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Wang J, Xue N, Pan W, Tu R, Li S, Zhang Y, Mao Y, Liu Y, Cheng H, Guo Y, Yuan W, Ni X, Wang M. Repurposing conformational changes in ANL superfamily enzymes to rapidly generate biosensors for organic and amino acids. Nat Commun 2023; 14:6680. [PMID: 37865661 PMCID: PMC10590383 DOI: 10.1038/s41467-023-42431-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/10/2023] [Indexed: 10/23/2023] Open
Abstract
Biosensors are powerful tools for detecting, real-time imaging, and quantifying molecules, but rapidly constructing diverse genetically encoded biosensors remains challenging. Here, we report a method to rapidly convert enzymes into genetically encoded circularly permuted fluorescent protein-based indicators to detect organic acids (GECFINDER). ANL superfamily enzymes undergo hinge-mediated ligand-coupling domain movement during catalysis. We introduce a circularly permuted fluorescent protein into enzymes hinges, converting ligand-induced conformational changes into significant fluorescence signal changes. We obtain 11 GECFINDERs for detecting phenylalanine, glutamic acid and other acids. GECFINDER-Phe3 and GECFINDER-Glu can efficiently and accurately quantify target molecules in biological samples in vitro. This method simplifies amino acid quantification without requiring complex equipment, potentially serving as point-of-care testing tools for clinical applications in low-resource environments. We also develop a GECFINDER-enabled droplet-based microfluidic high-throughput screening method for obtaining high-yield industrial strains. Our method provides a foundation for using enzymes as untapped blueprint resources for biosensor design, creation, and application.
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Affiliation(s)
- Jin Wang
- University of Chinese Academy of Sciences, 100049, Beijing, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- Haihe Laboratory of Synthetic Biology, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, 300308, Tianjin, China
| | - Ning Xue
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- Haihe Laboratory of Synthetic Biology, 300308, Tianjin, China
- Tianjin University of Science & Technology, 300457, Tianjin, China
| | - Wenjia Pan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, 300308, Tianjin, China
| | - Ran Tu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- College of Environmental and Resources, Chongqing Technology and Business University, 400067, Chongqing, China
| | - Shixin Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- Tianjin University of Science & Technology, 300457, Tianjin, China
| | - Yue Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, 300308, Tianjin, China
| | - Yufeng Mao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, 300308, Tianjin, China
| | - Ye Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, 300308, Tianjin, China
| | - Haijiao Cheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, 300308, Tianjin, China
| | - Yanmei Guo
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, 300308, Tianjin, China
| | - Wei Yuan
- University of Chinese Academy of Sciences, 100049, Beijing, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, 300308, Tianjin, China
| | - Xiaomeng Ni
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
| | - Meng Wang
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China.
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, 300308, Tianjin, China.
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2
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Tran JU, Brown BL. Structural Basis for Allostery in PLP-dependent Enzymes. Front Mol Biosci 2022; 9:884281. [PMID: 35547395 PMCID: PMC9081730 DOI: 10.3389/fmolb.2022.884281] [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: 02/26/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Pyridoxal 5′-phosphate (PLP)-dependent enzymes are found ubiquitously in nature and are involved in a variety of biological pathways, from natural product synthesis to amino acid and glucose metabolism. The first structure of a PLP-dependent enzyme was reported over 40 years ago, and since that time, there is a steady wealth of structural and functional information revealed for a wide array of these enzymes. A functional mechanism that is gaining more appreciation due to its relevance in drug design is that of protein allostery, where binding of a protein or ligand at a distal site influences the structure, organization, and function at the active site. Here, we present a review of current structure-based mechanisms of allostery for select members of each PLP-dependent enzyme family. Knowledge of these mechanisms may have a larger potential for identifying key similarities and differences among enzyme families that can eventually be exploited for therapeutic development.
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Affiliation(s)
- Jenny U Tran
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Breann L Brown
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States.,Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, United States
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3
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Verma D, Gupta V. New insights into the structure and function of an emerging drug target CysE. 3 Biotech 2021; 11:373. [PMID: 34367865 DOI: 10.1007/s13205-021-02891-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 06/09/2021] [Indexed: 11/24/2022] Open
Abstract
The antimicrobial resistant strains of several pathogens are major culprits of hospital-acquired nosocomial infections. An active and urgent action is necessary against these pathogens for the development of unique therapeutics. The cysteine biosynthetic pathway or genes (that are absent in humans) involved in the production of L-cysteine appear to be an attractive target for developing novel antibiotics. CysE, a Serine Acetyltransferase (SAT), catalyzes the first step of cysteine synthesis and is reported to be essential for the survival of persistence in several microbes including Mycobacterium tuberculosis. Structure determination provides fundamental insight into structure and function of protein and aid in drug design/discovery efforts. This review focuses on the overview of current knowledge of structure function, regulatory mechanism, and potential inhibitors (active site as well as allosteric site) of CysE. Despite having conserved structure, slight modification in CysE structure lead to altered the regulatory mechanism and hence affects the cysteine production. Due to its possible role in virulence and vital metabolism of pathogens makes it a potential target in the quest to develop novel therapeutics to treat multi-drug-resistant bacteria.
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Affiliation(s)
- Deepali Verma
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, Noida, Uttar Pradesh 201309 India
| | - Vibha Gupta
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, Noida, Uttar Pradesh 201309 India
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4
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A Competitive O-Acetylserine Sulfhydrylase Inhibitor Modulates the Formation of Cysteine Synthase Complex. Catalysts 2021. [DOI: 10.3390/catal11060700] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Cysteine is the main precursor of sulfur-containing biological molecules in bacteria and contributes to the control of the cell redox state. Hence, this amino acid plays an essential role in microbial survival and pathogenicity and the reductive sulfate assimilation pathway is considered a promising target for the development of new antibacterials. Serine acetyltransferase (SAT) and O-acetylserine sulfhydrylase (OASS-A), the enzymes catalyzing the last two steps of cysteine biosynthesis, engage in the formation of the cysteine synthase (CS) complex. The interaction between SAT and OASS-A finely tunes cysteine homeostasis, and the development of inhibitors targeting either protein–protein interaction or the single enzymes represents an attractive strategy to undermine bacterial viability. Given the peculiar mode of interaction between SAT and OASS-A, which exploits the insertion of SAT C-terminal sequence into OASS-A active site, we tested whether a recently developed competitive inhibitor of OASS-A exhibited any effect on the CS stability. Through surface plasmon resonance spectroscopy, we (i) determined the equilibrium constant for the Salmonella Typhimurium CS complex formation and (ii) demonstrated that the inhibitor targeting OASS-A active site affects CS complex formation. For comparison, the Escherichia coli CS complex was also investigated, with the aim of testing the potential broad-spectrum activity of the candidate antimicrobial compound.
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5
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Rosa B, Dickinson ER, Marchetti M, Campanini B, Pioselli B, Bettati S, Rand KD. Revealing the Dynamic Allosteric Changes Required for Formation of the Cysteine Synthase Complex by Hydrogen-Deuterium Exchange MS. Mol Cell Proteomics 2021; 20:100098. [PMID: 34022432 PMCID: PMC8253905 DOI: 10.1016/j.mcpro.2021.100098] [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: 04/10/2021] [Accepted: 05/14/2021] [Indexed: 11/30/2022] Open
Abstract
CysE and CysK, the last two enzymes of the cysteine biosynthetic pathway, engage in a bienzyme complex, cysteine synthase, with yet incompletely characterized three-dimensional structure and regulatory function. Being absent in mammals, the two enzymes and their complex are attractive targets for antibacterial drugs. We have used hydrogen/deuterium exchange MS to unveil how complex formation affects the conformational dynamics of CysK and CysE. Our results support a model where CysE is present in solution as a dimer of trimers, and each trimer can bind one CysK homodimer. When CysK binds to one CysE monomer, intratrimer allosteric communication ensures conformational and dynamic symmetry within the trimer. Furthermore, a long-range allosteric signal propagates through CysE to induce stabilization of the interface between the two CysE trimers, preparing the second trimer for binding the second CysK with a nonrandom orientation. These results provide new molecular insights into the allosteric formation of the cysteine synthase complex and could help guide antibacterial drug design. HDX-MS reveals complex formation impact on conformational dynamics of CysK and CysE. CysK binding ensures conformational symmetry within the CysE trimer. Long-range allostery propagates through CysE stabilizing the inter-trimer interface. Insights into the allostery of CS complex could help guide antibacterial drug design.
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Affiliation(s)
- Brenda Rosa
- Biopharmanet-TEC Interdepartmental Center, University di Parma, Parma, Italy
| | - Eleanor R Dickinson
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen O, Denmark
| | | | | | | | - Stefano Bettati
- Biopharmanet-TEC Interdepartmental Center, University di Parma, Parma, Italy; Department of Medicine and Surgery, University of Parma, Parma, Italy; Institute of Biophysics, CNR, Pisa, Italy.
| | - Kasper Dyrberg Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen O, Denmark.
