (MtPRS). Here, we report amplification, cloning, expression and purification of wild-type MtPRS. Glutaraldehyde cross-linking results suggest that MtPRS predominates as a hexamer, presenting varied oligomeric states due to distinct ligand binding. MtPRS activity measurements were carried out by a novel coupled continuous spectrophotometric assay. MtPRS enzyme activity could be detected in the absence of Pi. ADP, GDP and UMP inhibit MtPRS activity. Steady-state kinetics results indicate that MtPRS has broad substrate specificity, being able to accept ATP, GTP, CTP, and UTP as diphosphoryl group donors. Fluorescence spectroscopy data suggest that the enzyme mechanism for purine diphosphoryl donors follows a random order of substrate addition, and for pyrimidine diphosphoryl donors follows an ordered mechanism of substrate addition in which R5P binds first to free enzyme. An ordered mechanism for product dissociation is followed by MtPRS, in which PRPP is the first product to be released followed by the nucleoside monophosphate products to yield free enzyme for the next round of catalysis. The broad specificity for diphosphoryl group donors and detection of enzyme activity in the absence of Pi would suggest that MtPRS belongs to Class II PRS proteins. On the other hand, the hexameric quaternary structure and allosteric ADP inhibition would place MtPRS in Class I PRSs. Further data are needed to classify MtPRS as belonging to a particular family of PRS proteins. The data here presented should help augment our understanding of MtPRS mode of action. Current efforts are toward experimental structure determination of MtPRS to provide a solid foundation for the rational design of specific inhibitors of this enzyme.
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Affiliation(s)
- Ardala Breda
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Leonardo K. B. Martinelli
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Cristiano V. Bizarro
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Leonardo A. Rosado
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Caroline B. Borges
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Diógenes S. Santos
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail: (LB); (DSS)
| | - Luiz A. Basso
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail: (LB); (DSS)
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Hedstrom L. The dynamic determinants of reaction specificity in the IMPDH/GMPR family of (β/α)(8) barrel enzymes. Crit Rev Biochem Mol Biol 2012; 47:250-63. [PMID: 22332716 DOI: 10.3109/10409238.2012.656843] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The inosine monophosphate dehydrogenase (IMPDH)/guanosine monophosphate reductase (GMPR) family of (β/α)(8) enzymes presents an excellent opportunity to investigate how subtle changes in enzyme structure change reaction specificity. IMPDH and GMPR bind the same ligands with similar affinities and share a common set of catalytic residues. Both enzymes catalyze a hydride transfer reaction involving a nicotinamide cofactor hydride, and both reactions proceed via the same covalent intermediate. In the case of IMPDH, this intermediate reacts with water, while in GMPR it reacts with ammonia. In both cases, the two chemical transformations are separated by a conformational change. In IMPDH, the conformational change involves a mobile protein flap while in GMPR, the cofactor moves. Thus reaction specificity is controlled by differences in dynamics, which in turn are controlled by residues outside the active site. These findings have some intriguing implications for the evolution of the IMPDH/GMPR family.
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Affiliation(s)
- Lizbeth Hedstrom
- Departments of Biology and Chemistry, Brandeis University, Waltham, MA 02454, USA.
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Helicobacter pylori relies primarily on the purine salvage pathway for purine nucleotide biosynthesis. J Bacteriol 2011; 194:839-54. [PMID: 22194455 DOI: 10.1128/jb.05757-11] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Helicobacter pylori is a chronic colonizer of the gastric epithelium and plays a major role in the development of gastritis, peptic ulcer disease, and gastric cancer. In its coevolution with humans, the streamlining of the H. pylori genome has resulted in a significant reduction in metabolic pathways, one being purine nucleotide biosynthesis. Bioinformatic analysis has revealed that H. pylori lacks the enzymatic machinery for de novo production of IMP, the first purine nucleotide formed during GTP and ATP biosynthesis. This suggests that H. pylori must rely heavily on salvage of purines from the environment. In this study, we deleted several genes putatively involved in purine salvage and processing. The growth and survival of these mutants were analyzed in both nutrient-rich and minimal media, and the results confirmed the presence of a robust purine salvage pathway in H. pylori. Of the two phosphoribosyltransferase genes found in the H. pylori genome, only gpt appears to be essential, and an Δapt mutant strain was still capable of growth on adenine, suggesting that adenine processing via Apt is not essential. Deletion of the putative nucleoside phosphorylase gene deoD resulted in an inability of H. pylori to grow on purine nucleosides or the purine base adenine. Our results suggest a purine requirement for growth of H. pylori in standard media, indicating that H. pylori possesses the ability to utilize purines and nucleosides from the environment in the absence of a de novo purine nucleotide biosynthesis pathway.
