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Feregrino-Mondragón RD, Santiago-Martínez MG, Silva-Flores M, Encalada R, Reyes-Prieto A, Rodríguez-Zavala JS, Peña-Ocaña BA, Moreno-Sánchez R, Saavedra E, Jasso-Chávez R. Lactate oxidation is linked to energy conservation and to oxygen detoxification via a putative terminal cytochrome oxidase in Methanosarcina acetivorans. Arch Biochem Biophys 2023:109667. [PMID: 37327962 DOI: 10.1016/j.abb.2023.109667] [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: 12/27/2022] [Revised: 06/09/2023] [Accepted: 06/11/2023] [Indexed: 06/18/2023]
Abstract
The marine archaeon Methanosarcina acetivorans contains a putative NAD + -independent d-lactate dehydrogenase (D-iLDH/glycolate oxidase) encoded by the MA4631 gene, belonging to the FAD-oxidase C superfamily. Nucleotide sequences similar to MA4631 gene, were identified in other methanogens and Firmicutes with >90 and 35-40% identity, respectively. Therefore, the lactate metabolism in M. acetivorans is reported here. Cells subjected to intermittent pulses of oxygen (air-adapted; AA-Ma cells) consumed lactate only in combination with acetate, increasing methane production and biomass yield. In AA-Ma cells incubated with d-lactate plus [14C]-l-lactate, the radioactive label was found in methane, CO2 and glycogen, indicating that lactate metabolism fed both methanogenesis and gluconeogenesis. Moreover, d-lactate oxidation was coupled to O2-consumption which was sensitive to HQNO; also, AA-Ma cells showed high transcript levels of gene dld and those encoding subunits A (MA1006) and B (MA1007) of a putative cytochrome bd quinol oxidase, compared to anaerobic control cells. An E. coli mutant deficient in dld complemented with the MA4631 gene, grew with d-lactate as carbon source and showed membrane-bound d-lactate:quinone oxidoreductase activity. The product of the MA4631 gene is a FAD-containing monomer showing activity of iLDH with preference to d-lactate. The results suggested that air adapted M. acetivorans is able to co-metabolize lactate and acetate with associated oxygen consumption by triggering the transcription and synthesis of the D-iLDH and a putative cytochrome bd: methanophenazine (quinol) oxidoreductase. Biomass generation and O2 consumption, suggest a potentially new oxygen detoxification mechanism coupled to energy conservation in this methanogen.
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Affiliation(s)
| | - Michel Geovanni Santiago-Martínez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico; Department of Molecular and Cell Biology, The University of Connecticut, Storrs, 06269, Connecticut, USA
| | - Mayel Silva-Flores
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico
| | - Rusely Encalada
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico
| | - Adrián Reyes-Prieto
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - José S Rodríguez-Zavala
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico
| | - Betsy Anaid Peña-Ocaña
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico
| | - Rafael Moreno-Sánchez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico
| | - Ricardo Jasso-Chávez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico.
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Satomura T, Hayashi J, Ohshida T, Sakuraba H, Ohshima T, Suye SI. Enzymological characteristics of a novel archaeal dye-linked D-lactate dehydrogenase showing loose binding of FAD. Extremophiles 2018; 22:975-981. [PMID: 30206766 DOI: 10.1007/s00792-018-1054-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 09/06/2018] [Indexed: 11/26/2022]
Abstract
A gene-encoding a dye-linked D-lactate dehydrogenase (Dye-DLDH) homolog was identified in the genome of the hyperthermophilic archaeon Thermoproteus tenax. The gene was expressed in Escherichia coli and the product was purified to homogeneity. The recombinant protein exhibited highly thermostable Dye-DLDH activity. To date, four types of Dye-DLDH have been identified in hyperthermophilic archaea (in Aeropyrum pernix, Sulfolobus tokodaii, Archaeoglobus fulgidus, and Candidatus Caldiarchaeum subterraneum). The amino acid sequence of T. tenax Dye-DLDH showed the highest similarity (45%) to A. pernix Dye-DLDH, but neither contained a known FAD-binding motif. Nonetheless, both homologs required FAD for enzymatic activity, suggesting that FAD binds loosely to the enzyme and is easily released unlike in other Dye-DLDHs. Our findings indicate that Dye-DLDHs from T. tenax and A. pernix are a novel type of Dye-DLDH characterized by loose binding of FAD.
