1
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Dinh DM, Thomas LM, Karr EA. Crystal structure of a putative 3-hydroxypimelyl-CoA dehydrogenase, Hcd1, from Syntrophus aciditrophicus strain SB at 1.78 Å resolution. Acta Crystallogr F Struct Biol Commun 2023; 79:151-158. [PMID: 37227375 PMCID: PMC10231260 DOI: 10.1107/s2053230x23004399] [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: 03/28/2023] [Accepted: 05/20/2023] [Indexed: 05/26/2023] Open
Abstract
Syntrophus aciditrophicus strain SB is a model syntroph that degrades benzoate and alicyclic acids. The structure of a putative 3-hydroxypimelyl-CoA dehydrogenase from S. aciditrophicus strain SB (SaHcd1) was resolved at 1.78 Å resolution. SaHcd1 contains sequence motifs and structural features that belong to the short-chain dehydrogenase/reductase (SDR) family of NADPH-dependent oxidoreductases. SaHcd1 is proposed to concomitantly reduce NAD+ or NADP+ to NADH or NADPH, respectively, while converting 3-hydroxypimelyl-CoA to 3-oxopimeyl-CoA. Further enzymatic studies are needed to confirm the function of SaHcd1.
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Affiliation(s)
- David M. Dinh
- Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, Norman, OK 73019, USA
- Price Family Foundation Institute of Structural Biology, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Leonard M. Thomas
- Price Family Foundation Institute of Structural Biology, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, USA
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Elizabeth A. Karr
- Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, Norman, OK 73019, USA
- Price Family Foundation Institute of Structural Biology, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019, USA
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2
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Aygün C, Kocer S, Danış Ö, Cubuk S, Mutlu O. Heterologous expression, purification, and partial characterisation of the apicoplast protein 3-oxoacyl-[acyl-carrier-protein] reductase from Toxoplasma gondii. Protein Expr Purif 2023; 202:106187. [PMID: 36216219 DOI: 10.1016/j.pep.2022.106187] [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: 07/08/2022] [Revised: 10/02/2022] [Accepted: 10/03/2022] [Indexed: 11/05/2022]
Abstract
Recombinant expression and purification of proteins have become a staple of modern drug discovery as it enables more precise in vitro analyses of drug targets, which may help obtain biochemical and biophysical parameters of a known enzyme and even uncover unknown characteristics indicative of novel enzymatic functions. Such information is often necessary to prepare adequate screening assays and drug-discovery experiments in general. Toxoplasma gondii is an obligate protozoan parasite that is a member of the phylum Apicomplexa, can develop several neuro-degenerative symptoms and, in specific cases, certain death for human hosts. Its relict non-photosynthetic plastid, the apicoplast, harbours a unique de novo long-chain fatty acid synthesis pathway of a prokaryotic character, FASII. The FASII pathway shows plasticity and, is essential for many intracellular and membranal components, along with fatty acid uptake via salvaging from the host, therefore, its disruption causes parasite death. TgFabG, a FASII enzyme responsible for a single reduction step in the pathway, was recombinantly expressed, purified and biochemically and biophysically characterised in this study. The bioengineering hurdle of expressing the recombinant gene of a eukaryotic, signal peptide-containing protein in a prokaryotic system was overcome for the apicomplexan enzyme TgFabG, by truncating the N-terminal signal peptide. TgFabG was ultimately recombinantly produced in a plasmid expression vector from its 1131 base pair gene, purified as 260 and 272 amino acid proteins using a hexahistidine (6 × Histag) affinity chromatography and its biochemical (enzyme activity and kinetics) and biophysical characteristics were analysed in vitro.
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Affiliation(s)
- Can Aygün
- Marmara University, Faculty of Arts and Sciences, Department of Biology, 34722, Istanbul, Turkey
| | - Sinem Kocer
- Istanbul Yeni Yüzyıl University, Faculty of Pharmacy, Department of Pharmaceutical Biotechnology, 34010, Istanbul, Turkey
| | - Özkan Danış
- Marmara University, Faculty of Arts and Sciences, Department of Chemistry, 34722, Istanbul, Turkey
| | - Soner Cubuk
- Marmara University, Faculty of Arts and Sciences, Department of Chemistry, 34722, Istanbul, Turkey
| | - Ozal Mutlu
- Marmara University, Faculty of Arts and Sciences, Department of Biology, 34722, Istanbul, Turkey.
