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Fragment-Based Lead Discovery Strategies in Antimicrobial Drug Discovery. Antibiotics (Basel) 2023; 12:antibiotics12020315. [PMID: 36830226 PMCID: PMC9951956 DOI: 10.3390/antibiotics12020315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Fragment-based lead discovery (FBLD) is a powerful application for developing ligands as modulators of disease targets. This approach strategy involves identification of interactions between low-molecular weight compounds (100-300 Da) and their putative targets, often with low affinity (KD ~0.1-1 mM) interactions. The focus of this screening methodology is to optimize and streamline identification of fragments with higher ligand efficiency (LE) than typical high-throughput screening. The focus of this review is on the last half decade of fragment-based drug discovery strategies that have been used for antimicrobial drug discovery.
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2
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Prejanò M, Škerlová J, Stenmark P, Himo F. Reaction Mechanism of Human PAICS Elucidated by Quantum Chemical Calculations. J Am Chem Soc 2022; 144:14258-14268. [PMID: 35914774 PMCID: PMC9376930 DOI: 10.1021/jacs.2c05072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Human PAICS is a bifunctional enzyme that is involved
in the de novo purine biosynthesis, catalyzing the
conversion of
aminoimidazole ribonucleotide (AIR) into N-succinylcarboxamide-5-aminoimidazole
ribonucleotide (SAICAR). It comprises two distinct active sites, AIR
carboxylase (AIRc) where the AIR is initially converted to carboxyaminoimidazole
ribonucleotide (CAIR) by reaction with CO2 and SAICAR synthetase
(SAICARs) in which CAIR then reacts with an aspartate to form SAICAR,
in an ATP-dependent reaction. Human PAICS is a promising target for
the treatment of various types of cancer, and it is therefore of high
interest to develop a detailed understanding of its reaction mechanism.
In the present work, density functional theory calculations are employed
to investigate the PAICS reaction mechanism. Starting from the available
crystal structures, two large models of the AIRc and SAICARs active
sites are built and different mechanistic proposals for the carboxylation
and phosphorylation–condensation mechanisms are examined. For
the carboxylation reaction, it is demonstrated that it takes place
in a two-step mechanism, involving a C–C bond formation followed
by a deprotonation of the formed tetrahedral intermediate (known as
isoCAIR) assisted by an active site histidine residue. For the phosphorylation–condensation
reaction, it is shown that the phosphorylation of CAIR takes place
before the condensation reaction with the aspartate. It is further
demonstrated that the three active site magnesium ions are involved
in binding the substrates and stabilizing the transition states and
intermediates of the reaction. The calculated barriers are in good
agreement with available experimental data.
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Affiliation(s)
- Mario Prejanò
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Jana Škerlová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 160 00 Prague, Czech Republic
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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3
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Charoensutthivarakul S, Thomas SE, Curran A, Brown KP, Belardinelli JM, Whitehouse AJ, Acebrón-García-de-Eulate M, Sangan J, Gramani SG, Jackson M, Mendes V, Floto RA, Blundell TL, Coyne AG, Abell C. Development of Inhibitors of SAICAR Synthetase (PurC) from Mycobacterium abscessus Using a Fragment-Based Approach. ACS Infect Dis 2022; 8:296-309. [PMID: 35037462 PMCID: PMC7614835 DOI: 10.1021/acsinfecdis.1c00432] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mycobacterium abscessus (Mab) has emerged as a challenging threat to individuals with cystic fibrosis. Infections caused by this pathogen are often impossible to treat due to the intrinsic antibiotic resistance leading to lung malfunction and eventually death. Therefore, there is an urgent need to develop new drugs against novel targets in Mab to overcome drug resistance and subsequent treatment failure. In this study, SAICAR synthetase (PurC) from Mab was identified as a promising target for novel antibiotics. An in-house fragment library screen and a high-throughput X-ray crystallographic screen of diverse fragment libraries were explored to provide crucial starting points for fragment elaboration. A series of compounds developed from fragment growing and merging strategies, guided by crystallographic information and careful hit-to-lead optimization, have achieved potent nanomolar binding affinity against the enzyme. Some compounds also show a promising inhibitory effect against Mab and Mtb. This work utilizes a fragment-based design and demonstrates for the first time the potential to develop inhibitors against PurC from Mab.