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Affiliation(s)
- Takenori Satomura
- Division of Engineering, Faculty of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui, 910-8507, Japan.
- Organization for Life Science Advancement Programs, University of Fukui, 3-9-1 Bunkyo, Fukui, 910-8507, Japan.
| | - Junji Hayashi
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Biwako-Kusatsu Campus, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Tatsuya Ohshida
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0795, Japan
| | - Haruhiko Sakuraba
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0795, Japan
| | - Toshihisa Ohshima
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, Ohmiya, 5-16-1 Asahi-ku, Osaka, 535-8585, Japan
| | - Shin-Ichiro Suye
- Division of Engineering, Faculty of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui, 910-8507, Japan
- Organization for Life Science Advancement Programs, University of Fukui, 3-9-1 Bunkyo, Fukui, 910-8507, Japan
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Satomura T, Hayashi J, Sakamoto H, Nunoura T, Takaki Y, Takai K, Takami H, Ohshima T, Sakuraba H, Suye SI. d-Lactate electrochemical biosensor prepared by immobilization of thermostable dye-linked d-lactate dehydrogenase from Candidatus Caldiarchaeum subterraneum. J Biosci Bioeng 2018; 126:425-430. [PMID: 29691195 DOI: 10.1016/j.jbiosc.2018.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/30/2018] [Accepted: 04/02/2018] [Indexed: 11/30/2022]
Abstract
A stable d-lactate electrochemical sensing system was developed using a dye-linked d-lactate dehydrogenase (Dye-DLDH) from an uncultivated thermophilic archaeon, Candidatus Caldiarchaeum subterraneum. To develop the system, the putative gene encoding the Dye-DLDH from Ca. Caldiarchaeum subterraneum was overexpressed in Escherichia coli, and the expressed product was purified. The recombinant enzyme was a highly thermostable Dye-DLDH that retained full activity after incubation for 10 min at 70°C. The electrode for detection of d-lactate was prepared by immobilizing the thermostable Dye-DLDH and multi-walled carbon nanotube (MWCNT) within Nafion membrane. The electrocatalytic response of the electrode was clearly observed upon exposure to d-lactate. The electrode response to d-lactate was linear within the concentration range of 0.03-2.5 mM, and it showed little reduction in responsiveness after 50 days. This is the first report describing a d-lactate sensing system using a thermostable Dye-DLDH.
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Affiliation(s)
- Takenori Satomura
- Division of Engineering, Faculty of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan; Organization for Life Science Advancement Programs, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan.
| | - Junji Hayashi
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
| | - Hiroaki Sakamoto
- Tenure-Track Program for Innovative Research, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan
| | - Takuro Nunoura
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yoshihiro Takaki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Ken Takai
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Hideto Takami
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Toshihisa Ohshima
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technoligy, Ohmiya, 5-16-1 Asahi-ku, Ohsaka 535-8585 Japan
| | - Haruhiko Sakuraba
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
| | - Shin-Ichiro Suye
- Division of Engineering, Faculty of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan; Organization for Life Science Advancement Programs, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan
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4
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Wolf J, Stark H, Fafenrot K, Albersmeier A, Pham TK, Müller KB, Meyer BH, Hoffmann L, Shen L, Albaum SP, Kouril T, Schmidt-Hohagen K, Neumann-Schaal M, Bräsen C, Kalinowski J, Wright PC, Albers SV, Schomburg D, Siebers B. A systems biology approach reveals major metabolic changes in the thermoacidophilic archaeon Sulfolobus solfataricus in response to the carbon source L-fucose versus D-glucose. Mol Microbiol 2016; 102:882-908. [PMID: 27611014 DOI: 10.1111/mmi.13498] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2016] [Indexed: 12/01/2022]
Abstract
Archaea are characterised by a complex metabolism with many unique enzymes that differ from their bacterial and eukaryotic counterparts. The thermoacidophilic archaeon Sulfolobus solfataricus is known for its metabolic versatility and is able to utilize a great variety of different carbon sources. However, the underlying degradation pathways and their regulation are often unknown. In this work, the growth on different carbon sources was analysed, using an integrated systems biology approach. The comparison of growth on L-fucose and D-glucose allows first insights into the genome-wide changes in response to the two carbon sources and revealed a new pathway for L-fucose degradation in S. solfataricus. During growth on L-fucose major changes in the central carbon metabolic network, as well as an increased activity of the glyoxylate bypass and the 3-hydroxypropionate/4-hydroxybutyrate cycle were observed. Within the newly discovered pathway for L-fucose degradation the following key reactions were identified: (i) L-fucose oxidation to L-fuconate via a dehydrogenase, (ii) dehydration to 2-keto-3-deoxy-L-fuconate via dehydratase, (iii) 2-keto-3-deoxy-L-fuconate cleavage to pyruvate and L-lactaldehyde via aldolase and (iv) L-lactaldehyde conversion to L-lactate via aldehyde dehydrogenase. This pathway as well as L-fucose transport shows interesting overlaps to the D-arabinose pathway, representing another example for pathway promiscuity in Sulfolobus species.