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3
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Dutta D. Advance in Research on Mycobacterium tuberculosis FabG4 and Its Inhibitor. Front Microbiol 2018; 9:1184. [PMID: 29946302 PMCID: PMC6008564 DOI: 10.3389/fmicb.2018.01184] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/16/2018] [Indexed: 12/17/2022] Open
Abstract
Increasing evidence from recent reports of drug-resistant mycobacterial strains poses a challenge worldwide. Drug-resistant strains often undergo mutations, adopt alternative pathways, and express drug efflux pumps to reduce or eliminate drug doses. Besides these intrinsic resistance mechanisms, bacteria can evade drug doses by forming biofilms. Biofilms are the concerted growth of adherent microorganisms, which can also be formed at the air-water interface. The growth is supported by the extracellular polymer matrix which is self-produced by the microorganisms. Reduced metabolic activity in a nutrient-deficient environment in the biofilm may cause the microorganisms to take alternative pathways that can make the microorganisms recalcitrant to the drug doses. Recent works have shown that Mycobacterium tuberculosis expresses several proteins during its growth in biofilm, those when deleted, did not show any effect on mycobacterial growth in normal nutrient-sufficient conditions. Studying these unconventional proteins in mycobacterial biofilms is therefore of utmost importance. In this article, I will discuss one such mycobacterial biofilm-related protein FabG4 that is recently shown to be important for mycobacterial survival in the presence of antibiotic stressors and limited nutrient condition. In an attempt to find more effective FabG4 inhibitors and its importance in biofilm forming M. tuberculosis, present knowledge about FabG4 and its known inhibitors are discussed. Based on the existing data, a putative role of FabG4 is also suggested.
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Affiliation(s)
- Debajyoti Dutta
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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4
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Liu C, Qi J, Shan B, Ma Y. Tachyplesin Causes Membrane Instability That Kills Multidrug-Resistant Bacteria by Inhibiting the 3-Ketoacyl Carrier Protein Reductase FabG. Front Microbiol 2018; 9:825. [PMID: 29765362 PMCID: PMC5938390 DOI: 10.3389/fmicb.2018.00825] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/11/2018] [Indexed: 12/19/2022] Open
Abstract
Tachyplesin is a type of cationic β-hairpin antimicrobial peptide discovered in horseshoe crab approximately 30 years ago that is well known for both its potential antimicrobial activities against multidrug-resistant bacteria and its cytotoxicity to mammalian cells. Though its physical interactions with artificial membranes have been well studied, details of its physiological mechanism of action the physiological consequences of its action remain limited. By using the DNA-binding fluorescent dye propidium iodide to monitor membrane integrity, confocal microscopy to assess the intracellular location of FITC-tagged tachyplesin, and RNA sequencing of the differentially expressed genes in four Gram-negative bacteria (Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa) treated with lethal or sublethal concentrations of tachyplesin, we found that compared with levofloxacin-treated bacteria, tachyplesin-treated bacteria showed significant effects on the pathways underlying unsaturated fatty acid biosynthesis. Notably, RNA levels of the conserved and essential 3-ketoacyl carrier protein reductase in this pathway (gene FabG) were elevated in all of the four bacteria after tachyplesin treatment. In vitro tests including surface plasmon resonance and enzyme activity assays showed that tachyplesin could bind and inhibit 3-ketoacyl carrier protein reductase, which was consistent with molecular docking prediction results. As unsaturated fatty acids are important for membrane fluidity, our results provided one possible mechanism to explain how tachyplesin kills bacteria and causes cytotoxicity by targeting membranes, which may be helpful for designing more specific and safer antibiotics based on the function of tachyplesin.