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6
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Annunziato G, Spadini C, Franko N, Storici P, Demitri N, Pieroni M, Flisi S, Rosati L, Iannarelli M, Marchetti M, Magalhaes J, Bettati S, Mozzarelli A, Cabassi CS, Campanini B, Costantino G. Investigational Studies on a Hit Compound Cyclopropane-Carboxylic Acid Derivative Targeting O-Acetylserine Sulfhydrylase as a Colistin Adjuvant. ACS Infect Dis 2021; 7:281-292. [PMID: 33513010 DOI: 10.1021/acsinfecdis.0c00378] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Antibacterial adjuvants are of great significance, since they allow the therapeutic dose of conventional antibiotics to be lowered and reduce the insurgence of antibiotic resistance. Herein, we report that an O-acetylserine sulfhydrylase (OASS) inhibitor can be used as a colistin adjuvant to treat infections caused by Gram-positive and Gram-negative pathogens. A compound that binds OASS with a nM dissociation constant was tested as an adjuvant of colistin against six critical pathogens responsible for infections spreading worldwide, Escherichia coli, Salmonella enterica serovar Typhimurium, Klebisiella pneumoniae, Staphylococcus aureus, methicillin-resistant Staphylococcus aureus, and Staphylococcus pseudintermedius. The compound showed promising synergistic or additive activities against all of them. Knockout experiments confirmed the intracellular target engagement supporting the proposed mechanism of action. Moreover, compound toxicity was evaluated by means of its hemolytic activity against sheep defibrinated blood cells, showing a good safety profile. The 3D structure of the compound in complex with OASS was determined at 1.2 Å resolution by macromolecular crystallography, providing for the first time structural insights about the nature of the interaction between the enzyme and this class of competitive inhibitors. Our results provide a robust proof of principle supporting OASS as a potential nonessential antibacterial target to develop a new class of adjuvants and the structural basis for further structure-activity relationship studies.
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Affiliation(s)
- Giannamaria Annunziato
- P4T Group, Department of Food and Drugs, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Costanza Spadini
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, via del Taglio, 8, 43126 Parma, Italy
| | - Nina Franko
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drugs, University of Parma, via Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Paola Storici
- Elettra - Sincrotrone Trieste S.C.p.A., SS 14
- km 163,5 in AREA Science Park, 34149 Trieste, Italy
| | - Nicola Demitri
- Elettra - Sincrotrone Trieste S.C.p.A., SS 14
- km 163,5 in AREA Science Park, 34149 Trieste, Italy
| | - Marco Pieroni
- P4T Group, Department of Food and Drugs, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Sara Flisi
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, via del Taglio, 8, 43126 Parma, Italy
| | - Lucrezia Rosati
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, via del Taglio, 8, 43126 Parma, Italy
| | - Mattia Iannarelli
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, via del Taglio, 8, 43126 Parma, Italy
| | - Marialaura Marchetti
- Biopharmanet-TEC Interdepartmental Center, University of Parma, 43124 Parma, Italy
| | - Joana Magalhaes
- P4T Group, Department of Food and Drugs, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, via Volturno, 39, 43125 Parma, Italy
- Biopharmanet-TEC Interdepartmental Center, University of Parma, 43124 Parma, Italy
- Institute of Biophysics, CNR, 56124 Pisa, Italy
| | - Andrea Mozzarelli
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drugs, University of Parma, via Parco Area delle Scienze 23/A, 43124 Parma, Italy
- Biopharmanet-TEC Interdepartmental Center, University of Parma, 43124 Parma, Italy
- Institute of Biophysics, CNR, 56124 Pisa, Italy
| | - Clotilde Silvia Cabassi
- Operative Unit of Animals Infectious Diseases, Department of Veterinary Science, University of Parma, via del Taglio, 8, 43126 Parma, Italy
| | - Barbara Campanini
- Laboratory of Biochemistry and Molecular Biology, Department of Food and Drugs, University of Parma, via Parco Area delle Scienze 23/A, 43124 Parma, Italy
- Biopharmanet-TEC Interdepartmental Center, University of Parma, 43124 Parma, Italy
| | - Gabriele Costantino
- P4T Group, Department of Food and Drugs, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
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7
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Combination of SAXS and Protein Painting Discloses the Three-Dimensional Organization of the Bacterial Cysteine Synthase Complex, a Potential Target for Enhancers of Antibiotic Action. Int J Mol Sci 2019; 20:ijms20205219. [PMID: 31640223 PMCID: PMC6829319 DOI: 10.3390/ijms20205219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/10/2019] [Accepted: 09/17/2019] [Indexed: 01/03/2023] Open
Abstract
The formation of multienzymatic complexes allows for the fine tuning of many aspects of enzymatic functions, such as efficiency, localization, stability, and moonlighting. Here, we investigated, in solution, the structure of bacterial cysteine synthase (CS) complex. CS is formed by serine acetyltransferase (CysE) and O-acetylserine sulfhydrylase isozyme A (CysK), the enzymes that catalyze the last two steps of cysteine biosynthesis in bacteria. CysK and CysE have been proposed as potential targets for antibiotics, since cysteine and related metabolites are intimately linked to protection of bacterial cells against redox damage and to antibiotic resistance. We applied a combined approach of small-angle X-ray scattering (SAXS) spectroscopy and protein painting to obtain a model for the solution structure of CS. Protein painting allowed the identification of protein–protein interaction hotspots that were then used as constrains to model the CS quaternary assembly inside the SAXS envelope. We demonstrate that the active site entrance of CysK is involved in complex formation, as suggested by site-directed mutagenesis and functional studies. Furthermore, complex formation involves a conformational change in one CysK subunit that is likely transmitted through the dimer interface to the other subunit, with a regulatory effect. Finally, SAXS data indicate that only one active site of CysK is involved in direct interaction with CysE and unambiguously unveil the quaternary arrangement of CS.
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8
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Devi S, Tarique KF, Ali MF, Abdul Rehman SA, Gourinath S. Identification and characterization of Helicobacter pylori O-acetylserine-dependent cystathionine β-synthase, a distinct member of the PLP-II family. Mol Microbiol 2019; 112:718-739. [PMID: 31132312 DOI: 10.1111/mmi.14315] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2019] [Indexed: 02/02/2023]
Abstract
O-acetylserine sulfhydrylase (OASS) and cystathionine β-synthase (CBS) are members of the PLP-II family, and involved in L-cysteine production. OASS produces L-cysteine via a de novo pathway while CBS participates in the reverse transsulfuration pathway. O-acetylserine-dependent CBS (OCBS) was previously identified as a new member of the PLP-II family, which are predominantly seen in bacteria. The bacterium Helicobacter pylori possess only one OASS (hp0107) gene and we showed that the protein coded by this gene actually functions as an OCBS and utilizes L-homocysteine and O-acetylserine (OAS) to produce cystathionine. HpOCBS did not show CBS activity with the substrate L-serine and required OAS exclusively. The HpOCBS structure in complex with methionine showed a closed cleft state, explaining the initial mode of substrate binding. Sequence and structural analyses showed differences between the active sites of OCBS and CBS, and explain their different substrate preferences. We identified three hydrophobic residues near the active site of OCBS, corresponding to one serine and two tyrosine residues in CBSs. Mutational studies were performed on HpOCBS and Saccharomyces cerevisiae CBS. A ScCBS double mutant (Y158F/Y226V) did not display activity with L-serine, indicating indispensability of these polar residues for selecting substrate L-serine, however, did show activity with OAS.
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Affiliation(s)
- Suneeta Devi
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Khaja Faisal Tarique
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.,Public Health Research Institute, Rutgers, Newark, NJ, USA
| | - Mohammad Farhan Ali
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Syed Arif Abdul Rehman
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.,MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Samudrala Gourinath
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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9
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Insights into multifaceted activities of CysK for therapeutic interventions. 3 Biotech 2019; 9:44. [PMID: 30675454 DOI: 10.1007/s13205-019-1572-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 01/10/2019] [Indexed: 01/24/2023] Open
Abstract
CysK (O-acetylserine sulfhydrylase) is a pyridoxal-5' phosphate-dependent enzyme which catalyzes the second step of the de novo cysteine biosynthesis pathway by converting O-acetyl serine (OAS) into l-cysteine in the presence of sulfide. The first step of the cysteine biosynthesis involves formation of OAS from serine and acetyl CoA by CysE (serine acetyltransferase). Apart from role of CysK in cysteine biosynthesis, recent studies have revealed various additional roles of this enzyme in bacterial physiology. Other than the suggested regulatory role in cysteine production, other activities of CysK include involvement of CysK-in contact-dependent toxin activation in Gram-negative pathogens, as a transcriptional regulator of CymR by stabilizing the CymR-DNA interactions, in biofilm formation by providing cysteine and via another mechanism not yet understood, in ofloxacin and tellurite resistance as well as in cysteine desulfurization. Some of these activities involve binding of CysK to another cellular partner, where the complex is regulated by the availability of OAS and/or sulfide (H2S). The aim of this study is to present an overview of current knowledge of multiple functions performed by CysK and identifying structural features involved in alternate functions. Due to possible role in disease, promoting or inhibiting a "moonlighting" function of CysK could be a target for developing novel therapeutic interventions.