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Affiliation(s)
- Jacqueline Wolf
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Helge Stark
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Katharina Fafenrot
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Universität Duisburg-Essen, Essen, 45141, Germany
| | - Andreas Albersmeier
- Center for Biotechnology - CeBiTec, Universität Bielefeld, Bielefeld, 33615, Germany
| | - Trong K Pham
- Departement of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, S1 3JD, UK
| | - Katrin B Müller
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Benjamin H Meyer
- Molecular Biology of Archaea, Institute for Biology II - Microbiology, Universität Freiburg, Freiburg, 79104, Germany
| | - Lena Hoffmann
- Molecular Biology of Archaea, Institute for Biology II - Microbiology, Universität Freiburg, Freiburg, 79104, Germany
| | - Lu Shen
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Universität Duisburg-Essen, Essen, 45141, Germany
| | - Stefan P Albaum
- Center for Biotechnology - CeBiTec, Universität Bielefeld, Bielefeld, 33615, Germany
| | - Theresa Kouril
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Universität Duisburg-Essen, Essen, 45141, Germany
| | - Kerstin Schmidt-Hohagen
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Meina Neumann-Schaal
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Universität Duisburg-Essen, Essen, 45141, Germany
| | - Jörn Kalinowski
- Center for Biotechnology - CeBiTec, Universität Bielefeld, Bielefeld, 33615, Germany
| | - Phillip C Wright
- Departement of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, S1 3JD, UK
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute for Biology II - Microbiology, Universität Freiburg, Freiburg, 79104, Germany
| | - Dietmar Schomburg
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, 38106, Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Universität Duisburg-Essen, Essen, 45141, Germany
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5
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Min K, Yeon YJ, Um Y, Kim YH. Novel NAD-independent d-lactate dehydrogenases from Acetobacter aceti and Acidocella species MX-AZ02 as potential candidates for in vitro biocatalytic pyruvate production. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2015.10.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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6
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Gene Expression and Characterization of a Third Type of Dye-LinkedL-Proline Dehydrogenase from the Aerobic Hyperthermophilic Archaeon,Aeropyrum pernix. Biosci Biotechnol Biochem 2014; 76:589-93. [DOI: 10.1271/bbb.110775] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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7
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Kim S, Gu SA, Kim YH, Kim KJ. Crystal structure and thermodynamic properties of d-lactate dehydrogenase from Lactobacillus jensenii. Int J Biol Macromol 2014; 68:151-7. [PMID: 24794195 DOI: 10.1016/j.ijbiomac.2014.04.048] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 04/21/2014] [Accepted: 04/22/2014] [Indexed: 11/28/2022]
Abstract
The thermostable d-lactate dehydrogenase from Lactobacillus jensenii (Ljd-LDH) is a key enzyme in the production of the d-form of lactic acid from pyruvate concomitant with the oxidation of NADH to NAD(+). The polymers of d-lactic acid are used as biodegradable bioplastics. The crystal structures of Ljd-LDH and in complex with NAD(+) were determined at 2.13 and 2.60Å resolutions, respectively. The Ljd-LDH monomer consists of the N-terminal substrate-binding domain and the C-terminal NAD-binding domain. The Ljd-LDH forms a homodimeric structure, and the C-terminal NAD-binding domain mostly enables the dimerization of the enzyme. The NAD cofactor is bound to the GxGxxG NAD-binding motif located between the two domains. Structural comparisons of Ljd-LDH with other d-LDHs reveal that Ljd-LDH has unique amino acid residues at the linker region, which indicates that the open-close dynamics of Ljd-LDH might be different from that of other d-LDHs. Moreover, thermostability experiments showed that the T50(10) value of Ljd-LDH (54.5°C) was much higher than the commercially available d-lactate dehydrogenase (42.7°C). In addition, Ljd-LDH has at least a 7°C higher denaturation temperature compared to commercially available d-LDHs.