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Affiliation(s)
- Cunbao Liu
- Laboratory of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Jialong Qi
- Laboratory of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Bin Shan
- Department of Clinical Laboratory, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yanbing Ma
- Laboratory of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
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5
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Küssau T, Flipo M, Van Wyk N, Viljoen A, Olieric V, Kremer L, Blaise M. Structural rearrangements occurring upon cofactor binding in the Mycobacterium smegmatis β-ketoacyl-acyl carrier protein reductase MabA. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:383-393. [PMID: 29717709 DOI: 10.1107/s2059798318002917] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/19/2018] [Indexed: 12/14/2022]
Abstract
In mycobacteria, the ketoacyl-acyl carrier protein (ACP) reductase MabA (designated FabG in other bacteria) catalyzes the NADPH-dependent reduction of β-ketoacyl-ACP substrates to β-hydroxyacyl-ACP products. This first reductive step in the fatty-acid biosynthesis elongation cycle is essential for bacteria, which makes MabA/FabG an interesting drug target. To date, however, very few molecules targeting FabG have been discovered and MabA remains the only enzyme of the mycobacterial type II fatty-acid synthase that lacks specific inhibitors. Despite the existence of several MabA/FabG crystal structures, the structural rearrangement that occurs upon cofactor binding is still not fully understood. Therefore, unlocking this knowledge gap could help in the design of new inhibitors. Here, high-resolution crystal structures of MabA from Mycobacterium smegmatis in its apo, NADP+-bound and NADPH-bound forms are reported. Comparison of these crystal structures reveals the structural reorganization of the lid region covering the active site of the enzyme. The crystal structure of the apo form revealed numerous residues that trigger steric hindrance to the binding of NADPH and substrate. Upon NADPH binding, these residues are pushed away from the active site, allowing the enzyme to adopt an open conformation. The transition from an NADPH-bound to an NADP+-bound form is likely to facilitate release of the product. These results may be useful for subsequent rational drug design and/or for in silico drug-screening approaches targeting MabA/FabG.
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Affiliation(s)
- Tanja Küssau
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, 34293 Montpellier, France
| | - Marion Flipo
- Université de Lille, INSERM, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, 59000 Lille, France
| | - Niel Van Wyk
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, 34293 Montpellier, France
| | - Albertus Viljoen
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, 34293 Montpellier, France
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, 34293 Montpellier, France
| | - Mickaël Blaise
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, 34293 Montpellier, France
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6
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Domain swapping between FabGs deciphers the structural determinant for in-solution oligomerization and substrate binding. Biophys Chem 2018; 237:9-21. [PMID: 29625337 DOI: 10.1016/j.bpc.2018.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/15/2018] [Accepted: 03/19/2018] [Indexed: 01/02/2023]
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7
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Haft DH, Pierce PG, Mayclin SJ, Sullivan A, Gardberg AS, Abendroth J, Begley DW, Phan IQ, Staker BL, Myler PJ, Marathias VM, Lorimer DD, Edwards TE. Mycofactocin-associated mycobacterial dehydrogenases with non-exchangeable NAD cofactors. Sci Rep 2017; 7:41074. [PMID: 28120876 PMCID: PMC5264612 DOI: 10.1038/srep41074] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/12/2016] [Indexed: 01/08/2023] Open
Abstract
During human infection, Mycobacterium tuberculosis (Mtb) survives the normally bacteriocidal phagosome of macrophages. Mtb and related species may be able to combat this harsh acidic environment which contains reactive oxygen species due to the mycobacterial genomes encoding a large number of dehydrogenases. Typically, dehydrogenase cofactor binding sites are open to solvent, which allows NAD/NADH exchange to support multiple turnover. Interestingly, mycobacterial short chain dehydrogenases/reductases (SDRs) within family TIGR03971 contain an insertion at the NAD binding site. Here we present crystal structures of 9 mycobacterial SDRs in which the insertion buries the NAD cofactor except for a small portion of the nicotinamide ring. Line broadening and STD-NMR experiments did not show NAD or NADH exchange on the NMR timescale. STD-NMR demonstrated binding of the potential substrate carveol, the potential product carvone, the inhibitor tricyclazol, and an external redox partner 2,6-dichloroindophenol (DCIP). Therefore, these SDRs appear to contain a non-exchangeable NAD cofactor and may rely on an external redox partner, rather than cofactor exchange, for multiple turnover. Incidentally, these genes always appear in conjunction with the mftA gene, which encodes the short peptide MftA, and with other genes proposed to convert MftA into the external redox partner mycofactocin.