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Affiliation(s)
- Sitthivut Charoensutthivarakul
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.,School of Bioinnovation and Bio-based Product Intelligence, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Sherine E Thomas
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Amy Curran
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Karen P Brown
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge CB23 3RE, United Kingdom
| | - Juan M Belardinelli
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Andrew J Whitehouse
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | | | - Jaspar Sangan
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge CB23 3RE, United Kingdom
| | - Subramanian G Gramani
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682, United States
| | - Vitor Mendes
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - R Andres Floto
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge CB23 3RE, United Kingdom
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Anthony G Coyne
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Chris Abell
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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4
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Škerlová J, Unterlass J, Göttmann M, Marttila P, Homan E, Helleday T, Jemth AS, Stenmark P. Crystal structures of human PAICS reveal substrate and product binding of an emerging cancer target. J Biol Chem 2020; 295:11656-11668. [PMID: 32571877 DOI: 10.1074/jbc.ra120.013695] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/18/2020] [Indexed: 12/16/2022] Open
Abstract
The bifunctional human enzyme phosphoribosylaminoimidazole carboxylase and phosphoribosylaminoimidazolesuccinocarboxamide synthetase (PAICS) catalyzes two essential steps in the de novo purine biosynthesis pathway. PAICS is overexpressed in many cancers and could be a promising target for the development of cancer therapeutics. Here, using gene knockdowns and clonogenic survival and cell viability assays, we demonstrate that PAICS is required for growth and survival of prostate cancer cells. PAICS catalyzes the carboxylation of aminoimidazole ribonucleotide (AIR) and the subsequent conversion of carboxyaminoimidazole ribonucleotide (CAIR) and l-aspartate to N-succinylcarboxamide-5-aminoimidazole ribonucleotide (SAICAR). Of note, we present the first structures of human octameric PAICS in complexes with native ligands. In particular, we report the structure of PAICS with CAIR bound in the active sites of both domains and SAICAR bound in one of the SAICAR synthetase domains. Moreover, we report the PAICS structure with SAICAR and an ATP analog occupying the SAICAR synthetase active site. These structures provide insight into substrate and product binding and the architecture of the active sites, disclosing important structural information for rational design of PAICS inhibitors as potential anticancer drugs.
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Affiliation(s)
- Jana Škerlová
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Judith Unterlass
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Mona Göttmann
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Petra Marttila
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Evert Homan
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.,Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Ann-Sofie Jemth
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden .,Department of Experimental Medical Science, Lund University, Lund, Sweden
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5
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Thomas SE, Collins P, James RH, Mendes V, Charoensutthivarakul S, Radoux C, Abell C, Coyne AG, Floto RA, von Delft F, Blundell TL. Structure-guided fragment-based drug discovery at the synchrotron: screening binding sites and correlations with hotspot mapping. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2019; 377:20180422. [PMID: 31030650 PMCID: PMC6501894 DOI: 10.1098/rsta.2018.0422] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Structure-guided drug discovery emerged in the 1970s and 1980s, stimulated by the three-dimensional structures of protein targets that became available, mainly through X-ray crystal structure analysis, assisted by the development of synchrotron radiation sources. Structures of known drugs or inhibitors were used to guide the development of leads. The growth of high-throughput screening during the late 1980s and the early 1990s in the pharmaceutical industry of chemical libraries of hundreds of thousands of compounds of molecular weight of approximately 500 Da was impressive but still explored only a tiny fraction of the chemical space of the predicted 1040 drug-like compounds. The use of fragments with molecular weights less than 300 Da in drug discovery not only decreased the chemical space needing exploration but also increased promiscuity in binding targets. Here we discuss advances in X-ray fragment screening and the challenge of identifying sites where fragments not only bind but can be chemically elaborated while retaining their positions and binding modes. We first describe the analysis of fragment binding using conventional X-ray difference Fourier techniques, with Mycobacterium abscessus SAICAR synthetase (PurC) as an example. We observe that all fragments occupy positions predicted by computational hotspot mapping. We compare this with fragment screening at Diamond Synchrotron Light Source XChem facility using PanDDA software, which identifies many more fragment hits, only some of which bind to the predicted hotspots. Many low occupancy sites identified may not support elaboration to give adequate ligand affinity, although they will likely be useful in drug discovery as 'warm spots' for guiding elaboration of fragments bound at hotspots. We discuss implications of these observations for fragment screening at the synchrotron sources. This article is part of the theme issue 'Fifty years of synchrotron science: achievements and opportunities'.
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Affiliation(s)
- Sherine E. Thomas
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Patrick Collins
- Diamond Light Source (DLS), Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Rory Hennell James
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Vitor Mendes
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | | | - Chris Radoux
- The European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Anthony G. Coyne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - R. Andres Floto
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge CB23 3RE, UK
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC-Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Frank von Delft
- Diamond Light Source (DLS), Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
- e-mail:
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6
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Zantow J, Just S, Lagkouvardos I, Kisling S, Dübel S, Lepage P, Clavel T, Hust M. Mining gut microbiome oligopeptides by functional metaproteome display. Sci Rep 2016; 6:34337. [PMID: 27703179 PMCID: PMC5050496 DOI: 10.1038/srep34337] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/12/2016] [Indexed: 12/25/2022] Open
Abstract
Pathogen infections, autoimmune diseases, and chronic inflammatory disorders are associated with systemic antibody responses from the host immune system. Disease-specific antibodies can be important serum biomarkers, but the identification of antigens associated with specific immune reactions is challenging, in particular if complex communities of microorganisms are involved in the disease progression. Despite promising new diagnostic opportunities, the discovery of these serological markers becomes more difficult with increasing complexity of microbial communities. In the present work, we used a metagenomic M13 phage display approach to select immunogenic oligopeptides from the gut microbiome of transgenic mice suffering from chronic ileitis. We constructed three individual metaproteome phage display libraries with a library size of approximately 107 clones each. Using serum antibodies, we selected and validated three oligopeptides that induced specific antibody responses in the mouse model. This proof-of-concept study provides the first successful application of functional metaproteome display for the study of protein-protein interactions and the discovery of potential disease biomarkers.