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Affiliation(s)
- Sangwoo Kim
- School of Life Sciences, KNU Creative BioResearch Group (BK21 plus program), Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea; School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 689-798, Republic of Korea
| | - Sol-A Gu
- Department of Chemical Engineering, Kwangwoon University, Seoul 139-701, Republic of Korea
| | - Yong Hwan Kim
- Department of Chemical Engineering, Kwangwoon University, Seoul 139-701, Republic of Korea.
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group (BK21 plus program), Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea.
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Polysaccharide-degrading thermophiles generated by heterologous gene expression in Geobacillus kaustophilus HTA426. Appl Environ Microbiol 2013; 79:5151-8. [PMID: 23793634 DOI: 10.1128/aem.01506-13] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Thermophiles have important advantages over mesophiles as host organisms for high-temperature bioprocesses, functional production of thermostable enzymes, and efficient expression of enzymatic activities in vivo. To capitalize on these advantages of thermophiles, we describe here a new inducible gene expression system in the thermophile Geobacillus kaustophilus HTA426. Six promoter regions in the HTA426 genome were identified and analyzed for expression profiles using β-galactosidase reporter assay. This analysis identified a promoter region upstream of a putative amylose-metabolizing gene cluster that directed high-level expression of the reporter gene. The expression was >280-fold that without a promoter and was further enhanced 12-fold by maltose addition. In association with a multicopy plasmid, this promoter region was used to express heterologous genes. Several genes, including a gene whose product was insoluble when expressed in Escherichia coli, were successfully expressed as soluble proteins, with yields of 0.16 to 59 mg/liter, and conferred new functions to G. kaustophilus strains. Remarkably, cellulase and α-amylase genes conferred the ability to degrade cellulose paper and insoluble starch at high temperatures, respectively, generating thermophiles with the potential to degrade plant biomass. Our results demonstrate that this novel expression system expands the potential applications of G. kaustophilus.
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Jun C, Sa YS, Gu SA, Joo JC, Kim S, Kim KJ, Kim YH. Discovery and characterization of a thermostable d-lactate dehydrogenase from Lactobacillus jensenii through genome mining. Process Biochem 2013. [DOI: 10.1016/j.procbio.2012.11.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Sakuraba H, Satomura T, Kawakami R, Kim K, Hara Y, Yoneda K, Ohshima T. Crystal structure of novel dye-linked L-proline dehydrogenase from hyperthermophilic archaeon Aeropyrum pernix. J Biol Chem 2012; 287:20070-80. [PMID: 22511758 DOI: 10.1074/jbc.m111.319038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two types of dye-linked L-proline dehydrogenase (PDH1, α4β4-type hetero-octamer, and PDH2, αβγδ-type heterotetramer) have been identified so far in hyperthermophilic archaea. Here, we report the crystal structure of a third type of L-proline dehydrogenase, found in the aerobic hyperthermophilic archaeon Aeropyrum pernix, whose structure (homodimer) is much simpler than those of previously studied L-proline dehydrogenases. The structure was determined at a resolution of 1.92 Å. The asymmetric unit contained one subunit, and a crystallographic 2-fold axis generated the functional dimer. The overall fold of the subunit showed similarity to that of the PDH1 β-subunit, which is responsible for catalyzing L-proline dehydrogenation. However, the situation at the subunit-subunit interface of the A. pernix enzyme was totally different from that in PDH1. The presence of additional surface elements in the A. pernix enzyme contributes to a unique dimer association. Moreover, the C-terminal Leu(428), which is provided by a tail extending from the FAD-binding domain, shielded the active site, and an L-proline molecule was entrapped within the active site cavity. The K(m) value of a Leu(428) deletion mutant for L-proline was about 800 times larger than the K(m) value of the wild-type enzyme, although the k(cat) values did not differ much between the two enzymes. This suggests the C-terminal Leu(428) is not directly involved in catalysis, but it is essential for maintaining a high affinity for the substrate. This is the first description of an LPDH structure with L-proline bound, and it provides new insight into the substrate binding of LPDH.