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10
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Magalhães J, Franko N, Annunziato G, Welch M, Dolan SK, Bruno A, Mozzarelli A, Armao S, Jirgensons A, Pieroni M, Costantino G, Campanini B. Discovery of novel fragments inhibiting O-acetylserine sulphhydrylase by combining scaffold hopping and ligand-based drug design. J Enzyme Inhib Med Chem 2018; 33:1444-1452. [PMID: 30221554 PMCID: PMC6147075 DOI: 10.1080/14756366.2018.1512596] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Several bacteria rely on the reductive sulphur assimilation pathway, absent in mammals, to synthesise cysteine. Reduction of virulence and decrease in antibiotic resistance have already been associated with mutations on the genes that codify cysteine biosynthetic enzymes. Therefore, inhibition of cysteine biosynthesis has emerged as a promising strategy to find new potential agents for the treatment of bacterial infection. Following our previous efforts to explore OASS inhibition and to expand and diversify our library, a scaffold hopping approach was carried out, with the aim of identifying a novel fragment for further development. This novel chemical tool, endowed with favourable pharmacological characteristics, was successfully developed, and a preliminary Structure–Activity Relationship investigation was carried out.
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Affiliation(s)
- Joana Magalhães
- a P4T group, Department of Food and Drug , University of Parma , Parma , Italy
| | - Nina Franko
- b Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug , University of Parma , Parma , Italy
| | | | - Martin Welch
- c Department of Biochemistry , Cambridge University , Cambridge , United Kingdom
| | - Stephen K Dolan
- c Department of Biochemistry , Cambridge University , Cambridge , United Kingdom
| | - Agostino Bruno
- d Experimental Therapeutics Program , IFOM - The FIRC Institute for Molecular Oncology Foundation , Milano , Italy
| | - Andrea Mozzarelli
- b Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug , University of Parma , Parma , Italy.,e National Institute of Biostructures and Biosystems , Rome , Italy.,f Institute of Biophysics, CNR , Pisa , Italy
| | - Stefano Armao
- g Centro Interdipartimentale "Biopharmanet-tec", Università degli Studi di Parma , Parma , Italy
| | | | - Marco Pieroni
- a P4T group, Department of Food and Drug , University of Parma , Parma , Italy
| | - Gabriele Costantino
- a P4T group, Department of Food and Drug , University of Parma , Parma , Italy.,i Centro Interdipartimentale Misure (CIM)'G. Casnati', University of Parma , Parma , Italy
| | - Barbara Campanini
- b Laboratory of Biochemistry and Molecular Biology, Department of Food and Drug , University of Parma , Parma , Italy
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11
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Cytosolic Cysteine Synthase Switch Cysteine and Mimosine Production in Leucaena leucocephala. Appl Biochem Biotechnol 2018; 186:613-632. [PMID: 29691793 DOI: 10.1007/s12010-018-2745-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 03/21/2018] [Indexed: 10/17/2022]
Abstract
In higher plants, multiple copies of the cysteine synthase gene are present for cysteine biosynthesis. Some of these genes also have the potential to produce various kinds of β-substitute alanine. In the present study, we cloned a 1275-bp cDNA for cytosolic O-acetylserine(thiol)lyase (cysteine synthase) (Cy-OASTL) from Leucaena leucocephala. The purified protein product showed a dual function of cysteine and mimosine synthesis. Kinetics studies showed pH optima of 7.5 and 8.0, while temperature optima of 40 and 35 °C, respectively, for cysteine and mimosine synthesis. The kinetic parameters such as apparent Km, kcat were determined for both cysteine and mimosine synthesis with substrates O-acetylserine (OAS) and Na2S or 3-hydroxy-4-pyridone (3H4P). From the in vitro results with the common substrate OAS, the apparent kcat for Cys production is over sixfold higher than mimosine synthesis and the apparent Km is 3.7 times lower, suggesting Cys synthesis is the favored pathway.
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12
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Rashid MHU, Iwasaki H, Oogai S, Fukuta M, Parveen S, Hossain MA, Anai T, Oku H. Molecular characterization of cytosolic cysteine synthase in Mimosa pudica. JOURNAL OF PLANT RESEARCH 2018; 131:319-329. [PMID: 29181648 DOI: 10.1007/s10265-017-0986-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 09/21/2017] [Indexed: 06/07/2023]
Abstract
In the cysteine and mimosine biosynthesis process, O-acetyl-L-serine (OAS) is the common substrate. In the presence of O-acetylserine (thiol) lyase (OASTL, cysteine synthase) the reaction of OAS with sulfide produces cysteine, while with 3-hydroxy-4-pyridone (3H4P) produces mimosine. The enzyme OASTL can either catalyze Cys synthesis or both Cys and mimosine. A cDNA for cytosolic OASTL was cloned from M. pudica for the first time containing 1,410 bp nucleotides. The purified protein product from overexpressed bacterial cells produced Cys only, but not mimosine, indicating it is Cys specific. Kinetic studies revealed that pH and temperature optima for Cys production were 6.5 and 50 °C, respectively. The measured Km, Kcat, and Kcat Km-1 values were 159 ± 21 µM, 33.56 s-1, and 211.07 mM-1s-1 for OAS and 252 ± 25 µM, 32.99 s-1, and 130.91 mM-1s-1 for Na2S according to the in vitro Cys assay. The Cy-OASTL of Mimosa pudica is specific to Cys production, although it contains sensory roles in sulfur assimilation and the reduction network in the intracellular environment of M. pudica.
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Affiliation(s)
- Md Harun-Ur- Rashid
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
- Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
| | - Hironori Iwasaki
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Shigeki Oogai
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | - Masakazu Fukuta
- Graduate School of Agriculture, University of the Ryukyus, Okinawa, Japan.
| | - Shahanaz Parveen
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
- Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
| | - Md Amzad Hossain
- Graduate School of Agriculture, University of the Ryukyus, Okinawa, Japan
| | - Toyoaki Anai
- Faculty of Agriculture, Saga University, Saga, Japan
| | - Hirosuke Oku
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
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13
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Devi S, Abdul Rehman SA, Tarique KF, Gourinath S. Structural characterization and functional analysis of cystathionine β-synthase: an enzyme involved in the reverse transsulfuration pathway of Bacillus anthracis. FEBS J 2017; 284:3862-3880. [PMID: 28921884 DOI: 10.1111/febs.14273] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/31/2017] [Accepted: 09/13/2017] [Indexed: 01/29/2023]
Abstract
The reverse transsulfuration pathway has been reported to produce cysteine from homocysteine in eukaryotes ranging from protozoans to mammals while bacteria and plants produce cysteine via a de novo pathway. Interestingly, the bacterium Bacillus anthracis includes enzymes of the reverse transsulfuration pathway viz. cystathionine β-synthase [BaCBS, previously annotated to be an O-acetylserine sulfhydrylase (OASS)] and cystathionine γ-lyase. Here, we report the structure of BaCBS at a resolution of 2.2 Å. The enzyme was found to show CBS activity only with activated serine (O-acetylserine) and not with serine, and was also observed to display OASS activity but not serine sulfhydrylase activity. BaCBS was also found to produce hydrogen sulfide (H2 S) upon reaction of cysteine and homocysteine. A mutational study revealed Glu 220, conserved in CBS, to be necessary for generating H2 S. Structurally, BaCBS display a considerably more open active site than has been found for any other CBS or OASS, which was attributed to the presence of a helix at the junction of the C- and N-terminal domains. The root-mean-square deviation (RMSD) between the backbone Cα carbon atoms of BaCBS and those of other CBSs and OASSs were calculated to be greater than 3.0 Å. The pyridoxal 5'-phosphate at the active site was not traced, and appeared to be highly flexible due to the active site being wide open. Phylogenetic analysis revealed the presence of an O-acetylserine-dependent CBS in the bacterial domain and making separate clade from CBS and OASS indicating its evolution for specific function. DATABASE Structural data are available in the PDB under the accession number 5XW3.
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Affiliation(s)
- Suneeta Devi
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Syed A Abdul Rehman
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.,MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Khaja F Tarique
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.,Public Health Research Institute, Rutgers, Newark, NJ, USA
| | - Samudrala Gourinath
- Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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14
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Benoni R, Beck CM, Garza-Sánchez F, Bettati S, Mozzarelli A, Hayes CS, Campanini B. Activation of an anti-bacterial toxin by the biosynthetic enzyme CysK: mechanism of binding, interaction specificity and competition with cysteine synthase. Sci Rep 2017; 7:8817. [PMID: 28821763 PMCID: PMC5562914 DOI: 10.1038/s41598-017-09022-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/20/2017] [Indexed: 12/20/2022] Open
Abstract
Contact-dependent growth inhibition (CDI) is a wide-spread mechanism of inter-bacterial competition. CDI+ bacteria deliver CdiA-CT toxins into neighboring bacteria and produce specific immunity proteins that protect against self-intoxication. The CdiA-CT toxin from uropathogenic Escherichia coli 536 is a latent tRNase that is only active when bound to the cysteine biosynthetic enzyme CysK. Remarkably, the CysK:CdiA-CT binding interaction mimics the ‘cysteine synthase’ complex of CysK:CysE. The C-terminal tails of CysE and CdiA-CT each insert into the CysK active-site cleft to anchor the respective complexes. The dissociation constant for CysK:CdiA-CT (Kd ~ 11 nM) is comparable to that of the E. coli cysteine synthase complex (Kd ~ 6 nM), and both complexes bind through a two-step mechanism with a slow isomerization phase after the initial encounter. However, the second-order rate constant for CysK:CdiA-CT binding is two orders of magnitude slower than that of the cysteine synthase complex, suggesting that CysE should outcompete the toxin for CysK occupancy. However, we find that CdiA-CT can effectively displace CysE from pre-formed cysteine synthase complexes, enabling toxin activation even in the presence of excess competing CysE. This adventitious binding, coupled with the very slow rate of CysK:CdiA-CT dissociation, ensures robust nuclease activity in target bacteria.