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Affiliation(s)
- Jonas Zantow
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics - Department for Biotechnology, Germany
| | - Sarah Just
- Technische Universität München, ZIEL Institute for Food and Health, Freising, Germany
| | - Ilias Lagkouvardos
- Technische Universität München, ZIEL Institute for Food and Health, Freising, Germany
| | - Sigrid Kisling
- Technische Universität München, ZIEL Institute for Food and Health, Freising, Germany
| | - Stefan Dübel
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics - Department for Biotechnology, Germany
| | - Patricia Lepage
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Thomas Clavel
- Technische Universität München, ZIEL Institute for Food and Health, Freising, Germany
| | - Michael Hust
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics - Department for Biotechnology, Germany
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7
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Tuntland ML, Fung LWM. Substrate independent ATPase activity may complicate high throughput screening. Anal Biochem 2016; 510:18-20. [PMID: 27430931 DOI: 10.1016/j.ab.2016.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/13/2016] [Accepted: 07/14/2016] [Indexed: 10/21/2022]
Abstract
Inorganic phosphate release, [Pi], is often measured in an enzymatic reaction in a high throughput setting. Based on the published mechanism, we designed a protocol for our screening for inhibitors of SAICAR synthetase (PurC), and we found a gradual increase in [Pi] in positive control samples over the course of the day. Further investigation indicated that hydrolysis of ATP catalyzed by PurC, rather than substrate-related phosphate release, was responsible for a partial contribution to the signals in the control samples. Thus substrate-independent ATPase activity may complicate high throughput screening.
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Affiliation(s)
- Micheal L Tuntland
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - L W-M Fung
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA.
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8
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Barelier S, Sterling T, O’Meara MJ, Shoichet BK. The Recognition of Identical Ligands by Unrelated Proteins. ACS Chem Biol 2015; 10:2772-84. [PMID: 26421501 DOI: 10.1021/acschembio.5b00683] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The binding of drugs and reagents to off-targets is well-known. Whereas many off-targets are related to the primary target by sequence and fold, many ligands bind to unrelated pairs of proteins, and these are harder to anticipate. If the binding site in the off-target can be related to that of the primary target, this challenge resolves into aligning the two pockets. However, other cases are possible: the ligand might interact with entirely different residues and environments in the off-target, or wholly different ligand atoms may be implicated in the two complexes. To investigate these scenarios at atomic resolution, the structures of 59 ligands in 116 complexes (62 pairs in total), where the protein pairs were unrelated by fold but bound an identical ligand, were examined. In almost half of the pairs, the ligand interacted with unrelated residues in the two proteins (29 pairs), and in 14 of the pairs wholly different ligand moieties were implicated in each complex. Even in those 19 pairs of complexes that presented similar environments to the ligand, ligand superposition rarely resulted in the overlap of related residues. There appears to be no single pattern-matching "code" for identifying binding sites in unrelated proteins that bind identical ligands, though modeling suggests that there might be a limited number of different patterns that suffice to recognize different ligand functional groups.
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Affiliation(s)
- Sarah Barelier
- Department of Pharmaceutical
Chemistry, University of California San Francisco, 1700 Fourth
Street, Byers Hall, San Francisco, California 94158, United States
| | - Teague Sterling
- Department of Pharmaceutical
Chemistry, University of California San Francisco, 1700 Fourth
Street, Byers Hall, San Francisco, California 94158, United States
| | - Matthew J. O’Meara
- Department of Pharmaceutical
Chemistry, University of California San Francisco, 1700 Fourth
Street, Byers Hall, San Francisco, California 94158, United States
| | - Brian K. Shoichet
- Department of Pharmaceutical
Chemistry, University of California San Francisco, 1700 Fourth
Street, Byers Hall, San Francisco, California 94158, United States
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9
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Abstract
We review literature on the metabolism of ribo- and deoxyribonucleotides, nucleosides, and nucleobases in Escherichia coli and Salmonella,including biosynthesis, degradation, interconversion, and transport. Emphasis is placed on enzymology and regulation of the pathways, at both the level of gene expression and the control of enzyme activity. The paper begins with an overview of the reactions that form and break the N-glycosyl bond, which binds the nucleobase to the ribosyl moiety in nucleotides and nucleosides, and the enzymes involved in the interconversion of the different phosphorylated states of the nucleotides. Next, the de novo pathways for purine and pyrimidine nucleotide biosynthesis are discussed in detail.Finally, the conversion of nucleosides and nucleobases to nucleotides, i.e.,the salvage reactions, are described. The formation of deoxyribonucleotides is discussed, with emphasis on ribonucleotidereductase and pathways involved in fomation of dUMP. At the end, we discuss transport systems for nucleosides and nucleobases and also pathways for breakdown of the nucleobases.
