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Husain NAC, Jamaluddin H, Jonet MA. Functional and structural characterization of a thermostable flavin reductase from Geobacillus mahadii Geo-05. Int J Biol Macromol 2024; 275:133721. [PMID: 38986972 DOI: 10.1016/j.ijbiomac.2024.133721] [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: 12/02/2023] [Revised: 05/25/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
Flavin reductases play a vital role in catalyzing the reduction of flavin through NADH or NADPH oxidation. The gene encoding flavin reductase from the thermophilic bacterium Geobacillus mahadii Geo-05 (GMHpaC) was cloned, overexpressed in Escherichia coli BL21 (DE3) pLysS, and purified to homogeneity. The purified recombinant GMHpaC (Class II) contains chromogenic cofactors, evidenced by maximal absorbance peaks at 370 nm and 460 nm. GMHpaC stands out as the most thermostable and pH-tolerant flavin reductase reported to date, retaining up to 95 % catalytic activity after incubation at 70 °C for 30 min and maintaining over 80 % activity within a pH range of 2-12 for 30 min. Furthermore, GMHpaC's catalytic activity increases by 52 % with FMN as a co-factor compared to FAD and riboflavin. GMHpaC, coupled with 4-hydroxyphenylacetate-3-monooxygenase (GMHpaB) from G. mahadii Geo-05, enhances the hydroxylation of 4-hydroxyphenylacetate (HPA) by 85 %. The modeled structure of GMHpaC reveals relatively conserved flavin and NADH binding sites. Modeling and docking studies shed light on structural features and amino acid substitutions that determine GMHpaC's co-factor specificity. The remarkable thermostability, high catalytic activity, and general stability exhibited by GMHpaC position it as a promising enzyme candidate for various industrial applications.
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Affiliation(s)
- Nor Asyikin Che Husain
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia; Structural Biology & Functional Omics, Malaysian Genome and Vaccine Institute, 43000 Kajang, Selangor, Malaysia
| | - Haryati Jamaluddin
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia.
| | - Mohd Anuar Jonet
- Structural Biology & Functional Omics, Malaysian Genome and Vaccine Institute, 43000 Kajang, Selangor, Malaysia.
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2
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De Silva AJ, Sehgal R, Kim J, Bellizzi JJ. Steady-state kinetic analysis of halogenase-supporting flavin reductases BorF and AbeF reveals different kinetic mechanisms. Arch Biochem Biophys 2021; 704:108874. [PMID: 33862020 DOI: 10.1016/j.abb.2021.108874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/03/2021] [Accepted: 04/05/2021] [Indexed: 11/28/2022]
Abstract
The short-chain flavin reductases BorF and AbeF reduce FAD to FADH2, which is then used by flavin-dependent halogenases (BorH and AbeH respectively) to regioselectively chlorinate tryptophan in the biosynthesis of indolotryptoline natural products. Recombinant AbeF and BorF were overexpressed and purified as homodimers from E. coli, and copurified with substoichiometric amounts of FAD, which could be easily removed. AbeF and BorF can reduce FAD, FMN, and riboflavin in vitro and are selective for NADH over NADPH. Initial velocity studies in the presence and absence of inhibitors showed that BorF proceeds by a sequential ordered kinetic mechanism in which FAD binds first, while AbeF follows a random-ordered sequence of substrate binding. Fluorescence quenching experiments verified that NADH does not bind BorF in the absence of FAD, and that both AbeF and BorF bind FAD with higher affinity than FADH2. pH-rate profiles of BorF and AbeF were bell-shaped with maximum kcat at pH 7.5, and site-directed mutagenesis of BorF implicated His160 and Arg38 as contributing to the catalytic activity and the pH dependence.
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Affiliation(s)
- Aravinda J De Silva
- Department of Chemistry and Biochemistry, College of Natural Sciences and Mathematics, The University of Toledo Toledo, OH, 43606, USA
| | - Rippa Sehgal
- Department of Chemistry and Biochemistry, College of Natural Sciences and Mathematics, The University of Toledo Toledo, OH, 43606, USA
| | - Jennifer Kim
- Department of Chemistry and Biochemistry, College of Natural Sciences and Mathematics, The University of Toledo Toledo, OH, 43606, USA
| | - John J Bellizzi
- Department of Chemistry and Biochemistry, College of Natural Sciences and Mathematics, The University of Toledo Toledo, OH, 43606, USA.