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Affiliation(s)
- Haruhiko Sakuraba
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
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Kawakami R, Satomura T, Sakuraba H, Ohshima T. l-Proline dehydrogenases in hyperthermophilic archaea: distribution, function, structure, and application. Appl Microbiol Biotechnol 2011; 93:83-93. [DOI: 10.1007/s00253-011-3682-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 10/11/2011] [Accepted: 10/27/2011] [Indexed: 10/15/2022]
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Shibahara T, Satomura T, Kawakami R, Ohshima T, Sakuraba H. Crystallization and preliminary X-ray analysis of a dye-linked D-lactate dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1425-7. [PMID: 22102248 DOI: 10.1107/s1744309111036098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 09/05/2011] [Indexed: 11/11/2022]
Abstract
A dye-linked D-lactate dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix was crystallized using the hanging-drop vapour-diffusion method with polyethylene glycol 8000 as the precipitant. The crystals belonged to the monoclinic space group P2(1), with unit-cell parameters a = 63.4, b = 119.4, c = 70.2 Å, β = 112.0°, and diffracted to 2.0 Å resolution on the BL26B1 beamline at SPring-8. The overall R(merge) was 4.5% and the completeness was 99.8%.
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Affiliation(s)
- Takenori Shibahara
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Kita-gun, Kagawa 761-0795, Japan
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Satomura T, Sakuraba H, Hara Y, Ohshima T. Crystallization and preliminary X-ray analysis of a novel dye-linked L-proline dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1508-10. [PMID: 21045308 DOI: 10.1107/s1744309110036808] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 09/14/2010] [Indexed: 11/10/2022]
Abstract
A novel dye-linked L-proline dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix was crystallized using the sitting-drop vapour-diffusion method with polyethylene glycol 8000 as the precipitant. The crystals belonged to the tetragonal space group P4(1)2(1)2 or its enantiomorph P4(3)2(1)2, with unit-cell parameters a = b = 61.1, c = 276.3 Å, and diffracted to 2.87 Å resolution using a Cu Kα rotating-anode generator with an R-AXIS VII detector. The asymmetric unit contained one protein molecule, giving a crystal volume per enzyme mass (V(M)) of 2.75 Å(3) Da(-1) and a solvent content of 55.3%.
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Affiliation(s)
- Takenori Satomura
- Department of Materials Science, Yonago National College of Technology, 4448 Hikona-cho, Yonago, Tottori 683-8506, Japan
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14
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Satomura T, Zhang XD, Hara Y, Doi K, Sakuraba H, Ohshima T. Characterization of a novel dye-linked L-proline dehydrogenase from an aerobic hyperthermophilic archaeon, Pyrobaculum calidifontis. Appl Microbiol Biotechnol 2010; 89:1075-82. [PMID: 20936278 DOI: 10.1007/s00253-010-2914-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 09/07/2010] [Accepted: 09/09/2010] [Indexed: 11/28/2022]
Abstract
The activity of a dye-linked L-proline dehydrogenase (dye-L: -proDH) was found in the crude extract of an aerobic hyperthermophilic archaeon, Pyrobaculum calidifontis JCM 11548, and was purified 163-fold through four sequential chromatography steps. The enzyme has a molecular mass of about 108 kDa and is a homodimer with a subunit molecular mass of about 46 kDa. The enzyme retained more than 90% of its activity after incubation at 100 °C for 120 min (pH 7.5) or after incubation at pHs 4.5-9.0 for 30 min at 50 °C. The enzyme catalyzed L-proline dehydrogenation to Δ(1)-pyroline-5-carboxylate using 2,6-dichloroindophenol (DCIP) as the electron acceptor and the Michaelis constants for L-proline and DCIP were 1.67 and 0.026 mM, respectively. The prosthetic group on the enzyme was identified as flavin adenine dinucleotide by high-performance liquid chromatography. The subunit N-terminal amino acid sequence was MYDYVVVGAG. Using that sequence and previously reported genome information, the gene encoding the enzyme (Pcal_1655) was identified. The gene was then cloned and expressed in Escherichia coli and found to encode a polypeptide of 415 amino acids with a calculated molecular weight of 46,259. The dye-L-proDH gene cluster in P. calidifontis inherently differs from those in the other hyperthermophiles reported so far.
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Affiliation(s)
- Takenori Satomura
- Department of Materials Science, Yonago National College of Technology, 4448 Hikona-cho, Yonago, Tottori 683-8506, Japan
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