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10
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Tuntland ML, Wolf NM, Fung LWM. Differences in the purification and solution properties of PurC gene products from Streptococcus pneumoniae and Bacillus anthracis. Protein Expr Purif 2015; 114:143-8. [PMID: 26118696 DOI: 10.1016/j.pep.2015.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 04/02/2015] [Accepted: 05/14/2015] [Indexed: 11/24/2022]
Abstract
4-(N-succino)-5-aminoimidazole-4-carboxamide ribonucleotide synthetase (PurC) is a key enzyme in the de novo purine biosynthetic pathway of bacteria and an ideal target pathway for the discovery of antimicrobials. Bacillus anthracis (Ba) and Streptococcus pneumoniae (Sp) are two of the bacteria shown to be severe detriments to public health. To be able to carry out the experimentation that leads to drug discovery, high yields of pure soluble recombinant protein must first be obtained. We studied two recombinant PurC proteins from B. anthracis and S. pneumoniae, using Escherichia coli as the host cells. These two proteins, with very similar amino acid sequences, exhibit very different solution properties, leading to a large difference in yields during protein purification under the same conditions. The yield for SpPurC (>50mG per gram of cells) is ten times greater than that for BaPurC (<5mG per gram of cells). The BaPurC samples in solution consisted of oligomers and dimers, with dimers as its functional form. Comparing the yields of dimers, SpPurC is 25 times greater than that for BaPurC (∼2mG per gram of cell). Our studies suggest that the difference in exposed hydrophobic surface area is responsible for the difference in yields under the same conditions.
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Affiliation(s)
- Micheal L Tuntland
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Nina M Wolf
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Leslie W-M Fung
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA.
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11
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Catalytic pathway, substrate binding and stability in SAICAR synthetase: A structure and molecular dynamics study. J Struct Biol 2015; 191:22-31. [PMID: 26072057 DOI: 10.1016/j.jsb.2015.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 06/05/2015] [Accepted: 06/08/2015] [Indexed: 11/21/2022]
Abstract
The de novo purine biosynthesis is one of the highly conserved pathways among all organisms and is essential for the cell viability. A clear understanding of the enzymes in this pathway would pave way for the development of antimicrobial and anticancer drugs. Phosphoribosylaminoimidazole-succinocarboxamide (SAICAR) synthetase is one of the enzymes in this pathway that catalyzes ATP dependent ligation of carboxyaminoimidazole ribotide (CAIR) with l-aspartate (ASP). Here, we describe eight crystal structures of this enzyme, in C2221 and H3 space groups, bound to various substrates and substrate mimics from a hyperthermophilic archaea Pyrococcus horikoshii along with molecular dynamics simulations of the structures with substrates. Complexes exhibit minimal deviation from its apo structure. The CAIR binding site displays a preference for pyrimidine nucleotides. In the ADP·TMP·ASP complex, the ASP binds at a position equivalent to that found in Saccharomyces cerevisiae structure (PDB: 2CNU) and thus, clears the ambiguity regarding ASP's position. A possible mode for the inhibition of the enzyme by CTP and UTP, observed earlier in the yeast enzyme, is clearly illustrated in the structures bound to CMP and UMP. The ADP.Mg(2+)·PO4·CD/MP complex having a phosphate ion between the ATP and CAIR sites strengthens one of the two probable pathways (proposed in Escherichia coli study) of catalytic mechanism and suggests the possibility of a phosphorylation taking place before the ASP's attack on CAIR. Molecular dynamic simulations of this enzyme along with its substrates at 90°C reveal the relative strengths of substrate binding, possible antagonism and the role of Mg(2+) ions.
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12
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Datt M, Sharma A. Novel and unique domains in aminoacyl-tRNA synthetases from human fungal pathogens Aspergillus niger, Candida albicans and Cryptococcus neoformans. BMC Genomics 2014; 15:1069. [PMID: 25479903 PMCID: PMC4301749 DOI: 10.1186/1471-2164-15-1069] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 11/20/2014] [Indexed: 12/15/2022] Open
Abstract
Background Some species of fungi can cause serious human diseases, particularly to immuno-compromised individuals. Opportunistic fungal infections are a leading cause of mortality, and present an emerging challenge that requires development of new and effective therapeutics. Aminoacyl-tRNA synthetases (aaRSs) are indispensable components of cellular protein translation machinery and can be targeted for discovery of novel anti-fungal agents. Results Validation of aaRSs as potential drug targets in pathogenic microbes prompted us to investigate the genomic distribution of aaRSs within three fungi that infect humans – A. niger, C. albicans and C. neoformans. Hidden Markov Models were built for aaRSs and related proteins to search for homologues in these fungal genomes. Here, we provide a detailed and comprehensive annotation for 3 fungal genome aaRSs and their associated proteins. We delineate predicted localizations, subdomain architectures and prevalence of unusual motifs within these aaRSs. Several fungal aaRSs have unique domain appendages of unknown function e.g. A. niger AsxRS and C. neoformans TyrRS have additional domains that are absent from human homologs. Conclusions Detailed comparisons of fungal aaRSs with human homologs suggest key differences that could be exploited for specific drug targeting. Our cataloging and structural analyses provide a comprehensive foundation for experimentally dissecting fungal aaRSs that may enable development of new anti-fungal agents. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1069) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Amit Sharma
- Structural and Computational Biology group, International Center for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India.