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Pradhan SK, Singh NR, Dehury B, Panda D, Modi MK, Thatoi H. Insights into the mode of flavin mononucleotide binding and catalytic mechanism of bacterial chromate reductases: A molecular dynamics simulation study. J Cell Biochem 2019; 120:16990-17005. [PMID: 31131470 DOI: 10.1002/jcb.28960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/04/2019] [Accepted: 02/14/2019] [Indexed: 11/09/2022]
Abstract
Enzymes from natural sources protect the environment via complex biological mechanisms, which aid in reductive immobilization of toxic metals including chromium. Nevertheless, progress was being made in elucidating high-resolution crystal structures of reductases and their binding with flavin mononucleotide (FMN) to understand the underlying mechanism of chromate reduction. Therefore, herein, we employed molecular dynamics (MD) simulations, principal component analysis (PCA), and binding free energy calculations to understand the dynamics behavior of these enzymes with FMN. Six representative chromate reductases in monomeric and dimeric forms were selected to study the mode, dynamics, and energetic component that drive the FMN binding process. As evidenced by MD simulation, FMN prefers to bind the cervix formed between the catalytic domain surrounded by strong conserved hydrogen bonding, electrostatic, and hydrophobic contacts. The slight movement and reorientation of FMN resulted in breakage of some crucial H-bonds and other nonbonded contacts, which were well compensated with newly formed H-bonds, electrostatic, and hydrophobic interactions. The critical residues aiding in tight anchoring of FMN within dimer were found to be strongly conserved in the bacterial system. The molecular mechanics combined with the Poisson-Boltzmann surface area binding free energy of the monomer portrayed that the van der Waals and electrostatic energy contribute significantly to the total free energy, where, the polar solvation energy opposes the binding of FMN. The proposed proximity relationships between enzyme and FMN binding site presented in this study will open up better avenues to engineer enzymes with optimized chromate reductase activity for sustainable bioremediation of heavy metals.
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Affiliation(s)
- Sukanta Kumar Pradhan
- Department of Bioinformatics, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India.,Department of Biotechnology, School of Life Sciences, Ravenshaw University, Cuttack, Odisha, India
| | - Nihar Ranjan Singh
- Department of Botany, School of Life Sciences, Ravenshaw University, Cuttack, Odisha, India
| | - Budheswar Dehury
- Biomedical Informatics Centre, Regional Medical Research Centre (ICMR), Nalco Square, Chandrasekharpur, Bhubaneswar, Odisha, India.,Department of Chemistry, Technical University of Denmark, DK-2800 Kgs, Lyngby
| | - Debashis Panda
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Mahendra Kumar Modi
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - Hrudayanath Thatoi
- Department of Biotechnology, North Orissa University, Sriram Chandra Vihar, Takatpur, Baripada, Odisha, India
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Lasek R, Szuplewska M, Mitura M, Decewicz P, Chmielowska C, Pawłot A, Sentkowska D, Czarnecki J, Bartosik D. Genome Structure of the Opportunistic Pathogen Paracoccus yeei ( Alphaproteobacteria) and Identification of Putative Virulence Factors. Front Microbiol 2018; 9:2553. [PMID: 30410477 PMCID: PMC6209633 DOI: 10.3389/fmicb.2018.02553] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 10/05/2018] [Indexed: 12/17/2022] Open
Abstract
Bacteria of the genus Paracoccus are common components of the microbiomes of many naturally- and anthropogenically shaped environments. One species, Paracoccus yeei, is unique within the genus because it is associated with opportunistic human infections. Therefore, strains of P. yeei may serve as an interesting model to study the transition from a saprophytic to a pathogenic lifestyle in environmental bacteria. Unfortunately, knowledge concerning the biology, genetics and genomic content of P. yeei is fragmentary; also the mechanisms of pathogenicity of this bacterium remain unclear. In this study we provide the first insight into the genome composition and metabolic potential of a clinical isolate, P. yeei CCUG 32053. This strain has a multipartite genome (4,632,079 bp) composed of a circular chromosome plus eight extrachromosomal replicons pYEE1–8: 3 chromids and 5 plasmids, with a total size of 1,247,173 bp. The genome has been significantly shaped by the acquisition of genomic islands, prophages (Myoviridae and Siphoviridae phage families) and numerous insertion sequences (ISs) representing seven IS families. Detailed comparative analysis with other complete genomic sequences of Paracoccus spp. (including P. yeei FDAARGOS_252 and TT13, as well as non-pathogenic strains of other species in this genus) enabled us to identify P. yeei species-specific genes and to predict putative determinants of virulence. This is the first attempt to identify pathoadaptive genetic information of P. yeei and to estimate the role of the mobilome in the evolution of pathogenicity in this species.
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Affiliation(s)
- Robert Lasek
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Magdalena Szuplewska
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Monika Mitura
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Przemysław Decewicz
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Cora Chmielowska
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Aleksandra Pawłot
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Dorota Sentkowska
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jakub Czarnecki
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland
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Sepúlveda Cisternas I, Salazar JC, García-Angulo VA. Overview on the Bacterial Iron-Riboflavin Metabolic Axis. Front Microbiol 2018; 9:1478. [PMID: 30026736 PMCID: PMC6041382 DOI: 10.3389/fmicb.2018.01478] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 06/13/2018] [Indexed: 01/10/2023] Open
Abstract
Redox reactions are ubiquitous in biological processes. Enzymes involved in redox metabolism often use cofactors in order to facilitate electron-transfer reactions. Common redox cofactors include micronutrients such as vitamins and metals. By far, while iron is the main metal cofactor, riboflavin is the most important organic cofactor. Notably, the metabolism of iron and riboflavin seem to be intrinsically related across life kingdoms. In bacteria, iron availability influences expression of riboflavin biosynthetic genes. There is documented evidence for riboflavin involvement in surpassing iron-restrictive conditions in some species. This is probably achieved through increase in iron bioavailability by reduction of extracellular iron, improvement of iron uptake pathways and boosting hemolytic activity. In some cases, riboflavin may also work as replacement of iron as enzyme cofactor. In addition, riboflavin is involved in dissimilatory iron reduction during extracellular respiration by some species. The main direct metabolic relationships between riboflavin and iron in bacterial physiology are reviewed here.
