1
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Koper K, Han SW, Kothadia R, Salamon H, Yoshikuni Y, Maeda HA. Multisubstrate specificity shaped the complex evolution of the aminotransferase family across the tree of life. Proc Natl Acad Sci U S A 2024; 121:e2405524121. [PMID: 38885378 PMCID: PMC11214133 DOI: 10.1073/pnas.2405524121] [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: 04/02/2024] [Accepted: 05/14/2024] [Indexed: 06/20/2024] Open
Abstract
Aminotransferases (ATs) are an ancient enzyme family that play central roles in core nitrogen metabolism, essential to all organisms. However, many of the AT enzyme functions remain poorly defined, limiting our fundamental understanding of the nitrogen metabolic networks that exist in different organisms. Here, we traced the deep evolutionary history of the AT family by analyzing AT enzymes from 90 species spanning the tree of life (ToL). We found that each organism has maintained a relatively small and constant number of ATs. Mapping the distribution of ATs across the ToL uncovered that many essential AT reactions are carried out by taxon-specific AT enzymes due to wide-spread nonorthologous gene displacements. This complex evolutionary history explains the difficulty of homology-based AT functional prediction. Biochemical characterization of diverse aromatic ATs further revealed their broad substrate specificity, unlike other core metabolic enzymes that evolved to catalyze specific reactions today. Interestingly, however, we found that these AT enzymes that diverged over billion years share common signatures of multisubstrate specificity by employing different nonconserved active site residues. These findings illustrate that AT family enzymes had leveraged their inherent substrate promiscuity to maintain a small yet distinct set of multifunctional AT enzymes in different taxa. This evolutionary history of versatile ATs likely contributed to the establishment of robust and diverse nitrogen metabolic networks that exist throughout the ToL. The study provides a critical foundation to systematically determine diverse AT functions and underlying nitrogen metabolic networks across the ToL.
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Affiliation(s)
- Kaan Koper
- Department of Botany, University of Wisconsin-Madison, Madison, WI53706
| | - Sang-Woo Han
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Biotechnology, Konkuk University, Chungju27478, South Korea
| | - Ramani Kothadia
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Hugh Salamon
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Yasuo Yoshikuni
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Global Center for Food, Land, and Water Resources, Research Faculty of Agriculture, Hokkaido University, Hokkaido, Japan 060-8589
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo183-8538, Japan
| | - Hiroshi A. Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI53706
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2
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Zarin S, Shariq M, Rastogi N, Ahuja Y, Manjunath P, Alam A, Hasnain SE, Ehtesham NZ. Rv2231c, a unique histidinol phosphate aminotransferase from Mycobacterium tuberculosis, supports virulence by inhibiting host-directed defense. Cell Mol Life Sci 2024; 81:203. [PMID: 38698289 PMCID: PMC11065945 DOI: 10.1007/s00018-024-05200-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 02/02/2024] [Accepted: 03/04/2024] [Indexed: 05/05/2024]
Abstract
Nitrogen metabolism of M. tuberculosis is critical for its survival in infected host cells. M. tuberculosis has evolved sophisticated strategies to switch between de novo synthesis and uptake of various amino acids from host cells for metabolic demands. Pyridoxal phosphate-dependent histidinol phosphate aminotransferase-HspAT enzyme is critically required for histidine biosynthesis. HspAT is involved in metabolic synthesis of histidine, phenylalanine, tyrosine, tryptophan, and novobiocin. We showed that M. tuberculosis Rv2231c is a conserved enzyme with HspAT activity. Rv2231c is a monomeric globular protein that contains α-helices and β-sheets. It is a secretory and cell wall-localized protein that regulates critical pathogenic attributes. Rv2231c enhances the survival and virulence of recombinant M. smegmatis in infected RAW264.7 macrophage cells. Rv2231c is recognized by the TLR4 innate immune receptor and modulates the host immune response by suppressing the secretion of the antibacterial pro-inflammatory cytokines TNF, IL-12, and IL-6. It also inhibits the expression of co-stimulatory molecules CD80 and CD86 along with antigen presenting molecule MHC-I on macrophage and suppresses reactive nitrogen species formation, thereby promoting M2 macrophage polarization. Recombinant M. smegmatis expressing Rv2231c inhibited apoptosis in macrophages, promoting efficient bacterial survival and proliferation, thereby increasing virulence. Our results indicate that Rv2231c is a moonlighting protein that regulates multiple functions of M. tuberculosis pathophysiology to increase its virulence. These mechanistic insights can be used to better understand the pathogenesis of M. tuberculosis and to design strategies for tuberculosis mitigation.