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13
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Wolf NM, Abad-Zapatero C, Johnson ME, Fung LWM. Structures of SAICAR synthetase (PurC) from Streptococcus pneumoniae with ADP, Mg2+, AIR and Asp. ACTA ACUST UNITED AC 2014; 70:841-50. [PMID: 24598753 DOI: 10.1107/s139900471303366x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 12/12/2013] [Indexed: 11/10/2022]
Abstract
Streptococcus pneumoniae is a multidrug-resistant pathogen that is a target of considerable interest for antibacterial drug development. One strategy for drug discovery is to inhibit an essential metabolic enzyme. The seventh step of the de novo purine-biosynthesis pathway converts carboxyaminoimidazoleribonucleotide (CAIR) and L-aspartic acid (Asp) to 4-(N-succino)-5-aminoimidazole-4-carboxamide ribonucleotide (SAICAR) in the presence of adenosine 5'-triphosphate (ATP) using the enzyme PurC. PurC has been shown to be conditionally essential for bacterial replication. Two crystal structures of this essential enzyme from Streptococcus pneumoniae (spPurC) in the presence of adenosine 5'-diphosphate (ADP), Mg(2+), aminoimidazoleribonucleotide (AIR) and/or Asp have been obtained. This is the first structural study of spPurC, as well as the first of PurC from any species with Asp in the active site. Based on these findings, two model structures are proposed for the active site with all of the essential ligands (ATP, Mg(2+), Asp and CAIR) present, and a relay mechanism for the formation of the product SAICAR is suggested.
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Affiliation(s)
- Nina M Wolf
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Celerino Abad-Zapatero
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Michael E Johnson
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Leslie W-M Fung
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
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14
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Manjunath K, Sekar K. Molecular dynamics perspective on the protein thermal stability: a case study using SAICAR synthetase. J Chem Inf Model 2013; 53:2448-61. [PMID: 23962324 DOI: 10.1021/ci400306m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The enzyme SAICAR synthetase ligates aspartate with CAIR (5'-phosphoribosyl-4-carboxy-5-aminoimidazole) forming SAICAR (5-amino-4-imidazole-N-succinocarboxamide ribonucleotide) in the presence of ATP. In continuation with our previous study on the thermostability of this enzyme in hyper-/thermophiles based on the structural aspects, here, we present the dynamic aspects that differentiate the mesophilic (E. coli, E. chaffeensis), thermophilic (G. kaustophilus), and hyperthermophilic (M. jannaschii, P. horikoshii) SAICAR synthetases by carrying out a total of 11 simulations. The five functional dimers from the above organisms were simulated using molecular dynamics for a period of 50 ns each at 300 K, 363 K, and an additional simulation at 333 K for the thermophilic protein. The basic features like root-mean-square deviations, root-mean-square fluctuations, surface accessibility, and radius of gyration revealed the instability of mesophiles at 363 K. Mean square displacements establish the reduced flexibility of hyper-/thermophiles at all temperatures. At the simulations time scale considered here, the long-distance networks are considerably affected in mesophilic structures at 363 K. In mesophiles, a comparatively higher number of short-lived (having less percent existence time) Cα, hydrogen bonds, hydrophobic interactions are formed, and long-lived (with higher percentage existence time) contacts are lost. The number of time-averaged salt-bridges is at least 2-fold higher in hyperthermophiles at 363 K. The change in surface accessibility of salt-bridges at 363 K from 300 K is nearly doubled in mesophilic protein compared to proteins from other temperature classes.
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Affiliation(s)
- Kavyashree Manjunath
- Supercomputer Education and Research Centre, Indian Institute of Science , Bangalore, Karnataka 560 012, India
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15
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Taschner M, Basquin J, Benda C, Lorentzen E. Crystal structure of the invertebrate bifunctional purine biosynthesis enzyme PAICS at 2.8 Å resolution. Proteins 2013; 81:1473-8. [PMID: 23553965 DOI: 10.1002/prot.24296] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 03/13/2013] [Accepted: 03/17/2013] [Indexed: 11/11/2022]
Abstract
Two important steps of the de novo purine biosynthesis pathway are catalyzed by the 5-aminoimidazole ribonucleotide carboxylase and the 4-(N-succinylcarboxamide)-5-aminoimidazole ribonucleotide synthetase enzymes. In most eukaryotic organisms, these two activities are present in the bifunctional enzyme complex known as PAICS. We have determined the 2.8-Å resolution crystal structure of the 350-kDa invertebrate PAICS from insect cells (Trichoplusia ni) using single-wavelength anomalous dispersion methods. Comparison of insect PAICS to human and prokaryotic homologs provides insights into substrate binding and reveals a highly conserved enzymatic framework across divergent species.