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Affiliation(s)
- Daniel H Haft
- National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Phillip G Pierce
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Stephen J Mayclin
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Amy Sullivan
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Anna S Gardberg
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Darren W Begley
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Isabelle Q Phan
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Avenue North, Seattle WA 98109, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Avenue North, Seattle WA 98109, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Avenue North, Seattle WA 98109, USA.,University of Washington, Department of Medical Education and Biomedical Informatics &Department of Global Health, Seattle WA 98195, USA
| | - Vasilios M Marathias
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Donald D Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA.,Beryllium Discovery Corp., 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
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8
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Delineating Substrate Diversity of Disparate Short-Chain Dehydrogenase Reductase from Debaryomyces hansenii. PLoS One 2017; 12:e0170202. [PMID: 28107498 PMCID: PMC5249140 DOI: 10.1371/journal.pone.0170202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 12/30/2016] [Indexed: 11/19/2022] Open
Abstract
Short-chain dehydrogenase reductases (SDRs) have been utilized for catalyzing the reduction of many aromatic/aliphatic prochiral ketones to their respective alcohols. However, there is a paucity of data that elucidates their innate biological role and diverse substrate space. In this study, we executed an in-depth biochemical characterization and substrate space mapping (with 278 prochiral ketones) of an unannotated SDR (DHK) from Debaryomyces hansenii and compared it with structurally and functionally characterized SDR Synechococcus elongatus. PCC 7942 FabG to delineate its industrial significance. It was observed that DHK was significantly more efficient than FabG, reducing a diverse set of ketones albeit at higher conversion rates. Comparison of the FabG structure with a homology model of DHK and a docking of substrate to both structures revealed the presence of additional flexible loops near the substrate binding site of DHK. The comparative elasticity of the cofactor and substrate binding site of FabG and DHK was experimentally substantiated using differential scanning fluorimetry. It is postulated that the loop flexibility may account for the superior catalytic efficiency of DHK although the positioning of the catalytic triad is conserved.
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9
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Dissecting the Structural Elements for the Activation of β-Ketoacyl-(Acyl Carrier Protein) Reductase from Vibrio cholerae. J Bacteriol 2015; 198:463-76. [PMID: 26553852 DOI: 10.1128/jb.00360-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 11/03/2015] [Indexed: 01/22/2023] Open
Abstract
UNLABELLED β-Ketoacyl-(acyl carrier protein) reductase (FabG) catalyzes the key reductive reaction in the elongation cycle of fatty acid synthesis (FAS), which is a vital metabolic pathway in bacteria and a promising target for new antibiotic development. The activation of the enzyme is usually linked to the formation of a catalytic triad and cofactor binding, and crystal structures of FabG from different organisms have been captured in either the active or inactive conformation. However, the structural elements which enable activation of FabG require further exploration. Here we report the findings of structural, enzymatic, and binding studies of the FabG protein found in the causative agent of cholera, Vibrio cholerae (vcFabG). vcFabG exists predominantly as a dimer in solution and is able to self-associate to form tetramers, which is the state seen in the crystal structure. The formation of the tetramer may be promoted by the presence of the cofactor NADP(H). The transition between the dimeric and tetrameric states of vcFabG is related to changes in the conformations of the α4/α5 helices on the dimer-dimer interface. Two glycine residues adjacent to the dimer interface (G92 and G141) are identified to be the hinge for the conformational changes, while the catalytic tyrosine (Y155) and a glutamine residue that forms hydrogen bonds to both loop β4-α4 and loop β5-α5 (Q152) stabilize the active conformation. The functions of the aforementioned residues were confirmed by binding and enzymatic assays for the corresponding mutants. IMPORTANCE This paper describes the results of structural, enzymatic, and binding studies of FabG from Vibrio cholerae (vcFabG). In this work, we dissected the structural elements responsible for the activation of vcFabG. The structural information provided here is essential for the development of antibiotics specifically targeting bacterial FabG, especially for the multidrug-resistant strains of V. cholerae.
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10
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Banerjee DR, Biswas R, Das AK, Basak A. Design, synthesis and characterization of dual inhibitors against new targets FabG4 and HtdX of Mycobacterium tuberculosis. Eur J Med Chem 2015; 100:223-34. [PMID: 26092447 DOI: 10.1016/j.ejmech.2015.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 05/21/2015] [Accepted: 06/03/2015] [Indexed: 10/23/2022]
Abstract
Herein, we present dual inhibitors of new targets FabG4 and HtdX for the first time. In this work, eight compounds have been designed, synthesized, characterized and evaluated for bio-activities. Amongst them, six compounds have shown inhibitory activities. Three of them (12-14) demonstrate dual inhibition of both FabG4 and HtdX at low micromolar concentration. In addition, the dual inhibitors show good anti-mycobacterial properties against both planktonic growth and biofilm culture of Mycobacterium species. This study is an important addition to tuberculosis drug discovery because it explores two new enzymes as drug targets and presents their dual inhibitors as good candidates for pre-clinical trials.