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Franco TMA, Rostirolla DC, Ducati RG, Lorenzini DM, Basso LA, Santos DS. Biochemical characterization of recombinant guaA-encoded guanosine monophosphate synthetase (EC 6.3.5.2) from Mycobacterium tuberculosis H37Rv strain. Arch Biochem Biophys 2011; 517:1-11. [PMID: 22119138 DOI: 10.1016/j.abb.2011.11.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 11/08/2011] [Accepted: 11/09/2011] [Indexed: 12/29/2022]
Abstract
Administration of the current tuberculosis (TB) vaccine to newborns is not a reliable route for preventing TB in adults. The conversion of XMP to GMP is catalyzed by guaA-encoded GMP synthetase (GMPS), and deletions in the Shiguella flexneri guaBA operon led to an attenuated auxotrophic strain. Here we present the cloning, expression, and purification of recombinant guaA-encoded GMPS from Mycobacterium tuberculosis (MtGMPS). Mass spectrometry data, oligomeric state determination, steady-state kinetics, isothermal titration calorimetry (ITC), and multiple sequence alignment are also presented. The homodimeric MtGMPS catalyzes the conversion of XMP, MgATP, and glutamine into GMP, ADP, PP(i), and glutamate. XMP, NH(4)(+), and Mg(2+) displayed positive homotropic cooperativity, whereas ATP and glutamine displayed hyperbolic saturation curves. The activity of ATP pyrophosphatase domain is independent of glutamine amidotransferase domain, whereas the latter cannot catalyze hydrolysis of glutamine to NH(3) and glutamate in the absence of substrates. ITC data suggest random order of binding of substrates, and PP(i) is the last product released. Sequence comparison analysis showed conservation of both Cys-His-Glu catalytic triad of N-terminal Class I amidotransferase and of amino acid residues of the P-loop of the N-type ATP pyrophosphatase family.
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Affiliation(s)
- Tathyana Mar A Franco
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
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Patton GC, Stenmark P, Gollapalli DR, Sevastik R, Kursula P, Flodin S, Schuler H, Swales CT, Eklund H, Himo F, Nordlund P, Hedstrom L. Cofactor mobility determines reaction outcome in the IMPDH and GMPR (β-α)8 barrel enzymes. Nat Chem Biol 2011; 7:950-8. [PMID: 22037469 PMCID: PMC4552316 DOI: 10.1038/nchembio.693] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 08/22/2011] [Indexed: 12/13/2022]
Abstract
Inosine monophosphate dehydrogenase (IMPDH) and guanosine monophosphate reductase (GMPR) belong to the same structural family, share a common set of catalytic residues and bind the same ligands. The structural and mechanistic features that determine reaction outcome in the IMPDH and GMPR family have not been identified. Here we show that the GMPR reaction uses the same intermediate E-XMP* as IMPDH, but in this reaction the intermediate reacts with ammonia instead of water. A single crystal structure of human GMPR type 2 with IMP and NADPH fortuitously captures three different states, each of which mimics a distinct step in the catalytic cycle of GMPR. The cofactor is found in two conformations: an 'in' conformation poised for hydride transfer and an 'out' conformation in which the cofactor is 6 Å from IMP. Mutagenesis along with substrate and cofactor analog experiments demonstrate that the out conformation is required for the deamination of GMP. Remarkably, the cofactor is part of the catalytic machinery that activates ammonia.
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Affiliation(s)
- Gregory C. Patton
- Department of Biology, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Pål Stenmark
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | | | - Robin Sevastik
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Petri Kursula
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Susanne Flodin
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Herwig Schuler
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Colin T. Swales
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Hans Eklund
- Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala Biomedical Center, P.O. Box 590, SE-751 24 Uppsala, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Pär Nordlund
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
- School of Biological Sciences, Nanyang Technological University, 61 Nanyang Drive Singapore 639798
| | - Lizbeth Hedstrom
- Department of Biology, Brandeis University, 415 South Street, Waltham, MA 02453, USA
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
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