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Affiliation(s)
- Michael Taschner
- Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, Martinsried, Germany
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16
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Manjunath K, Kanaujia SP, Kanagaraj S, Jeyakanthan J, Sekar K. Structure of SAICAR synthetase from Pyrococcus horikoshii OT3: Insights into thermal stability. Int J Biol Macromol 2013; 53:7-19. [DOI: 10.1016/j.ijbiomac.2012.10.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 10/25/2012] [Accepted: 10/26/2012] [Indexed: 10/27/2022]
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17
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Brown AM, Hoopes SL, White RH, Sarisky CA. Purine biosynthesis in archaea: variations on a theme. Biol Direct 2011; 6:63. [PMID: 22168471 PMCID: PMC3261824 DOI: 10.1186/1745-6150-6-63] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2011] [Accepted: 12/14/2011] [Indexed: 11/10/2022] Open
Abstract
Background The ability to perform de novo biosynthesis of purines is present in organisms in all three domains of life, reflecting the essentiality of these molecules to life. Although the pathway is quite similar in eukaryotes and bacteria, the archaeal pathway is more variable. A careful manual curation of genes in this pathway demonstrates the value of manual curation in archaea, even in pathways that have been well-studied in other domains. Results We searched the Integrated Microbial Genome system (IMG) for the 17 distinct genes involved in the 11 steps of de novo purine biosynthesis in 65 sequenced archaea, finding 738 predicted proteins with sequence similarity to known purine biosynthesis enzymes. Each sequence was manually inspected for the presence of active site residues and other residues known or suspected to be required for function. Many apparently purine-biosynthesizing archaea lack evidence for a single enzyme, either glycinamide ribonucleotide formyltransferase or inosine monophosphate cyclohydrolase, suggesting that there are at least two more gene variants in the purine biosynthetic pathway to discover. Variations in domain arrangement of formylglycinamidine ribonucleotide synthetase and substantial problems in aminoimidazole carboxamide ribonucleotide formyltransferase and inosine monophosphate cyclohydrolase assignments were also identified. Manual curation revealed some overly specific annotations in the IMG gene product name, with predicted proteins without essential active site residues assigned product names implying enzymatic activity (21 proteins, 2.8% of proteins inspected) or Enzyme Commission (E. C.) numbers (57 proteins, 7.7%). There were also 57 proteins (7.7%) assigned overly generic names and 78 proteins (10.6%) without E.C. numbers as part of the assigned name when a specific enzyme name and E. C. number were well-justified. Conclusions The patchy distribution of purine biosynthetic genes in archaea is consistent with a pathway that has been shaped by horizontal gene transfer, duplication, and gene loss. Our results indicate that manual curation can improve upon automated annotation for a small number of automatically-annotated proteins and can reveal a need to identify further pathway components even in well-studied pathways. Reviewers This article was reviewed by Dr. Céline Brochier-Armanet, Dr Kira S Makarova (nominated by Dr. Eugene Koonin), and Dr. Michael Galperin.
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Affiliation(s)
- Anne M Brown
- Department of Chemistry, Roanoke College, Salem, VA 24153, USA
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18
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Lowe CD, Mello LV, Samatar N, Martin LE, Montagnes DJS, Watts PC. The transcriptome of the novel dinoflagellate Oxyrrhis marina (Alveolata: Dinophyceae): response to salinity examined by 454 sequencing. BMC Genomics 2011; 12:519. [PMID: 22014029 PMCID: PMC3209475 DOI: 10.1186/1471-2164-12-519] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 10/20/2011] [Indexed: 11/30/2022] Open
Abstract
Background The heterotrophic dinoflagellate Oxyrrhis marina is increasingly studied in experimental, ecological and evolutionary contexts. Its basal phylogenetic position within the dinoflagellates make O. marina useful for understanding the origin of numerous unusual features of the dinoflagellate lineage; its broad distribution has lent O. marina to the study of protist biogeography; and nutritive flexibility and eurytopy have made it a common lab rat for the investigation of physiological responses of marine heterotrophic flagellates. Nevertheless, genome-scale resources for O. marina are scarce. Here we present a 454-based transcriptome survey for this organism. In addition, we assess sequence read abundance, as a proxy for gene expression, in response to salinity, an environmental factor potentially important in determining O. marina spatial distributions. Results Sequencing generated ~57 Mbp of data which assembled into 7, 398 contigs. Approximately 24% of contigs were nominally identified by BLAST. A further clustering of contigs (at ≥ 90% identity) revealed 164 transcript variant clusters, the largest of which (Phosphoribosylaminoimidazole-succinocarboxamide synthase) was composed of 28 variants displaying predominately synonymous variation. In a genomic context, a sample of 5 different genes were demonstrated to occur as tandem repeats, separated by short (~200-340 bp) inter-genic regions. For HSP90 several intergenic variants were detected suggesting a potentially complex genomic arrangement. In response to salinity, analysis of 454 read abundance highlighted 9 and 20 genes over or under expressed at 50 PSU, respectively. However, 454 read abundance and subsequent qPCR validation did not correlate well - suggesting that measures of gene expression via ad hoc analysis of sequence read abundance require careful interpretation. Conclusion Here we indicate that tandem gene arrangements and the occurrence of multiple transcribed gene variants are common and indicate potentially complex genomic arrangements in O. marina. Comparison of the reported data set with existing O. marina and other dinoflagellates ESTs indicates little sequence overlap likely as a result of the relatively limited extent of genome scale sequence data currently available for the dinoflagellates. This is one of the first 454-based transcriptome surveys of an ancestral dinoflagellate taxon and will undoubtedly prove useful for future comparative studies aimed at reconstructing the origin of novel features of the dinoflagellates.