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Affiliation(s)
- Roberto Benoni
- Dipartimento di Medicina e Chirurgia, Università di Parma, Parma, Italy.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha, Czech Republic
| | - Christina M Beck
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA.,Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fernando Garza-Sánchez
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Stefano Bettati
- Dipartimento di Medicina e Chirurgia, Università di Parma, Parma, Italy.,Istituto Nazionale Biostrutture e Biosistemi, Rome, Italy
| | - Andrea Mozzarelli
- Istituto Nazionale Biostrutture e Biosistemi, Rome, Italy.,Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Parma, Italy
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA. .,Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA, USA.
| | - Barbara Campanini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Parma, Italy.
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15
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Hoque MN, Das G. Overview of the strategic approaches for the solid-state recognition of hydrated anions. CrystEngComm 2017. [DOI: 10.1039/c6ce02438f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Pieroni M, Annunziato G, Beato C, Wouters R, Benoni R, Campanini B, Pertinhez TA, Bettati S, Mozzarelli A, Costantino G. Rational Design, Synthesis, and Preliminary Structure–Activity Relationships of α-Substituted-2-Phenylcyclopropane Carboxylic Acids as Inhibitors of Salmonella typhimurium O-Acetylserine Sulfhydrylase. J Med Chem 2016; 59:2567-78. [DOI: 10.1021/acs.jmedchem.5b01775] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | | | | | | | | | | | | | - Stefano Bettati
- Department
of Neurosciences, University of Parma, Via Volturno, 39, 43125 Parma, Italy
- National Institute of Biostructures and Biosystems, Viale delle Medaglie d’Oro 305, 00136 Rome, Italy
| | - Andrea Mozzarelli
- National Institute of Biostructures and Biosystems, Viale delle Medaglie d’Oro 305, 00136 Rome, Italy
- Institute of Biophysics, CNR, /o
Area di Ricerca San Cataldo, Via G. Moruzzi N° 1, 56124 Pisa, Italy
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17
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Abstract
The synthesis of L-cysteine from inorganic sulfur is the predominant mechanism by which reduced sulfur is incorporated into organic compounds. L-cysteineis used for protein and glutathione synthesis and serves as the primary source of reduced sulfur in L-methionine, lipoic acid, thiamin, coenzyme A (CoA), molybdopterin, and other organic molecules. Sulfate and thiosulfate uptake in E. coli and serovar Typhimurium are achieved through a single periplasmic transport system that utilizes two different but similar periplasmic binding proteins. Kinetic studies indicate that selenate and selenite share a single transporter with sulfate, but molybdate also has a separate transport system. During aerobic growth, the reduction of sulfite to sulfide is catalyzed by NADPH-sulfite reductase (SiR), and serovar Typhimurium mutants lacking this enzyme accumulate sulfite from sulfate, implying that sulfite is a normal intermediate in assimilatory sulfate reduction. L-Cysteine biosynthesis in serovar Typhimurium and E. coli ceases almost entirely when cells are grown on L-cysteine or L-cystine, owing to a combination of end product inhibition of serine transacetylase by L-cysteine and a gene regulatory system known as the cysteine regulon, wherein genes for sulfate assimilation and alkanesulfonate utilization are expressed only when sulfur is limiting. In vitro studies with the cysJIH, cysK, and cysP promoters have confirmed that they are inefficient at forming transcription initiation complexes without CysB and N-acetyl-L-serine. Activation of the tauA and ssuE promoters requires Cbl. It has been proposed that the three serovar Typhimurium anaerobic reductases for sulfite, thiosulfate, and tetrathionate may function primarily in anaerobic respiration.
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18
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Campanini B, Benoni R, Bettati S, Beck CM, Hayes CS, Mozzarelli A. Moonlighting O-acetylserine sulfhydrylase: New functions for an old protein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1184-93. [PMID: 25731080 DOI: 10.1016/j.bbapap.2015.02.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/18/2015] [Accepted: 02/20/2015] [Indexed: 12/13/2022]
Abstract
O-acetylserine sulfhydrylase A (CysK) is the pyridoxal 5'-phosphate-dependent enzyme that catalyzes the final reaction of cysteine biosynthesis in bacteria. CysK was initially identified in a complex with serine acetyltransferase (CysE), which catalyzes the penultimate reaction in the synthetic pathway. This "cysteine synthase" complex is stabilized by insertion of the CysE C-terminus into the active-site of CysK. Remarkably, the CysK/CysE binding interaction is conserved in most bacterial and plant systems. For the past 40years, CysK was thought to function exclusively in cysteine biosynthesis, but recent studies have revealed a repertoire of additional "moonlighting" activities for this enzyme. CysK and its paralogs influence transcription in both Gram-positive bacteria and the nematode Caenorhabditis elegans. CysK also activates an antibacterial nuclease toxin produced by uropathogenic Escherichia coli. Intriguingly, each moonlighting activity requires a binding partner that invariably mimics the C-terminus of CysE to interact with the CysK active site. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications.
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Affiliation(s)
| | - Roberto Benoni
- Dipartimento di Neuroscienze, Università di Parma, Parma, Italy
| | - Stefano Bettati
- Dipartimento di Neuroscienze, Università di Parma, Parma, Italy; National Institute of Biostructures and Biosystems, Rome, Italy
| | - Christina M Beck
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA.
| | - Andrea Mozzarelli
- Dipartimento di Farmacia, Università di Parma, Parma, Italy; National Institute of Biostructures and Biosystems, Rome, Italy; Institute of Biophysics, CNR, Pisa, Italy
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19
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Wei L, Wang Q, Wu H, Ji C, Zhao J. Proteomic and metabolomic responses of Pacific oyster Crassostrea gigas to elevated pCO2 exposure. J Proteomics 2015; 112:83-94. [DOI: 10.1016/j.jprot.2014.08.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/25/2014] [Accepted: 08/11/2014] [Indexed: 01/11/2023]
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20
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Marchetti M, Bruno S, Campanini B, Bettati S, Peracchi A, Mozzarelli A. Regulation of human serine racemase activity and dynamics by halides, ATP and malonate. Amino Acids 2014; 47:163-73. [PMID: 25331425 DOI: 10.1007/s00726-014-1856-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 10/09/2014] [Indexed: 02/03/2023]
Abstract
D-Serine is a non-proteinogenic amino acid that acts as a co-agonist of the NMDA receptors in the central nervous system. D-Serine is produced by human serine racemase (hSR), a homodimeric pyridoxal 5'-phosphate (PLP)-dependent enzyme that also catalyzes the physiologically relevant β-elimination of both L- and D-serine to pyruvate and ammonia. After improving the protein purification yield and stability, which had so far limited the biochemical characterization of hSR, we found that the catalytic activity is affected by halides, in the order fluoride > chloride > bromide. On the contrary, iodide elicited a complete inhibition, accompanied by a modulation of the tautomeric equilibrium of the internal aldimine. We also investigated the reciprocal effects of ATP and malonate, an inhibitor that reversibly binds at the active site, 20 Å away from the ATP-binding site. ATP increased ninefold the affinity of hSR for malonate and malonate increased 100-fold that of ATP, confirming an allosteric interaction between the two binding sites. To further investigate this allosteric communication, we probed the active site accessibility by quenching of the coenzyme fluorescence in the absence and presence of ATP. We found that ATP stabilizes a closed conformation of the external aldimine Schiff base, suggesting a possible mechanism for ATP-induced hSR activation.
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21
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Luo YH, Song WT, Ge SW, Sun BW. Inorganic anions dependent orientation of ammonium cations in crown ether–ammonium cation–inorganic anion system. Polyhedron 2014. [DOI: 10.1016/j.poly.2013.11.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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22
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Luo YH, Wu DE, Song WT, Ge SW, Sun BW. Positions of amino groups on ammonium salts tunes the conformations of crown ethers: crystal structures, Hirshfeld surfaces and spectroscopic studies. CrystEngComm 2014. [DOI: 10.1039/c4ce00150h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The position of the amino group on the ammonium salt plays a key role in the supramolecular structure and conformation of the crown ether.