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Affiliation(s)
- Sheeba Zarin
- Institute of Molecular Medicine, Jamia Hamdard, Hamdard Nagar, New Delhi, India
- Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, 201310, India
| | - Mohd Shariq
- Cell Signaling and Inflammation Biology Lab, ICMR-National Institute of Pathology, New Delhi, 110029, India
| | - Nilisha Rastogi
- Cell Signaling and Inflammation Biology Lab, ICMR-National Institute of Pathology, New Delhi, 110029, India
| | - Yashika Ahuja
- Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, 201310, India
| | - P Manjunath
- Cell Signaling and Inflammation Biology Lab, ICMR-National Institute of Pathology, New Delhi, 110029, India
| | - Anwar Alam
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, 201310, India
| | - Seyed Ehtesham Hasnain
- Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, 201310, India.
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, 110016, India.
| | - Nasreen Zafar Ehtesham
- Department of Life Science, School of Basic Sciences and Research, Sharda University, Greater Noida, Uttar Pradesh, 201310, India.
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3
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Kaur H, Kalia M, Singh V, Taneja N. Identification of novel inhibitors against Escherichia coli utilizing HisC as a target from histidine biosynthesis pathway. J Biomol Struct Dyn 2023; 41:9907-9914. [PMID: 36416560 DOI: 10.1080/07391102.2022.2148319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/10/2022] [Indexed: 11/24/2022]
Abstract
Escherichia coli is a gram-negative bacterial pathogen that poses a significant challenge both clinically and epidemiologically. Large numbers of multi-drug resistant E. coli have emerged in the last decade, because of the selection pressure generated by the inadequate use of antibiotics. Although research to combat antibiotic resistance has been going on extensively but still lags in the rate of development of newer antibiotics. Therefore, newer approaches are required to speed up the rate of discovery of antibiotics. Computational methods for screening of inhibitors have made a significant contribution to the discovery of novel antimicrobials. The present study utilized histidinol-phospho aminotransferase (HisC) as a target. HisC is an enzyme that plays a crucial role in the biosynthesis of histidine and its absence in mammals makes it an attractive drug target. A ZINC library of 5000 natural compounds was screened against HisC (PDB ID: 1FG7) using PyRx and the first 500 hits were selected for secondary screening after sorting the result on the basis of binding score. Fifteen compounds passed the secondary filter ADME and out of these five passed toxicity filters; the best among five hits was selected on the basis of its binding score and inhibition constants. Further, molecular dynamics simulations and free binding were computed of selected five compounds and two natural compounds ZINC402598829 and ZINC31157928 complexed with HisC were found as highly stable. Overall, our results indicated that these natural sources could be used as potential HisC inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Harpreet Kaur
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Manmohit Kalia
- Department of Biology, State University of New York, Binghamton, NY, USA
| | - Vikram Singh
- School of Computational Biology and Bioinformatics, Central University of Himachal Pradesh, Dharamshala, Himachal Pradesh, India
| | - Neelam Taneja
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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4
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Rutkiewicz M, Nogues I, Witek W, Angelaccio S, Contestabile R, Ruszkowski M. Insights into the substrate specificity, structure, and dynamics of plant histidinol-phosphate aminotransferase (HISN6). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:759-773. [PMID: 36842242 DOI: 10.1016/j.plaphy.2023.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/01/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Histidinol-phosphate aminotransferase is the sixth protein (hence HISN6) in the histidine biosynthetic pathway in plants. HISN6 is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the reversible conversion of imidazole acetol phosphate into L-histidinol phosphate (HOLP). Here, we show that plant HISN6 enzymes are closely related to the orthologs from Chloroflexota. The studied example, HISN6 from Medicago truncatula (MtHISN6), exhibits a surprisingly high affinity for HOLP, which is much higher than reported for bacterial homologs. Moreover, unlike the latter, MtHISN6 does not transaminate phenylalanine. High-resolution crystal structures of MtHISN6 in the open and closed states, as well as the complex with HOLP and the apo structure without PLP, bring new insights into the enzyme dynamics, pointing at a particular role of a string-like fragment that oscillates near the active site and participates in the HOLP binding. When MtHISN6 is compared to bacterial orthologs with known structures, significant differences arise in or near the string region. The high affinity of MtHISN6 appears linked to the particularly tight active site cavity. Finally, a virtual screening against a library of over 1.3 mln compounds revealed three sites in the MtHISN6 structure with the potential to bind small molecules. Such compounds could be developed into herbicides inhibiting plant HISN6 enzymes absent in animals, which makes them a potential target for weed control agents.