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Affiliation(s)
- Chris D Lowe
- Department of Evolution, Ecology, and Behaviour, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
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Cheng X, Lu G, Qi J, Cheng H, Gao F, Wang J, Yan J. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of SAICAR synthase from Streptococcus suis serotype 2. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:909-912. [PMID: 20693665 PMCID: PMC2917288 DOI: 10.1107/s1744309110020518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 05/29/2010] [Indexed: 05/29/2023]
Abstract
Phosphoribosylaminoimidazole-succinocarboxamide synthase (SAICAR synthase) plays an essential role in the de novo biosynthesis of purine nucleotides. In this study, the SAICAR synthase from Streptococcus suis was cloned and overexpressed in Escherichia coli. The subsequent product was purified and crystallized using the hanging-drop vapour-diffusion method. The crystals diffracted to 2.8 A resolution and belonged to space group P2, with unit-cell parameters a=70.2, b=52.2, c=153.9 A, beta=102.8 degrees.
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Affiliation(s)
- Xia Cheng
- Key Laboratory of Environment Veterinary Science, Shanxi Agricultural University, Shanxi, People’s Republic of China
| | - Guangwen Lu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Hao Cheng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Feng Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Jundong Wang
- Key Laboratory of Environment Veterinary Science, Shanxi Agricultural University, Shanxi, People’s Republic of China
| | - Jinghua Yan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
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20
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Manjunath K, Jeyakanthan J, Nakagawa N, Shinkai A, Yoshimura M, Kuramitsu S, Yokoyama S, Sekar K. Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of the putative SAICAR synthetase (PH0239) from Pyrococcus horikoshii OT3. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:180-3. [PMID: 20124717 DOI: 10.1107/s1744309109052026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Accepted: 12/03/2009] [Indexed: 11/10/2022]
Abstract
The study of proteins involved in de novo biosynthesis of purine nucleotides is central in the development of antibiotics and anticancer drugs. In view of this, a protein from the hyperthermophile Pyrococcus horikoshii OT3 was isolated, purified and crystallized using the microbatch method. Its primary structure was found to be similar to that of SAICAR synthetase, which catalyses the seventh step of de novo purine biosynthesis. A diffraction-quality crystal was obtained using Hampton Research Crystal Screen II condition No. 34, consisting of 0.05 M cadmium sulfate hydrate, 0.1 M HEPES buffer pH 7.5 and 1.0 M sodium acetate trihydrate, with 40%(v/v) 1,4-butanediol as an additive. The crystal belonged to space group P3(1), with unit-cell parameters a = b = 95.62, c = 149.13 A. Assuming the presence of a hexamer in the asymmetric unit resulted in a Matthews coefficient (V(M)) of 2.3 A(3) Da(-1), corresponding to a solvent content of about 46%. A detailed study of this protein will yield insights into structural stability at high temperatures and should be highly relevant to the development of antibiotics and anticancer drugs targeting the biosynthesis of purine nucleotides.
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Affiliation(s)
- Kavyashree Manjunath
- Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India
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21
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Schmelz S, Kadi N, McMahon SA, Song L, Oves-Costales D, Oke M, Liu H, Johnson KA, Carter LG, Botting CH, White MF, Challis GL, Naismith JH. AcsD catalyzes enantioselective citrate desymmetrization in siderophore biosynthesis. Nat Chem Biol 2009; 5:174-82. [PMID: 19182782 PMCID: PMC2644304 DOI: 10.1038/nchembio.145] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Accepted: 01/12/2009] [Indexed: 01/12/2023]
Abstract
Bacterial pathogens need to scavenge iron from their host for growth and proliferation during infection. They have evolved several strategies to do this, one being the biosynthesis and excretion of small, high-affinity iron chelators known as siderophores. The biosynthesis of siderophores is an important area of study, not only for potential therapeutic intervention, but also to illuminate new enzyme chemistries. Two general pathways for siderophore biosynthesis exist: the well-characterized nonribosomal peptide synthetase (NRPS)-dependent pathway and the NRPS-independent (NIS) pathway, which relies on a different family of sparsely-investigated synthetases. Here, we report structural and biochemical studies of AcsD from Pectobacterium (formerly Erwinia) chrysanthemi, a NIS synthetase involved in achromobactin biosynthesis. The structures of ATP and citrate complexes provide a mechanistic rationale for stereospecific formation of an enzyme-bound (3R)-citryl-adenylate, which reacts with L-serine to form a likely achromobactin precursor. AcsD is a novel acyl adenylate-forming enzyme with a new fold and chemical catalysis strategy.