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Affiliation(s)
- Yang-Hui Luo
- School of Chemistry and Chemical Engineering
- Southeast University
- Nanjing, PR China
| | - Dong-En Wu
- School of Chemistry and Chemical Engineering
- Southeast University
- Nanjing, PR China
| | - Wen-Tao Song
- School of Chemistry and Chemical Engineering
- Southeast University
- Nanjing, PR China
| | - Shu-Wang Ge
- School of Chemistry and Chemical Engineering
- Southeast University
- Nanjing, PR China
| | - Bai-Wang Sun
- School of Chemistry and Chemical Engineering
- Southeast University
- Nanjing, PR China
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23
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Paul M, Dastidar P. Coordination polymers derived from pyridyl carboxylate ligands having an amide backbone: an attempt towards the selective separation of CuII cation following in situ crystallization under competitive conditions. CrystEngComm 2014. [DOI: 10.1039/c4ce00733f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Selective separation of CuII following in situ crystallization of coordination polymers derived from a pyridyl amide carboxylate ligand was achieved.
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Affiliation(s)
- Mithun Paul
- Department of Organic Chemistry
- Indian Association for the Cultivation of Science
- Kolkata-700032, India
| | - Parthasarathi Dastidar
- Department of Organic Chemistry
- Indian Association for the Cultivation of Science
- Kolkata-700032, India
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24
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Spyrakis F, Singh R, Cozzini P, Campanini B, Salsi E, Felici P, Raboni S, Benedetti P, Cruciani G, Kellogg GE, Cook PF, Mozzarelli A. Isozyme-specific ligands for O-acetylserine sulfhydrylase, a novel antibiotic target. PLoS One 2013; 8:e77558. [PMID: 24167577 PMCID: PMC3805590 DOI: 10.1371/journal.pone.0077558] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 09/03/2013] [Indexed: 01/06/2023] Open
Abstract
The last step of cysteine biosynthesis in bacteria and plants is catalyzed by O-acetylserine sulfhydrylase. In bacteria, two isozymes, O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B, have been identified that share similar binding sites, although the respective specific functions are still debated. O-acetylserine sulfhydrylase plays a key role in the adaptation of bacteria to the host environment, in the defense mechanisms to oxidative stress and in antibiotic resistance. Because mammals synthesize cysteine from methionine and lack O-acetylserine sulfhydrylase, the enzyme is a potential target for antimicrobials. With this aim, we first identified potential inhibitors of the two isozymes via a ligand- and structure-based in silico screening of a subset of the ZINC library using FLAP. The binding affinities of the most promising candidates were measured in vitro on purified O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B from Salmonella typhimurium by a direct method that exploits the change in the cofactor fluorescence. Two molecules were identified with dissociation constants of 3.7 and 33 µM for O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B, respectively. Because GRID analysis of the two isoenzymes indicates the presence of a few common pharmacophoric features, cross binding titrations were carried out. It was found that the best binder for O-acetylserine sulfhydrylase-B exhibits a dissociation constant of 29 µM for O-acetylserine sulfhydrylase-A, thus displaying a limited selectivity, whereas the best binder for O-acetylserine sulfhydrylase-A exhibits a dissociation constant of 50 µM for O-acetylserine sulfhydrylase-B and is thus 8-fold selective towards the former isozyme. Therefore, isoform-specific and isoform-independent ligands allow to either selectively target the isozyme that predominantly supports bacteria during infection and long-term survival or to completely block bacterial cysteine biosynthesis.
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Affiliation(s)
| | - Ratna Singh
- Department of Pharmacy, University of Parma, Parma, Italy
| | - Pietro Cozzini
- Department of Food Sciences, University of Parma, Parma, Italy
- National Institute of Biostructures and Biosystems, Rome, Italy
| | - Barbara Campanini
- Department of Pharmacy, University of Parma, Parma, Italy
- * E-mail: (BC); (AM)
| | - Enea Salsi
- Department of Pharmacy, University of Parma, Parma, Italy
| | - Paolo Felici
- Department of Pharmacy, University of Parma, Parma, Italy
| | - Samanta Raboni
- Department of Pharmacy, University of Parma, Parma, Italy
| | | | | | - Glen E. Kellogg
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Paul F. Cook
- Department of Biochemistry, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Andrea Mozzarelli
- Department of Pharmacy, University of Parma, Parma, Italy
- National Institute of Biostructures and Biosystems, Rome, Italy
- * E-mail: (BC); (AM)
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25
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Kalyani JN, Bisht S, Lakshmikanth M, Murthy MRN, Savithri HS. Identification of key amino acid residues in the catalytic mechanism of diaminopropionate ammonialyase from Salmonella typhimurium. FEBS J 2013; 280:5039-51. [PMID: 23927374 DOI: 10.1111/febs.12474] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 07/16/2013] [Accepted: 07/29/2013] [Indexed: 01/15/2023]
Abstract
Diaminopropionate ammonialyase (DAPAL), a fold-type II pyridoxal 5'-phosphate-dependent enzyme, catalyzes the α,β-elimination of diaminopropionate (DAP) to pyruvate and ammonia. DAPAL was able to utilize both d- and l-DAP as substrates with almost equal efficiency. Mutational analysis of functionally important residues such as Thr385, Asp125 and Asp194 was carried out to understand the mechanism by which the isomers are hydrolyzed. Further, the putative residues involved in the formation of disulfide bond Cys271 and Cys299 were also mutated. T385S, T385D sDAPAL were as active with dl-DAP as substrate as sDAPAL, whereas the later exhibited a threefold increase in catalytic efficiency with d-Ser as substrate. Further analysis of these mutants suggested that DAPAL might follow an anti-E2 mechanism of catalysis that does not involve the formation of a quinonoid intermediate. Of the two mutants of Asp125, D125E showed complete loss of activity with d-DAP as substrate, whereas the reaction with l-DAP was not affected significantly, demonstrating that Asp125 was essential for abstraction of protons from the d-isomer. By contrast, mutational analysis of Asp194 showed that the residue may not be directly involved in proton abstraction from l-DAP. sDAPAL does not form a disulfide bond in solution, although the position of Cys299 and Cys271 in the modeled structure of sDAPAL favored the formation of a disulfide bond. Further, unlike eDAPAL, sDAPAL could be activated by monovalent cations. Mutation of the cysteine residues showed that Cys271 may be involved in coordinating the monovalent cation, as observed in the case of other fold-type II enzymes.
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Affiliation(s)
- Josyula N Kalyani
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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26
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Nath JK, Baruah JB. Water assisted anion chains and anion dependent fluorescence emission in salts of N,N′-bis(3-imidazol-1-ylpropyl)naphthalenediimide. NEW J CHEM 2013. [DOI: 10.1039/c3nj00034f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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27
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Spyrakis F, Felici P, Bayden AS, Salsi E, Miggiano R, Kellogg GE, Cozzini P, Cook PF, Mozzarelli A, Campanini B. Fine tuning of the active site modulates specificity in the interaction of O-acetylserine sulfhydrylase isozymes with serine acetyltransferase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:169-81. [DOI: 10.1016/j.bbapap.2012.09.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 09/10/2012] [Accepted: 09/12/2012] [Indexed: 10/27/2022]
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28
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Yamamoto K, Oshima T, Nonaka G, Ito H, Ishihama A. Induction of the Escherichia colicysK gene by genetic and environmental factors. FEMS Microbiol Lett 2011; 323:88-95. [DOI: 10.1111/j.1574-6968.2011.02364.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 05/20/2011] [Accepted: 07/14/2011] [Indexed: 11/28/2022] Open
Affiliation(s)
| | - Taku Oshima
- Graduate School of Information Sciences; Nara Institute of Science and Technology; Ikoma; Nara; Japan
| | - Gen Nonaka
- Research Institute for Bioscience Products and Fine Chemicals; Ajinomoto Co.; Kawasaki; Kanagawa; Japan
| | - Hisao Ito
- Research Institute for Bioscience Products and Fine Chemicals; Ajinomoto Co.; Kawasaki; Kanagawa; Japan
| | - Akira Ishihama
- Department of Frontier Bioscience and Research Center for Micro-Nano Technology; Hosei University; Koganei; Tokyo; Japan
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29
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Mozzarelli A, Bettati S, Campanini B, Salsi E, Raboni S, Singh R, Spyrakis F, Kumar VP, Cook PF. The multifaceted pyridoxal 5'-phosphate-dependent O-acetylserine sulfhydrylase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1497-510. [PMID: 21549222 DOI: 10.1016/j.bbapap.2011.04.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 04/17/2011] [Accepted: 04/20/2011] [Indexed: 12/14/2022]
Abstract
Cysteine is the final product of the reductive sulfate assimilation pathway in bacteria and plants and serves as the precursor for all sulfur-containing biological compounds, such as methionine, S-adenosyl methionine, iron-sulfur clusters and glutathione. Moreover, in several microorganisms cysteine plays a role as a reducing agent, eventually counteracting host oxidative defense strategies. Cysteine is synthesized by the PLP-dependent O-acetylserine sulfhydrylase, a dimeric enzyme belonging to the fold type II, catalyzing a beta-replacement reaction. In this review, the spectroscopic properties, catalytic mechanism, three-dimensional structure, conformational changes accompanying catalysis, determinants of enzyme stability, role of selected amino acids in catalysis, and the regulation of enzyme activity by ligands and interaction with serine acetyltransferase, the preceding enzyme in the biosynthetic pathway, are described. Given the key biological role played by O-acetylserine sulfhydrylase in bacteria, inhibitors with potential antibiotic activity have been developed. This article is part of a Special Issue entitled: Pyridoxal Phospate Enzymology.