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Affiliation(s)
- Maria Rutkiewicz
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Isabel Nogues
- Research Institute on Terrestrial Ecosystems, National Research Council, Monterotondo Scalo, Rome, Italy
| | - Wojciech Witek
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Sebastiana Angelaccio
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Rome, Italy
| | - Roberto Contestabile
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Rome, Italy
| | - Milosz Ruszkowski
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
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5
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Kumar D, Jha B, Bhatia I, Ashraf A, Dwivedy A, Biswal BK. Characterization of a triazole scaffold compound as an inhibitor of Mycobacterium tuberculosis imidazoleglycerol-phosphate dehydratase. Proteins 2021; 90:3-17. [PMID: 34288118 DOI: 10.1002/prot.26181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/24/2021] [Accepted: 07/11/2021] [Indexed: 11/11/2022]
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of human tuberculosis (TB), employs ten enzymes including imidazoleglycerol-phosphate dehydratase (IGPD) for de novo biosynthesis of histidine. The absence of histidine-biosynthesis in humans combined with its essentiality for Mtb makes the enzymes of this pathway major anti-TB drug targets. We explored the inhibitory potential of a small molecule β-(1,2,4-Triazole-3-yl)-DL-alanine (DLA) against Mtb IGPD. DLA exhibits an in vitro inhibitory efficacy in the lower micromolar range. Higher-resolution crystal structures of native and substrate-bound Mtb IGPD provided additional structural features of this important drug target. Crystal structure of IGPD-DLA complex at a resolution of 1.75 Å, confirmed that DLA locks down the function of the enzyme by binding in the active site pocket of the IGPD mimicking the substrate-binding mode to a high degree. In our biochemical study, DLA showed an efficient inhibition of Mtb IGPD. Furthermore, DLA also showed bactericidal activity against Mtb and Mycobacterium smegmatis and inhibited their growth in respective culture medium. Importantly, owing to the favorable ADME and physicochemical properties, it serves as an important lead molecule for further derivatizations.
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Affiliation(s)
- Deepak Kumar
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi, India.,Department of Zoology, University of Rajasthan, JLN Marg, Jaipur, Rajasthan, India
| | - Bhavya Jha
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi, India.,Department of Zoology, GDM Mahavidyalaya, Patliputra University, Kankarbagh, Patna, Bihar, India
| | - Indu Bhatia
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi, India
| | - Anam Ashraf
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi, India
| | - Abhisek Dwivedy
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi, India
| | - Bichitra Kumar Biswal
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi, India
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6
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Kaur H, Kalia M, Singh V, Modgil V, Mohan B, Taneja N. In silico identification and characterization of promising drug targets in highly virulent uropathogenic Escherichia coli strain CFT073 by protein-protein interaction network analysis. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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7
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Aspartate aminotransferase Rv3722c governs aspartate-dependent nitrogen metabolism in Mycobacterium tuberculosis. Nat Commun 2020; 11:1960. [PMID: 32327655 PMCID: PMC7181641 DOI: 10.1038/s41467-020-15876-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/31/2020] [Indexed: 01/01/2023] Open
Abstract
Gene rv3722c of Mycobacterium tuberculosis is essential for in vitro growth, and encodes a putative pyridoxal phosphate-binding protein of unknown function. Here we use metabolomic, genetic and structural approaches to show that Rv3722c is the primary aspartate aminotransferase of M. tuberculosis, and mediates an essential but underrecognized role in metabolism: nitrogen distribution. Rv3722c deficiency leads to virulence attenuation in macrophages and mice. Our results identify aspartate biosynthesis and nitrogen distribution as potential species-selective drug targets in M. tuberculosis.