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Affiliation(s)
- Stefan Schmelz
- Scottish Structural Proteomics Facility and Centre for Biomolecular Sciences, The University of St Andrews, Scotland KY16 9ST, UK
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22
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Abstract
Purine biosynthesis requires ten enzymatic transformations to generate inosine monophosphate. PurF, PurD, PurL, PurM, PurC, and PurB are common to all pathways, while PurN or PurT, PurK/PurE-I or PurE-II, PurH or PurP, and PurJ or PurO catalyze the same steps in different organisms. X-ray crystal structures are available for all 15 purine biosynthetic enzymes, including 7 ATP-dependent enzymes, 2 amidotransferases and 2 tetrahydrofolate-dependent enzymes. Here we summarize the structures of the purine biosynthetic enzymes, discuss similarities and differences, and present arguments for pathway evolution. Four of the ATP-dependent enzymes belong to the ATP-grasp superfamily and 2 to the PurM superfamily. The amidotransferases are unrelated, with one utilizing an N-terminal nucleophileglutaminase and the other utilizing a triad glutaminase. Likewise the tetrahydrofolate-dependent enzymes are unrelated. Ancestral proteins may have included a broad specificity enzyme instead of PurD, PurT, PurK, PurC, and PurP, and a separate enzyme instead of PurM and PurL.
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Affiliation(s)
- Y. Zhang
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, NY 14853 USA
| | - M. Morar
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, NY 14853 USA
| | - S. E. Ealick
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, NY 14853 USA
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23
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Zhang Y, White RH, Ealick SE. Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii. Biochemistry 2007; 47:205-17. [PMID: 18069798 DOI: 10.1021/bi701406g] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Purine biosynthesis requires 10 enzymatic steps in higher organisms, while prokaryotes require an additional enzyme for step 6. In most organisms steps 9 and 10 are catalyzed by the purH gene product, a bifunctional enzyme with both 5-formaminoimidazole-4-carboxamide ribonucleotide (FAICAR) synthase and inosine monophosphate (IMP) cyclohydrolase activity. Recently it was discovered that Archaea utilize different enzymes to catalyze steps 9 and 10. An ATP-dependent FAICAR synthetase is encoded by the purP gene, and IMP cyclohydrolase is encoded by the purO gene. We have determined the X-ray crystal structures of FAICAR synthetase from Methanocaldococcus jannaschii complexed with various ligands, including the tertiary substrate complex and product complex. The enzyme belongs to the ATP grasp superfamily and is predicted to use a formyl phosphate intermediate formed by an ATP-dependent phosphorylation. In addition, we have determined the structures of a PurP orthologue from Pyrococcus furiosus, which is functionally unclassified, in three crystal forms. With approximately 50% sequence identity, P. furiosus PurP is structurally homologous to M. jannaschii PurP. A phylogenetic analysis was performed to explore the possible role of this functionally unclassified PurP.
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Affiliation(s)
- Yang Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA
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Li SX, Tong YP, Xie XC, Wang QH, Zhou HN, Han Y, Zhang ZY, Gao W, Li SG, Zhang XC, Bi RC. Octameric structure of the human bifunctional enzyme PAICS in purine biosynthesis. J Mol Biol 2006; 366:1603-14. [PMID: 17224163 DOI: 10.1016/j.jmb.2006.12.027] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2006] [Revised: 12/07/2006] [Accepted: 12/13/2006] [Indexed: 11/24/2022]
Abstract
Phosphoribosylaminoimidazole carboxylase/phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS) is an important bifunctional enzyme in de novo purine biosynthesis in vertebrate with both 5-aminoimidazole ribonucleotide carboxylase (AIRc) and 4-(N-succinylcarboxamide)-5-aminoimidazole ribonucleotide synthetase (SAICARs) activities. It becomes an attractive target for rational anticancer drug design, since rapidly dividing cancer cells rely heavily on the purine de novo pathway for synthesis of adenine and guanine, whereas normal cells favor the salvage pathway. Here, we report the crystal structure of human PAICS, the first in the entire PAICS family, at 2.8 A resolution. It revealed that eight PAICS subunits, each composed of distinct AIRc and SAICARs domains, assemble a compact homo-octamer with an octameric-carboxylase core and four symmetric periphery dimers formed by synthetase domains. Based on structural comparison and functional complementation analyses, the active sites of SAICARs and AIRc were identified, including a putative substrate CO(2)-binding site. Furthermore, four symmetry-related, separate tunnel systems in the PAICS octamer were found that connect the active sites of AIRc and SAICARs. This study illustrated the octameric nature of the bifunctional enzyme. Each carboxylase active site is formed by structural elements from three AIRc domains, demonstrating that the octamer structure is essential for the carboxylation activity. Furthermore, the existence of the tunnel system implies a mechanism of intermediate channeling and suggests that the quaternary structure arrangement is crucial for effectively executing the sequential reactions. In addition, this study provides essential structural information for designing PAICS-specific inhibitors for use in cancer chemotherapy.
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Affiliation(s)
- Shu-Xing Li
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
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