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Affiliation(s)
- Andrea Mozzarelli
- Department of Biochemistry and Molecular Biology, University of Parma, Parma, Italy
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30
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Joseph R, Rao CP. Ion and Molecular Recognition by Lower Rim 1,3-Di-conjugates of Calix[4]arene as Receptors. Chem Rev 2011; 111:4658-702. [DOI: 10.1021/cr1004524] [Citation(s) in RCA: 281] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Roymon Joseph
- Bioinorganic Laboratory, Department of Chemistry, Indian Institute of Technology, Bombay, Mumbai 400 076, India
| | - Chebrolu Pulla Rao
- Bioinorganic Laboratory, Department of Chemistry, Indian Institute of Technology, Bombay, Mumbai 400 076, India
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31
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32
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Exploring O-acetylserine sulfhydrylase-B isoenzyme from Salmonella typhimurium by fluorescence spectroscopy. Arch Biochem Biophys 2011; 505:178-85. [DOI: 10.1016/j.abb.2010.10.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 10/04/2010] [Accepted: 10/04/2010] [Indexed: 11/19/2022]
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33
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Collier DM, Snyder PM. Identification of epithelial Na+ channel (ENaC) intersubunit Cl- inhibitory residues suggests a trimeric alpha gamma beta channel architecture. J Biol Chem 2010; 286:6027-32. [PMID: 21149458 DOI: 10.1074/jbc.m110.198127] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The extracellular domain of the epithelial Na(+) channel (ENaC) is exposed to a wide range of anion concentrations in the kidney. We have previously demonstrated that extracellular Cl(-) inhibits ENaC activity. To identify sites involved in Cl(-) inhibition, we mutated residues in the extracellular domain of α-, β-, and γENaC that are homologous to the Cl(-) binding site in acid-sensing ion channel 1a and tested the effect of Cl(-) on the activity of ENaC expressed in Xenopus oocytes. We identified two Cl(-) inhibitory sites in ENaC. One is formed by residues in the thumb domain of αENaC and the palm domain of βENaC. Mutation of residues at this interface decreased Cl(-) inhibition and decreased Na(+) self-inhibition. The second site is formed by residues at the interface of the thumb domain of βENaC and the palm domain of γENaC. Mutation of these residues also decreased Cl(-) inhibition yet had no effect on Na(+) self-inhibition. In contrast, mutations in the thumb domain of γENaC and palm of αENaC had little or no effect on Cl(-) inhibition or Na(+) self-inhibition. The data demonstrate that Cl(-) inhibits ENaC activity by two distinct Na(+)-dependent and Na(+)-independent mechanisms that correspond to the two functional Cl(-) inhibitory sites. Furthermore, based on the effects of mutagenesis on Cl(-) inhibition, the additive nature of mutations, and on differences in the mechanisms of Cl(-) inhibition, the data support a model in which ENaC subunits assemble in an αγβ orientation (listed clockwise when viewed from the top).
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Affiliation(s)
- Daniel M Collier
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, Iowa 52242, USA
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Tian H, Guan R, Salsi E, Campanini B, Bettati S, Kumar VP, Karsten WE, Mozzarelli A, Cook PF. Identification of the structural determinants for the stability of substrate and aminoacrylate external Schiff bases in O-acetylserine sulfhydrylase-A. Biochemistry 2010; 49:6093-103. [PMID: 20550197 DOI: 10.1021/bi100473v] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
O-Acetylserine sulfhydrylase is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the final step in the cysteine biosynthetic pathway in enteric bacteria and plants, the replacement of the beta-acetoxy group of O-acetyl-L-serine (OAS) by a thiol to give L-cysteine. Previous studies of the K41A mutant enzyme showed L-methionine bound in an external Schiff base (ESB) linkage to PLP as the enzyme was isolated. The mutant enzyme exists in a closed form, optimizing the orientation of the cofactor PLP and properly positioning active site functional groups for reaction. The trigger for closing the active site upon formation of the ESB is thought to be interaction of the substrate alpha-carboxylate with the substrate-binding loop comprised of T68, S69, G70, and N71, and Q142, which is positioned above the cofactor as one looks into the active site. To probe the contribution of these residues to the active site closing and orientation of PLP in the ESB, T68, S69, N71, and Q142 were changed to alanine. Absorbance, fluorescence, near UV-visible CD, and (31)P NMR spectral studies and pre-steady state kinetic studies were used to characterize the mutant enzymes. All of the mutations affect closure of the active site, but to differing extents. In addition, the site appears to be more hydrophilic given that the ESBs do not exhibit a significant amount of the enolimine tautomer. No buildup of the alpha-aminoacrylate intermediate (AA) is observed for the T68A and Q142A mutant enzymes. However, pyruvate is produced at a rate much greater than that of the wild-type enzyme. Data suggest that T68 and Q142 play a role in stabilizing the AA. Both residues donate a hydrogen bond to one of the carboxylate oxygens of the methionine ESB and may also be responsible for the proper orientation of the ESB to generate the AA. The S69A and N71A mutants exhibit formation of the AA, but the rate constant for its formation from the ESB is decreased by 1 order of magnitude compared to that of the wild type. S69 donates a hydrogen bond to the substrate carboxylate in the ESB, while N71 donates hydrogen bonds to O3' of the cofactor and the carboxylate of the ESB; these side chains may also affect the orientation of the ESB. Data suggest that interaction of intermediates with the substrate-binding loop and Q142 gives a properly aligned Michaelis complex and facilitates the beta-elimination reaction.
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Affiliation(s)
- Hui Tian
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, Oklahoma 73018, USA
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Salsi E, Campanini B, Bettati S, Raboni S, Roderick SL, Cook PF, Mozzarelli A. A two-step process controls the formation of the bienzyme cysteine synthase complex. J Biol Chem 2010; 285:12813-22. [PMID: 20164178 DOI: 10.1074/jbc.m109.075762] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The regulation of enzyme activity through the transient formation of multiprotein assemblies plays an important role in the control of biosynthetic pathways. One of the first regulatory complexes to be discovered was cysteine synthase (CS), formed by the pyridoxal 5'-phosphate-dependent enzyme O-acetylserine sulfhydrylase (OASS) and serine acetyltransferase (SAT). These enzymes are at the branch point of the sulfur, carbon, and nitrogen assimilation pathways. Understanding the mechanism of complex formation helps to clarify the role played by CS in the regulation of sulfur assimilation in bacteria and plants. To this goal, stopped-flow fluorescence spectroscopy was used to characterize the interaction of SAT with OASS, at different temperatures and pH values, and in the presence of the physiological regulators cysteine and bisulfide. Results shed light on the mechanism of complex formation and regulation, so far poorly understood. Cysteine synthase assembly occurs via a two-step mechanism involving rapid formation of an encounter complex between the two enzymes, followed by a slow conformational change. The conformational change likely results from the closure of the active site of OASS upon binding of the SAT C-terminal peptide. Bisulfide, the second substrate and a feedback inhibitor of OASS, stabilizes the CS complex mainly by decreasing the back rate of the isomerization step. Cysteine, the product of the OASS reaction and a SAT inhibitor, slightly affects the kinetics of CS formation leading to destabilization of the complex.