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Affiliation(s)
- Deb Ranjan Banerjee
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Rupam Biswas
- Department of Biotechnology, Indian Institute of Technology, Kharagpur 721302, India
| | - Amit K Das
- Department of Biotechnology, Indian Institute of Technology, Kharagpur 721302, India.
| | - Amit Basak
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India; School of Bioscience, Indian Institute of Technology, Kharagpur 721302, India.
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11
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Inhibition of M. tuberculosis β-ketoacyl CoA reductase FabG4 (Rv0242c) by triazole linked polyphenol–aminobenzene hybrids: Comparison with the corresponding gallate counterparts. Bioorg Med Chem Lett 2015; 25:1343-7. [DOI: 10.1016/j.bmcl.2015.01.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 12/16/2014] [Accepted: 01/07/2015] [Indexed: 11/19/2022]
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12
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Shah BS, Tetu SG, Harrop SJ, Paulsen IT, Mabbutt BC. Structure of a short-chain dehydrogenase/reductase (SDR) within a genomic island from a clinical strain of Acinetobacter baumannii. Acta Crystallogr F Struct Biol Commun 2014; 70:1318-23. [PMID: 25286932 PMCID: PMC4188072 DOI: 10.1107/s2053230x14019785] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 09/02/2014] [Indexed: 11/10/2022] Open
Abstract
Over 15% of the genome of an Australian clinical isolate of Acinetobacter baumannii occurs within genomic islands. An uncharacterized protein encoded within one island feature common to this and other International Clone II strains has been studied by X-ray crystallography. The 2.4 Å resolution structure of SDR-WM99c reveals it to be a new member of the classical short-chain dehydrogenase/reductase (SDR) superfamily. The enzyme contains a nucleotide-binding domain and, like many other SDRs, is tetrameric in form. The active site contains a catalytic tetrad (Asn117, Ser146, Tyr159 and Lys163) and water molecules occupying the presumed NADP cofactor-binding pocket. An adjacent cleft is capped by a relatively mobile helical subdomain, which is well positioned to control substrate access.
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Affiliation(s)
- Bhumika S. Shah
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Research Park Drive, Sydney, NSW 2109, Australia
| | - Sasha G. Tetu
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Research Park Drive, Sydney, NSW 2109, Australia
| | - Stephen J. Harrop
- School of Physics, University of New South Wales, Sydney, NSW 2052, Australia
| | - Ian T. Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Research Park Drive, Sydney, NSW 2109, Australia
| | - Bridget C. Mabbutt
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Research Park Drive, Sydney, NSW 2109, Australia
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13
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Lord DM, Baran AU, Wood TK, Peti W, Page R. BdcA, a protein important for Escherichia coli biofilm dispersal, is a short-chain dehydrogenase/reductase that binds specifically to NADPH. PLoS One 2014; 9:e105751. [PMID: 25244619 PMCID: PMC4171110 DOI: 10.1371/journal.pone.0105751] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 07/25/2014] [Indexed: 02/07/2023] Open
Abstract
The Escherichia coli protein BdcA (previously referred to as YjgI) plays a key role in the dispersal of cells from bacterial biofilms, and its constitutive activation provides an attractive therapeutic target for dismantling these communities. In order to investigate the function of BdcA at a molecular level, we integrated structural and functional studies. Our 2.05 Å structure of BdcA shows that it is a member of the NAD(P)(H)-dependent short-chain dehydrogenase/reductase (SDR) superfamily. Structural comparisons with other members of the SDR family suggested that BdcA binds NADP(H). This was demonstrated experimentally using thermal denaturation studies, which showed that BcdA binds specifically to NADPH. Subsequent ITC experiments further confirmed this result and reported a Kd of 25.9 µM. Thus, BdcA represents the newest member of the limited number of oxidoreductases shown to be involved in quorum sensing and biofilm dispersal.