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8
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Madani A, Ridenour JN, Martin BP, Paudel RR, Abdul Basir A, Le Moigne V, Herrmann JL, Audebert S, Camoin L, Kremer L, Spilling CD, Canaan S, Cavalier JF. Cyclipostins and Cyclophostin Analogues as Multitarget Inhibitors That Impair Growth of Mycobacterium abscessus. ACS Infect Dis 2019; 5:1597-1608. [PMID: 31299146 DOI: 10.1021/acsinfecdis.9b00172] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Twelve new Cyclophostin and Cyclipostins analogues (CyC19-30) were synthesized, thus extending our series to 38 CyCs. Their antibacterial activities were evaluated against four pathogenic mycobacteria (Mycobacterium abscessus, Mycobacterium marinum, Mycobacterium bovis BCG, and Mycobacterium tuberculosis) and two Gram negative bacteria. The CyCs displayed very low toxicity toward host cells and were only active against mycobacteria. Importantly, several CyCs were active against extracellular M. abscessus (CyC17/CyC18β/CyC25/CyC26) or intramacrophage residing mycobacteria (CyC7(α,β)/CyC8(α,β)) with minimal inhibitory concentrations (MIC50) values comparable to or better than those of amikacin or imipenem, respectively. An activity-based protein profiling combined with mass spectrometry allowed identification of the potential target enzymes of CyC17/CyC26, mostly being involved in lipid metabolism and/or in cell wall biosynthesis. Overall, these results strengthen the selective activity of the CyCs against mycobacteria, including the most drug-resistant M. abscessus, through the cumulative inhibition of a large number of Ser- and Cys-enzymes participating in key physiological processes.
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Affiliation(s)
- Abdeldjalil Madani
- Aix-Marseille Université, CNRS, LISM, Institut de Microbiologie de la Méditerranée, Marseille, France 13402 Cedex 20
| | - Jeremy N. Ridenour
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Benjamin P. Martin
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Rishi R. Paudel
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Anosha Abdul Basir
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Vincent Le Moigne
- APHP, GHU PIFO, Hôpital Raymond-Poincaré−Hôpital Ambroise-Paré, 92100 Boulogne-Billancourt, France
| | - Jean-Louis Herrmann
- APHP, GHU PIFO, Hôpital Raymond-Poincaré−Hôpital Ambroise-Paré, 92100 Boulogne-Billancourt, France
- 2I, UVSQ, INSERM UMR 1173, Université Paris-Saclay, 78035 Versailles, France
| | - Stéphane Audebert
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, 13273 Marseille Cedex 09, France
| | - Luc Camoin
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, 13273 Marseille Cedex 09, France
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, 34293 Montpellier, France
- IRIM, INSERM, 34293 Montpellier, France
| | - Christopher D. Spilling
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Stéphane Canaan
- Aix-Marseille Université, CNRS, LISM, Institut de Microbiologie de la Méditerranée, Marseille, France 13402 Cedex 20
| | - Jean-François Cavalier
- Aix-Marseille Université, CNRS, LISM, Institut de Microbiologie de la Méditerranée, Marseille, France 13402 Cedex 20
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9
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Liang J, Han Q, Tan Y, Ding H, Li J. Current Advances on Structure-Function Relationships of Pyridoxal 5'-Phosphate-Dependent Enzymes. Front Mol Biosci 2019; 6:4. [PMID: 30891451 PMCID: PMC6411801 DOI: 10.3389/fmolb.2019.00004] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 01/25/2019] [Indexed: 12/23/2022] Open
Abstract
Pyridoxal 5′-phosphate (PLP) functions as a coenzyme in many enzymatic processes, including decarboxylation, deamination, transamination, racemization, and others. Enzymes, requiring PLP, are commonly termed PLP-dependent enzymes, and they are widely involved in crucial cellular metabolic pathways in most of (if not all) living organisms. The chemical mechanisms for PLP-mediated reactions have been well elaborated and accepted with an emphasis on the pure chemical steps, but how the chemical steps are processed by enzymes, especially by functions of active site residues, are not fully elucidated. Furthermore, the specific mechanism of an enzyme in relation to the one for a similar class of enzymes seems scarcely described or discussed. This discussion aims to link the specific mechanism described for the individual enzyme to the same types of enzymes from different species with aminotransferases, decarboxylases, racemase, aldolase, cystathionine β-synthase, aromatic phenylacetaldehyde synthase, et al. as models. The structural factors that contribute to the reaction mechanisms, particularly active site residues critical for dictating the reaction specificity, are summarized in this review.