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Affiliation(s)
- Enea Salsi
- Dipartimento di Biochimica e Biologia Molecolare, Università di Parma, 43100 Parma, Italy
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D’Souza F, Subbaiyan NK, Xie Y, Hill JP, Ariga K, Ohkubo K, Fukuzumi S. Anion-Complexation-Induced Stabilization of Charge Separation. J Am Chem Soc 2009; 131:16138-46. [DOI: 10.1021/ja9048306] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Francis D’Souza
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260-0051, WPI Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science, Namiki 1-1, Tsukuba, Ibaraki 305-0044, Japan, Key Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science & Technology, Shanghai 200237, P. R. China, and Graduate School of Engineering, Osaka University, SORST (JST), Suita, Osaka 565-0871, Japan
| | - Navaneetha K. Subbaiyan
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260-0051, WPI Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science, Namiki 1-1, Tsukuba, Ibaraki 305-0044, Japan, Key Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science & Technology, Shanghai 200237, P. R. China, and Graduate School of Engineering, Osaka University, SORST (JST), Suita, Osaka 565-0871, Japan
| | - Yongshu Xie
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260-0051, WPI Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science, Namiki 1-1, Tsukuba, Ibaraki 305-0044, Japan, Key Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science & Technology, Shanghai 200237, P. R. China, and Graduate School of Engineering, Osaka University, SORST (JST), Suita, Osaka 565-0871, Japan
| | - Jonathan P. Hill
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260-0051, WPI Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science, Namiki 1-1, Tsukuba, Ibaraki 305-0044, Japan, Key Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science & Technology, Shanghai 200237, P. R. China, and Graduate School of Engineering, Osaka University, SORST (JST), Suita, Osaka 565-0871, Japan
| | - Katsuhiko Ariga
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260-0051, WPI Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science, Namiki 1-1, Tsukuba, Ibaraki 305-0044, Japan, Key Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science & Technology, Shanghai 200237, P. R. China, and Graduate School of Engineering, Osaka University, SORST (JST), Suita, Osaka 565-0871, Japan
| | - Kei Ohkubo
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260-0051, WPI Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science, Namiki 1-1, Tsukuba, Ibaraki 305-0044, Japan, Key Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science & Technology, Shanghai 200237, P. R. China, and Graduate School of Engineering, Osaka University, SORST (JST), Suita, Osaka 565-0871, Japan
| | - Shunichi Fukuzumi
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260-0051, WPI Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science, Namiki 1-1, Tsukuba, Ibaraki 305-0044, Japan, Key Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science & Technology, Shanghai 200237, P. R. China, and Graduate School of Engineering, Osaka University, SORST (JST), Suita, Osaka 565-0871, Japan
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Liu CW, Sarkar B, Huang YJ, Liao PK, Wang JC, Saillard JY, Kahlal S. Octanuclear Copper(I) Clusters Inscribed in a Se12 Icosahedron: Anion-Induced Modulation of the Core Size and Symmetry. J Am Chem Soc 2009; 131:11222-33. [DOI: 10.1021/ja904089t] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C. W. Liu
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan 97401, R.O.C., Department of Chemistry, Soochow University, Taipei, Taiwan 111, R.O.C., and UMR-CNRS 6226 “Sciences Chimiques de Rennes”, Université de Rennes 1, 35042 Rennes cedex, France
| | - Bijay Sarkar
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan 97401, R.O.C., Department of Chemistry, Soochow University, Taipei, Taiwan 111, R.O.C., and UMR-CNRS 6226 “Sciences Chimiques de Rennes”, Université de Rennes 1, 35042 Rennes cedex, France
| | - Yao-Jheng Huang
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan 97401, R.O.C., Department of Chemistry, Soochow University, Taipei, Taiwan 111, R.O.C., and UMR-CNRS 6226 “Sciences Chimiques de Rennes”, Université de Rennes 1, 35042 Rennes cedex, France
| | - Ping-Kuei Liao
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan 97401, R.O.C., Department of Chemistry, Soochow University, Taipei, Taiwan 111, R.O.C., and UMR-CNRS 6226 “Sciences Chimiques de Rennes”, Université de Rennes 1, 35042 Rennes cedex, France
| | - Ju-Chun Wang
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan 97401, R.O.C., Department of Chemistry, Soochow University, Taipei, Taiwan 111, R.O.C., and UMR-CNRS 6226 “Sciences Chimiques de Rennes”, Université de Rennes 1, 35042 Rennes cedex, France
| | - Jean-Yves Saillard
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan 97401, R.O.C., Department of Chemistry, Soochow University, Taipei, Taiwan 111, R.O.C., and UMR-CNRS 6226 “Sciences Chimiques de Rennes”, Université de Rennes 1, 35042 Rennes cedex, France
| | - Samia Kahlal
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan 97401, R.O.C., Department of Chemistry, Soochow University, Taipei, Taiwan 111, R.O.C., and UMR-CNRS 6226 “Sciences Chimiques de Rennes”, Université de Rennes 1, 35042 Rennes cedex, France
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38
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Feldman-Salit A, Wirtz M, Hell R, Wade RC. A Mechanistic Model of the Cysteine Synthase Complex. J Mol Biol 2009; 386:37-59. [DOI: 10.1016/j.jmb.2008.08.075] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Revised: 08/07/2008] [Accepted: 08/20/2008] [Indexed: 11/17/2022]
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39
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Ågren D, Schnell R, Oehlmann W, Singh M, Schneider G. Cysteine Synthase (CysM) of Mycobacterium tuberculosis Is an O-Phosphoserine Sulfhydrylase. J Biol Chem 2008; 283:31567-74. [DOI: 10.1074/jbc.m804877200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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40
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A catalytic mechanism that explains a low catalytic activity of serine dehydratase like-1 from human cancer cells: Crystal structure and site-directed mutagenesis studies. Biochim Biophys Acta Gen Subj 2008; 1780:809-18. [DOI: 10.1016/j.bbagen.2008.01.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 01/29/2008] [Accepted: 01/30/2008] [Indexed: 11/23/2022]
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41
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Tai CH, Rabeh WM, Guan R, Schnackerz KD, Cook PF. Role of Histidine-152 in cofactor orientation in the PLP-dependent O-acetylserine sulfhydrylase reaction. Arch Biochem Biophys 2008; 472:115-25. [DOI: 10.1016/j.abb.2008.01.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Revised: 01/07/2008] [Accepted: 01/10/2008] [Indexed: 11/24/2022]
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42
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Chinthalapudi K, Kumar M, Kumar S, Jain S, Alam N, Gourinath S. Crystal structure of native O-acetyl-serine sulfhydrylase from Entamoeba histolytica and its complex with cysteine: Structural evidence for cysteine binding and lack of interactions with serine acetyl transferase. Proteins 2008; 72:1222-32. [DOI: 10.1002/prot.22013] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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43
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Hell R, Wirtz M. Metabolism of Cysteine in Plants and Phototrophic Bacteria. SULFUR METABOLISM IN PHOTOTROPHIC ORGANISMS 2008. [DOI: 10.1007/978-1-4020-6863-8_4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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44
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Zocher G, Wiesand U, Schulz GE. High resolution structure and catalysis of O-acetylserine sulfhydrylase isozyme B from Escherichia coli. FEBS J 2007; 274:5382-9. [PMID: 17894825 DOI: 10.1111/j.1742-4658.2007.06063.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The crystal structure of the dimeric O-acetylserine sulfhydrylase isozyme B from Escherichia coli (CysM), complexed with the substrate analog citrate, has been determined at 1.33 A resolution by X-ray diffraction analysis. The C1-carboxylate of citrate was bound at the carboxylate position of O-acetylserine, whereas the C6-carboxylate adopted two conformations. The activity of the enzyme and of several active center mutants was determined using an assay based on O-acetylserine and thio-nitrobenzoate (TNB). The unnatural substrate TNB was modeled into the reported structure. The substrate model and the observed mutant activities may facilitate future protein engineering attempts designed to broaden the substrate spectrum of the enzyme. A comparison of the reported structure with previously published CysM structures revealed large conformational changes. One of the crystal forms contained two dimers, each of which comprised one subunit in a closed and one in an open conformation. Although the homodimer asymmetry was most probably caused by crystal packing, it indicates that the enzyme can adopt such a state in solution, which may be relevant for the catalytic reaction.
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Affiliation(s)
- Georg Zocher
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Freiburg im Breisgau, Germany
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45
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Dufe V, Ingner D, Heby O, Khomutov A, Persson L, Al-Karadaghi S. A structural insight into the inhibition of human and Leishmania donovani ornithine decarboxylases by 1-amino-oxy-3-aminopropane. Biochem J 2007; 405:261-8. [PMID: 17407445 PMCID: PMC1904517 DOI: 10.1042/bj20070188] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The critical role of polyamines in key processes such as cell growth, differentiation and macromolecular synthesis makes the enzymes involved in their synthesis potential targets in the treatment of certain types of cancer and parasitic diseases. Here we present a study on the inhibition of human and Leishmania donovani ODC (ornithine decarboxylase), the first committed enzyme in the polyamine biosynthesis pathway, by APA (1-amino-oxy-3-aminopropane). The present study shows APA to be a potent inhibitor of both human and L. donovani ODC with a K(i) value of around 1.0 nM. We also show that L. donovani ODC binds the substrate, the co-enzyme pyridoxal 5'-phosphate and the irreversible inhibitor alpha-difluoromethylornithine (a curative agent of West African sleeping sickness) with less affinity than human ODC. We have also determined the three-dimensional structure of human ODC in complex with APA, which revealed the mode of the inhibitor binding to the enzyme. In contrast with earlier reports, the structure showed no indication of oxime formation between APA and PLP (pyridoxal 5'-phosphate). Homology modelling suggests a similar mode of binding of APA to L. donovani ODC. A comparison of the ODC-APA-PLP structure with earlier ODC structures also shows that the protease-sensitive loop (residues 158-168) undergoes a large conformational change and covers the active site of the protein. The understanding of the structural mode of APA binding may constitute the basis for the development of more specific inhibitors of L. donovani ODC.