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Affiliation(s)
- Dana M. Lord
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, United States of America
- Graduate Program in Molecular Pharmacology and Physiology, Brown University, Providence, Rhode Island, United States of America
| | - Ayse Uzgoren Baran
- Department of Molecular Pharmacology, Physiology and Biotechnology and Department of Chemistry, Brown University, Providence, Rhode Island, United States of America
| | - Thomas K. Wood
- Department of Chemical Engineering and Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Wolfgang Peti
- Department of Molecular Pharmacology, Physiology and Biotechnology and Department of Chemistry, Brown University, Providence, Rhode Island, United States of America
| | - Rebecca Page
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, United States of America
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14
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Venkatesan R, Sah-Teli SK, Awoniyi LO, Jiang G, Prus P, Kastaniotis AJ, Hiltunen JK, Wierenga RK, Chen Z. Insights into mitochondrial fatty acid synthesis from the structure of heterotetrameric 3-ketoacyl-ACP reductase/3R-hydroxyacyl-CoA dehydrogenase. Nat Commun 2014; 5:4805. [DOI: 10.1038/ncomms5805] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 07/24/2014] [Indexed: 12/19/2022] Open
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15
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Wang H, Zhang H, Zou Y, Mi Y, Lin S, Xie Z, Yan Y, Zhang H. Structural Insight into the Tetramerization of an Iterative Ketoreductase SiaM through Aromatic Residues in the Interfaces. PLoS One 2014; 9:e97996. [PMID: 24901639 PMCID: PMC4046962 DOI: 10.1371/journal.pone.0097996] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 04/23/2014] [Indexed: 11/19/2022] Open
Affiliation(s)
- Hua Wang
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, Hubei, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Huaidong Zhang
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, Hubei, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yi Zou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yanling Mi
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, Hubei, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhixiong Xie
- College of Life Sciences, Wuhan University, Wuhan, Hubei, China
| | - Yunjun Yan
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, Hubei, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Houjin Zhang
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, Hubei, China
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
- * E-mail:
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16
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Xu Y, Li H, Jin YH, Fan J, Sun F. Dimerization interface of 3-hydroxyacyl-CoA dehydrogenase tunes the formation of its catalytic intermediate. PLoS One 2014; 9:e95965. [PMID: 24763278 PMCID: PMC3999109 DOI: 10.1371/journal.pone.0095965] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 04/02/2014] [Indexed: 12/13/2022] Open
Abstract
3-hydroxyacyl-CoA dehydrogenase (HAD, EC 1.1.1.35) is a homodimeric enzyme localized in the mitochondrial matrix, which catalyzes the third step in fatty acid β-oxidation. The crystal structures of human HAD and subsequent complexes with cofactor/substrate enabled better understanding of HAD catalytic mechanism. However, numerous human diseases were found related to mutations at HAD dimerization interface that is away from the catalytic pocket. The role of HAD dimerization in its catalytic activity needs to be elucidated. Here, we solved the crystal structure of Caenorhabditis elegans HAD (cHAD) that is highly conserved to human HAD. Even though the cHAD mutants (R204A, Y209A and R204A/Y209A) with attenuated interactions on the dimerization interface still maintain a dimerization form, their enzymatic activities significantly decrease compared to that of the wild type. Such reduced activities are in consistency with the reduced ratios of the catalytic intermediate formation. Further molecular dynamics simulations results reveal that the alteration of the dimerization interface will increase the fluctuation of a distal region (a.a. 60–80) that plays an important role in the substrate binding. The increased fluctuation decreases the stability of the catalytic intermediate formation, and therefore the enzymatic activity is attenuated. Our study reveals the molecular mechanism about the essential role of the HAD dimerization interface in its catalytic activity via allosteric effects.
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Affiliation(s)
- Yingzhi Xu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - He Li
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, Jilin University, Changchun, China
| | - Ying-Hua Jin
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, Jilin University, Changchun, China
| | - Jun Fan
- Department of Physics and Materials Science, City University of Hong Kong, Hong Kong SAR, China
- * E-mail: (FS); (JF)
| | - Fei Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (FS); (JF)
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17
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Nanson JD, Forwood JK. Crystallization and preliminary X-ray diffraction analysis of FabG from Yersinia pestis. Acta Crystallogr F Struct Biol Commun 2014; 70:101-4. [PMID: 24419628 PMCID: PMC3943095 DOI: 10.1107/s2053230x13033402] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 12/09/2013] [Indexed: 11/11/2022] Open
Abstract
The type II fatty-acid biosynthesis pathway of bacteria provides enormous potential for antibacterial drug development owing to the structural differences between this and the type I fatty-acid biosynthesis system found in mammals. β-Ketoacyl-ACP reductase (FabG) is responsible for the reduction of the β-ketoacyl group linked to acyl carrier protein (ACP), and is essential for the formation of fatty acids and bacterial survival. Here, the cloning, expression, purification, crystallization and diffraction of FabG from Yersinia pestis (ypFabG), the highly virulent causative agent of plague, are reported. Recombinant FabG was expressed, purified to homogeneity and crystallized via the hanging-drop vapour-diffusion technique. Diffraction data were collected at the Australian Synchrotron to 2.30 Å resolution. The crystal displayed P2(1)2(1)2(1) symmetry, with unit-cell parameters a = 68.22, b = 98.68, c = 169.84 Å, and four ypFabG molecules in the asymmetric unit.