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Affiliation(s)
- Ignacio Sepúlveda Cisternas
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Juan C Salazar
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Víctor A García-Angulo
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
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Yuenyao A, Petchyam N, Kamonsutthipaijit N, Chaiyen P, Pakotiprapha D. Crystal structure of the flavin reductase of Acinetobacter baumannii p-hydroxyphenylacetate 3-hydroxylase (HPAH) and identification of amino acid residues underlying its regulation by aromatic ligands. Arch Biochem Biophys 2018; 653:24-38. [PMID: 29940152 DOI: 10.1016/j.abb.2018.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 06/07/2018] [Accepted: 06/21/2018] [Indexed: 10/28/2022]
Abstract
The first step in the degradation of p-hydroxyphenylacetic acid (HPA) is catalyzed by the two-component enzyme p-hydroxyphenylacetate 3-hydroxylase (HPAH). The two components of Acinetobacter baumannii HPAH are known as C1 and C2, respectively. C1 is a flavin reductase that uses NADH to generate reduced flavin mononucleotide (FMNH-), which is used by C2 in the hydroxylation of HPA. Interestingly, although HPA is not directly involved in the reaction catalyzed by C1, the presence of HPA dramatically increases the FMN reduction rate. Amino acid sequence analysis revealed that C1 contains two domains: an N-terminal flavin reductase domain, and a C-terminal MarR domain. Although MarR proteins typically function as transcription regulators, the MarR domain of C1 was found to play an auto-inhibitory role. Here, we report a crystal structure of C1 and small-angle X-ray scattering (SAXS) studies that revealed that C1 undergoes a substantial conformational change in the presence of HPA, concomitant with the increase in the rate of flavin reduction. Amino acid residues that are important for HPA binding and regulation of C1 activity were identified by site-directed mutagenesis. Amino acid sequence similarity analysis revealed several as yet uncharacterized flavin reductases with N- or C-terminal fusions.
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Affiliation(s)
- Anan Yuenyao
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Nopphon Petchyam
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | | | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science, Mahidol University, Bangkok, 10400, Thailand; School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand
| | - Danaya Pakotiprapha
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
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Heine T, Scholtissek A, Westphal AH, van Berkel WJH, Tischler D. N-terminus determines activity and specificity of styrene monooxygenase reductases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1770-1780. [PMID: 28888693 DOI: 10.1016/j.bbapap.2017.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/10/2017] [Accepted: 09/05/2017] [Indexed: 10/18/2022]
Abstract
Styrene monooxygenases (SMOs) are two-enzyme systems that catalyze the enantioselective epoxidation of styrene to (S)-styrene oxide. The FADH2 co-substrate of the epoxidase component (StyA) is supplied by an NADH-dependent flavin reductase (StyB). The genome of Rhodococcus opacus 1CP encodes two SMO systems. One system, which we define as E1-type, displays homology to the SMO from Pseudomonas taiwanensis VLB120. The other system, originally reported as a fused system (RoStyA2B), is defined as E2-type. Here we found that E1-type RoStyB is inhibited by FMN, while RoStyA2B is known to be active with FMN. To rationalize the observed specificity of RoStyB for FAD, we generated an artificial reductase, designated as RoStyBart, in which the first 22 amino acid residues of RoStyB were joined to the reductase part of RoStyA2B, while the oxygenase part (A2) was removed. RoStyBart mainly purified as apo-protein and mimicked RoStyB in being inhibited by FMN. Pre-incubation with FAD yielded a turnover number at 30°C of 133.9±3.5s-1, one of the highest rates observed for StyB reductases. RoStyBart holo-enzyme switches to a ping-pong mechanism and fluorescence analysis indicated for unproductive binding of FMN to the second (co-substrate) binding site. In summary, it is shown for the first time that optimization of the N-termini of StyB reductases allows the evolution of their activity and specificity.
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Affiliation(s)
- Thomas Heine
- Environmental Microbiology, Interdisciplinary Ecological Center, TU Bergakadmie Freiberg, Leipziger Straße 29, 09599 Freiberg, Germany; Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - Anika Scholtissek
- Environmental Microbiology, Interdisciplinary Ecological Center, TU Bergakadmie Freiberg, Leipziger Straße 29, 09599 Freiberg, Germany; Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Willem J H van Berkel
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dirk Tischler
- Environmental Microbiology, Interdisciplinary Ecological Center, TU Bergakadmie Freiberg, Leipziger Straße 29, 09599 Freiberg, Germany.
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