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Affiliation(s)
- Jing Liang
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Qian Han
- Laboratory of Tropical Veterinary Medicine and Vector Biology, Hainan Key Laboratory of Sustainable Utilization of Tropical Bioresources, Institute of Agriculture and Forestry, Hainan University, Haikou, China
| | - Yang Tan
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Haizhen Ding
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Jianyong Li
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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10
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Jha B, Kumar D, Sharma A, Dwivedy A, Singh R, Biswal BK. Identification and structural characterization of a histidinol phosphate phosphatase from Mycobacterium tuberculosis. J Biol Chem 2018; 293:10102-10118. [PMID: 29752410 PMCID: PMC6028948 DOI: 10.1074/jbc.ra118.002299] [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: 02/22/2018] [Revised: 05/10/2018] [Indexed: 01/07/2023] Open
Abstract
The absence of a histidine biosynthesis pathway in humans, coupled with histidine essentiality for survival of the important human pathogen Mycobacterium tuberculosis (Mtb), underscores the importance of the bacterial enzymes of this pathway as major antituberculosis drug targets. However, the identity of the mycobacterial enzyme that functions as the histidinol phosphate phosphatase (HolPase) of this pathway remains to be established. Here, we demonstrate that the enzyme encoded by the Rv3137 gene, belonging to the inositol monophosphatase (IMPase) family, functions as the Mtb HolPase and specifically dephosphorylates histidinol phosphate. The crystal structure of Rv3137 in apo form enabled us to dissect its distinct structural features. Furthermore, the holo-complex structure revealed that a unique cocatalytic multizinc-assisted mode of substrate binding and catalysis is the hallmark of Mtb HolPase. Interestingly, the enzyme-substrate complex structure unveiled that although monomers possess individual catalytic sites they share a common product-exit channel at the dimer interface. Furthermore, target-based screening against HolPase identified several small-molecule inhibitors of this enzyme. Taken together, our study unravels the missing enzyme link in the Mtb histidine biosynthesis pathway, augments our current mechanistic understanding of histidine production in Mtb, and has helped identify potential inhibitors of this bacterial pathway.
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Affiliation(s)
- Bhavya Jha
- From the Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi 110067, India and
| | - Deepak Kumar
- From the Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi 110067, India and
| | - Arun Sharma
- Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India
| | - Abhisek Dwivedy
- From the Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi 110067, India and
| | - Ramandeep Singh
- Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India
| | - Bichitra Kumar Biswal
- From the Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi 110067, India and , Recipient of funding from the National Institute of Immunology, New Delhi, India. To whom correspondence should be addressed. Tel.:
91-11-26703705; Fax:
91-11-26742125; E-mail:
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11
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Park YJ, Kenney GE, Schachner LF, Kelleher NL, Rosenzweig AC. Repurposed HisC Aminotransferases Complete the Biosynthesis of Some Methanobactins. Biochemistry 2018; 57:3515-3523. [PMID: 29694778 PMCID: PMC6019534 DOI: 10.1021/acs.biochem.8b00296] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Methanobactins (Mbns) are ribosomally produced, post-translationally modified bacterial natural products with a high affinity for copper. MbnN, a pyridoxal 5'-phosphate-dependent aminotransferase, performs a transamination reaction that is the last step in the biosynthesis of Mbns produced by several Methylosinus species. Our bioinformatic analyses indicate that MbnNs likely derive from histidinol-phosphate aminotransferases (HisCs), which play a key role in histidine biosynthesis. A comparison of the HisC active site with the predicted MbnN structure suggests that MbnN's active site is altered to accommodate the larger and more hydrophobic substrates necessary for Mbn biosynthesis. Moreover, we have confirmed that MbnN is capable of catalyzing the final transamination step in Mbn biosynthesis in vitro and in vivo. We also demonstrate that without this final modification, Mbn exhibits significantly decreased stability under physiological conditions. An examination of other Mbns and Mbn operons suggests that N-terminal protection of this family of natural products is of critical importance and that several different means of N-terminal stabilization have evolved independently in Mbn subfamilies.
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Affiliation(s)
- Yun Ji Park
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Grace E. Kenney
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Luis F. Schachner
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L. Kelleher
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C. Rosenzweig
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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