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Affiliation(s)
- Jeffrey David Nanson
- School of Biomedical Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia
| | - Jade Kenneth Forwood
- School of Biomedical Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia
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18
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Banerjee DR, Dutta D, Saha B, Bhattacharyya S, Senapati K, Das AK, Basak A. Design, synthesis and characterization of novel inhibitors against mycobacterial β-ketoacyl CoA reductase FabG4. Org Biomol Chem 2014; 12:73-85. [DOI: 10.1039/c3ob41676c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Cukier CD, Hope AG, Elamin AA, Moynie L, Schnell R, Schach S, Kneuper H, Singh M, Naismith JH, Lindqvist Y, Gray DW, Schneider G. Discovery of an allosteric inhibitor binding site in 3-Oxo-acyl-ACP reductase from Pseudomonas aeruginosa. ACS Chem Biol 2013; 8:2518-27. [PMID: 24015914 PMCID: PMC3833349 DOI: 10.1021/cb4005063] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
3-Oxo-acyl-acyl carrier protein (ACP) reductase (FabG) plays a key role in the bacterial fatty acid synthesis II system in pathogenic microorganisms, which has been recognized as a potential drug target. FabG catalyzes reduction of a 3-oxo-acyl-ACP intermediate during the elongation cycle of fatty acid biosynthesis. Here, we report gene deletion experiments that support the essentiality of this gene in P. aeruginosa and the identification of a number of small molecule FabG inhibitors with IC50 values in the nanomolar to low micromolar range and good physicochemical properties. Structural characterization of 16 FabG-inhibitor complexes by X-ray crystallography revealed that the compounds bind at a novel allosteric site located at the FabG subunit-subunit interface. Inhibitor binding relies primarily on hydrophobic interactions, but specific hydrogen bonds are also observed. Importantly, the binding cavity is formed upon complex formation and therefore would not be recognized by virtual screening approaches. The structure analysis further reveals that the inhibitors act by inducing conformational changes that propagate to the active site, resulting in a displacement of the catalytic triad and the inability to bind NADPH.
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Affiliation(s)
- Cyprian D. Cukier
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | | | - Ayssar A. Elamin
- LIONEX Diagnostics and Therapeutics GmbH, D-38126 Braunschweig, Germany
| | - Lucile Moynie
- Biomedical
Sciences Research Complex, University of St. Andrews, St. Andrews KY16 9ST, U.K
| | - Robert Schnell
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Susanne Schach
- LIONEX Diagnostics and Therapeutics GmbH, D-38126 Braunschweig, Germany
| | | | - Mahavir Singh
- LIONEX Diagnostics and Therapeutics GmbH, D-38126 Braunschweig, Germany
| | - James H. Naismith
- Biomedical
Sciences Research Complex, University of St. Andrews, St. Andrews KY16 9ST, U.K
| | - Ylva Lindqvist
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | | | - Gunter Schneider
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
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20
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Wang Y, Ma S. Recent Advances in Inhibitors of Bacterial Fatty Acid Synthesis Type II (FASII) System Enzymes as Potential Antibacterial Agents. ChemMedChem 2013; 8:1589-608. [DOI: 10.1002/cmdc.201300209] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 06/30/2013] [Indexed: 12/25/2022]
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21
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Crystal structure of hexanoyl-CoA bound to β-ketoacyl reductase FabG4 of Mycobacterium tuberculosis. Biochem J 2013; 450:127-39. [PMID: 23163771 DOI: 10.1042/bj20121107] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
FabGs, or β-oxoacyl reductases, are involved in fatty acid synthesis. The reaction entails NADPH/NADH-mediated conversion of β-oxoacyl-ACP (acyl-carrier protein) into β-hydroxyacyl-ACP. HMwFabGs (high-molecular-weight FabG) form a phylogenetically separate group of FabG enzymes. FabG4, an HMwFabG from Mycobacterium tuberculosis, contains two distinct domains, an N-terminal 'flavodoxintype' domain and a C-terminal oxoreductase domain. The catalytically active C-terminal domain utilizes NADH to reduce β-oxoacyl-CoA to β-hydroxyacyl-CoA. In the present study the crystal structures of the FabG4-NADH binary complex and the FabG4-NAD+-hexanoyl-CoA ternary complex have been determined to understand the substrate specificity and catalytic mechanism of FabG4. This is the first report to demonstrate how FabG4 interacts with its coenzyme NADH and hexanoyl-CoA that mimics an elongating fattyacyl chain covalently linked with CoA. Structural analysis shows that the binding of hexanoyl-CoA within the active site cavity of FabG significantly differs from that of the C16 fattyacyl substrate bound to mycobacterial FabI [InhA (enoyl-ACP reductase)]. The ternary complex reveals that both loop I and loop II interact with the phosphopantetheine moiety of CoA or ACP to align the covalently linked fattyacyl substrate near the active site. Structural data ACP inhibition studies indicate that FabG4 can accept both CoA- and ACP-based fattyacyl substrates. We have also shown that in the FabG4 dimer Arg146 and Arg445 of one monomer interact with the C-terminus of the second monomer to play pivotal role in substrate association and catalysis.