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Affiliation(s)
- Veronica T. Dufe
- *Department of Molecular Biophysics, Lund University, S-221 00 Lund, Sweden
| | - Daniel Ingner
- *Department of Molecular Biophysics, Lund University, S-221 00 Lund, Sweden
| | - Olle Heby
- †Department of Molecular Biology, Umeå University, S-901 87 Umeå, Sweden
| | - Alex R. Khomutov
- ‡Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Lo Persson
- §Department of Experimental Medical Science, Lund University, S-221 84 Lund, Sweden
- Correspondence may be addressed to either of these authors (email or )
| | - Salam Al-Karadaghi
- *Department of Molecular Biophysics, Lund University, S-221 00 Lund, Sweden
- Correspondence may be addressed to either of these authors (email or )
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46
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Chattopadhyay A, Meier M, Ivaninskii S, Burkhard P, Speroni F, Campanini B, Bettati S, Mozzarelli A, Rabeh WM, Li L, Cook PF. Structure, Mechanism, and Conformational Dynamics of O-Acetylserine Sulfhydrylase from Salmonella typhimurium: Comparison of A and B Isozymes. Biochemistry 2007; 46:8315-30. [PMID: 17583914 DOI: 10.1021/bi602603c] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
O-Acetylserine sulfhydrylase is a pyridoxal 5'-phosphate-dependent enzyme that catalyzes the final step in the cysteine biosynthetic pathway in enteric bacteria and plants, the replacement of the beta-acetoxy group of O-acetyl-l-serine by a thiol to give l-cysteine. Two isozymes are found in Salmonella typhimurium, with the A-isozyme expressed under aerobic and the B-isozyme expressed under anaerobic conditions. The structure of O-acetylserine sulfhydrylase B has been solved to 2.3 A and exhibits overall a fold very similar to that of the A-isozyme. The main difference between the two isozymes is the more hydrophilic active site of the B-isozyme with two ionizable residues, C280 and D281, replacing the neutral residues S300 and P299, respectively, in the A-isozyme. D281 is above the re face of the cofactor and is within hydrogen-bonding distance to Y286, while C280 is located about 3.4 A from the pyridine nitrogen (N1) of the internal Schiff base. The B-isozyme has a turnover number (V/Et) 12.5-fold higher than the A-isozyme and an approximately 10-fold lower Km for O-acetyl-l-serine. Studies of the first half-reaction by rapid-scanning stopped-flow indicate a first-order conversion of the internal Schiff base to the alpha-aminoacrylate intermediate at any concentration of O-acetyl-l-serine. The Kd values for formation of the external Schiff base with cysteine and serine, obtained by spectral titration, are pH dependent and exhibit a pKa of 7.0-7.5 (for a group that must be unprotonated for optimum binding) with values, above pH 8.0, of about 3.0 and 30.0 mM, respectively. In both cases the neutral enolimine is favored at high pH. Failure to observe the pKa for the alpha-amines of cysteine and serine in the pKESB vs pH profile suggests a compensatory effect resulting from titration of a group on the enzyme with a pKa in the vicinity of the alpha-amine's pKa. The pH dependence of the first-order rate constant for decay of the alpha-aminoacrylate intermediate to give pyruvate and ammonia gives a pKa of about 9 for the active site lysine (K41), a pH unit higher than that of the A-isozyme. The difference in pH dependence of the pKESB for cysteine and serine, the higher pKa for K41, and the preference for the neutral species at high pH compared to the A-isozyme can be explained by titration of C280 to give the thiolate. Subtle conformational differences between O-acetylserine sulfhydrylase A and O-acetylserine sulfhydrylase B are detected by comparing the absorption and emission spectra of the internal aldimine in the absence and presence of the product acetate and of the external aldimine with l-serine. The two isozymes show a different equilibrium distribution of the enolimine and ketoenamine tautomers, likely as a result of a more polar active site for O-acetylserine sulfhydrylase B. The distribution of cofactor tautomers is dramatically affected by the ligation state of the enzyme. In the presence of acetate, which occupies the alpha-carboxylate subsite, the equilibrium between tautomers is shifted toward the ketoenamine tautomer, as a result of a conformational change affecting the structure of the active site. This finding, in agreement with structural data, suggests for the O-acetylserine sulfhydrylase B-isozyme a higher degree of conformational flexibility linked to catalysis.
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Affiliation(s)
- Arundhati Chattopadhyay
- Institute of Materials Science, University of Connecticut, 97 North Eagleville Road, Storrs, Connecticut 06269-3136, USA
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Kumaran S, Jez JM. Thermodynamics of the Interaction between O-Acetylserine Sulfhydrylase and the C-Terminus of Serine Acetyltransferase. Biochemistry 2007; 46:5586-94. [PMID: 17425333 DOI: 10.1021/bi7001168] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cysteine biosynthesis in plants is partly regulated by the physical association of O-acetylserine sulfhydrylase (OASS) and serine acetyltransferase (SAT). Interaction of OASS and SAT requires only the 10 C-terminal residues of SAT. Here we analyze the thermodynamics of formation of a complex of Arabidopsis thaliana OASS (AtOASS) and the C-terminal ligand of AtSAT (C10 peptide) as a function of temperature and salt concentration using fluorescence spectroscopy and isothermal titration calorimetry (ITC). Our results suggest that the C-terminus of AtSAT provides the major contribution to the total binding energy in the plant cysteine synthase complex. The C10 peptide binds to the AtOASS homodimer in a 2:1 complex. Interaction between AtOASS and the C10 peptide is tight (Kd = 5-100 nM) over a range of temperatures (10-35 degrees C) and NaCl concentrations (0.02-1.3 M). AtOASS binding of the C10 peptide displays negative cooperativity at higher temperatures. ITC studies reveal compensating changes in the enthalpy and entropy of binding that also depend on temperature. The enthalpy of interaction has a significant temperature dependence (DeltaCp = -401 cal mol-1 K-1). The heat capacity change and salt dependence studies suggest that hydrophobic interactions drive formation of the AtOASS.C10 peptide complex. The potential regulatory effect of temperature on the plant cysteine synthase complex is discussed.
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Affiliation(s)
- Sangaralingam Kumaran
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, Missouri 63132, USA
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48
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Abstract
Pyridoxal 5'-phosphate (PLP)-dependent enzymes represent about 4% of the enzymes classified by the Enzyme Commission. The versatility of PLP in carrying out a large variety of reactions exploiting the electron sink effect of the pyridine ring, the conformational changes accompanying the chemical steps and stabilizing distinct catalytic intermediates, and the spectral properties of the different coenzyme-substrate derivatives signaling the reaction progress, are some of the features that have attracted our interest to investigate the structure-dynamics-function relationships of PLP-dependent enzymes. To this goal, an integrated approach combining biochemical, biophysical, computational, and molecular biology methods was used. The extensive work carried out on two enzymes, tryptophan synthase and O-acetylserine sulfhydrylase, is presented and discussed as representative of other PLP-dependent enzymes we have investigated. Finally, perspectives of PLP-dependent enzymes functional genomics and drug targeting highlight the continuous novelty of an "old" class of enzymes.
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Affiliation(s)
- Andrea Mozzarelli
- Department of Biochemistry and Molecular Biology, University of Parma, 43100 Parma, Italy.
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Campanini B, Speroni F, Salsi E, Cook PF, Roderick SL, Huang B, Bettati S, Mozzarelli A. Interaction of serine acetyltransferase with O-acetylserine sulfhydrylase active site: evidence from fluorescence spectroscopy. Protein Sci 2005; 14:2115-24. [PMID: 15987896 PMCID: PMC2279323 DOI: 10.1110/ps.051492805] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Revised: 05/09/2005] [Accepted: 05/09/2005] [Indexed: 10/25/2022]
Abstract
Serine acetyltransferase is a key enzyme in the sulfur assimilation pathway of bacteria and plants, and is known to form a bienzyme complex with O-acetylserine sulfhydrylase, the last enzyme in the cysteine biosynthetic pathway. The biological function of the complex and the mechanism of reciprocal regulation of the constituent enzymes are still poorly understood. In this work the effect of complex formation on the O-acetylserine sulfhydrylase active site has been investigated exploiting the fluorescence properties of pyridoxal 5'-phosphate, which are sensitive to the cofactor microenvironment and to conformational changes within the protein matrix. The results indicate that both serine acetyltransferase and its C-terminal decapeptide bind to the alpha-carboxyl subsite of O-acetylserine sulfhydrylase, triggering a transition from an open to a closed conformation. This finding suggests that serine acetyltransferase can inhibit O-acetylserine sulfhydrylase catalytic activity with a double mechanism, the competition with O-acetylserine for binding to the enzyme active site and the stabilization of a closed conformation that is less accessible to the natural substrate.
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Affiliation(s)
- Barbara Campanini
- Department of Biochemistry and Molecular Biology, Univeristy of Parma, 43100 Parma, Italy
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Claus MT, Zocher GE, Maier THP, Schulz GE. Structure of theO-Acetylserine Sulfhydrylase Isoenzyme CysM fromEscherichia coli†,‡. Biochemistry 2005; 44:8620-6. [PMID: 15952768 DOI: 10.1021/bi050485+] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enzyme O-acetylserine sulfhydrylase participates in the biosynthesis of l-cysteine in bacteria and plants. The structure of isoenzyme B (CysM) from Escherichia coli was established in a hexagonal crystal form at 2.7 A resolution (wild-type) and in a merohedrally twinned tetragonal crystal form at 2.1 A resolution (surface mutant). Structural superpositions revealed the variations with respect to isoenzyme A (CysK) and explained the different substrate specificities. A geometric model of the reaction catalyzed by CysM is proposed. Both isoenzymes are used for the production of l-amino acid derivatives as building blocks for the synthesis of peptides and peptidomimetic drugs. Since the structure of CysM revealed a remarkable main chain variation at the active center, it constitutes a further starting point for engineering mutants with novel substrate specificities.
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Affiliation(s)
- Michael T Claus
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstrasse 21, D-79104 Freiburg im Breisgau, Germany
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