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22
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Rosado LA, Caceres RA, de Azevedo WF, Basso LA, Santos DS. Role of Serine140 in the mode of action of Mycobacterium tuberculosis β-ketoacyl-ACP Reductase (MabA). BMC Res Notes 2012; 5:526. [PMID: 23006410 PMCID: PMC3519566 DOI: 10.1186/1756-0500-5-526] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 09/14/2012] [Indexed: 11/10/2022] Open
Abstract
Background Tuberculosis (TB) still remains one of the most deadly infectious diseases in the world. Mycobacterium tuberculosis β-ketoacyl-ACP Reductase (MabA) is a member of the fatty acid elongation system type II, providing precursors of mycolic acids that are essential to the bacterial cell growth and survival. MabA has been shown to be essential for M. tuberculosis survival and to play a role in intracellular signal transduction of bacilli. Findings Here we describe site-directed mutagenesis, recombinant protein expression and purification, steady-state kinetics, fluorescence spectroscopy, and molecular modeling for S140T and S140A mutant MabA enzymes. No enzyme activity could be detected for S140T and S140A. Although the S140T protein showed impaired NADPH binding, the S140A mutant could bind to NADPH. Computational predictions for NADPH binding affinity to WT, S140T and S140A MabA proteins were consistent with fluorescence spectroscopy data. Conclusions The results suggest that the main role of the S140 side chain of MabA is in catalysis. The S140 side chain appears to also play an indirect role in NADPH binding. Interestingly, NADPH titrations curves shifted from sigmoidal for WT to hyperbolic for S140A, suggesting that the S140 residue may play a role in displacing the pre-existing equilibrium between two forms of MabA in solution. The results here reported provide a better understanding of the mode of action of MabA that should be useful to guide the rational (function-based) design of inhibitors of MabA enzyme activity which, hopefully, could be used as lead compounds with anti-TB action.
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Affiliation(s)
- Leonardo A Rosado
- Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Pontifícia Universidade Católica do Rio Grande do Sul, Av. Ipiranga 6681, Porto Alegre, RS 90619-900, Brazil
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Dutta D, Bhattacharyya S, Das AK. Crystallization and preliminary X-ray diffraction analysis of the high molecular weight ketoacyl reductase FabG4 complexed with NADH. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:786-9. [PMID: 22750865 PMCID: PMC3388922 DOI: 10.1107/s1744309112020301] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 05/05/2012] [Indexed: 11/11/2022]
Abstract
FabG4 from Mycobacterium tuberculosis belongs to the high molecular weight ketoacyl reductases (HMwFabGs). The enzyme requires NADH for β-ketoacyl reductase activity. The protein was overexpressed, purified to homogeneity and crystallized as a FabG4-NADH complex. A mountable FabG4:NADH complex crystal diffracted to 2.59 Å resolution and belonged to space group P1, with unit-cell parameters a = 63.07, b = 71.03, c = 92.92 Å, α = 105.02, β = 97.06, γ = 93.66°. The Matthews coefficient suggested the presence of four monomers in the unit cell. In addition, a self-rotation function revealed the presence of two twofold NCS axes and one fourfold NCS axis. At χ = 180° the highest peak corresponds to the twofold NCS between two monomers, whereas the second peak corresponds to the twofold NCS between two dimers.
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Affiliation(s)
- Debajyoti Dutta
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, Kharagpur 721 302, India
| | - Sudipta Bhattacharyya
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, Kharagpur 721 302, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, Kharagpur 721 302, India
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