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Kim S, Lee SH, Kim IK, Seo H, Kim KJ. Structural insight into a molecular mechanism of methenyltetrahydrofolate cyclohydrolase from Methylobacterium extorquens AM1. Int J Biol Macromol 2022; 202:234-240. [PMID: 35051495 DOI: 10.1016/j.ijbiomac.2022.01.072] [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: 10/01/2021] [Revised: 01/06/2022] [Accepted: 01/10/2022] [Indexed: 11/28/2022]
Abstract
Bioconversion of the C1 compounds into value-added products is one of the CO2-reducing strategies. In particular, because CO2 can be easily converted into formate, the efficient and direct bioconversion of CO2 through formate assimilation is attracting attention. The tetrahydrofolate (THF) cycle is the highly efficient reconstructed formate assimilation pathway, and 5,10-methenyltetrahydrofolate cyclohydrolase (FchA) is an essential enzyme involved in the THF cycle. In this study, a kinetic analysis of FchA from Methylobacterium extorquens AM1 (MeFchA) was performed and revealed that the enzyme has much higher cyclization than hydrolyzation activity, making it an optimal enzyme for formate assimilation. The crystal structure of MeFchA in the apo- and the THF-complexed forms was also determined, revealing that the substrate-binding site of the enzyme has three differently charged regions to stabilize the three differently charged moieties of the formyl-THF substrate. The residues involved in the substrate binding were also verified through site-directed mutagenesis. This study provides a biochemical and structural basis for the molecular mechanism underlying formate assimilation.
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Affiliation(s)
- Seongmin Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seul Hoo Lee
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Il-Kwon Kim
- KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hogyun Seo
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea; Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Kyoung-Jin Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea.
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Watanabe T, Shima S. MvhB-type Polyferredoxin as an Electron-transfer Chain in Putative Redox-enzyme Complexes. CHEM LETT 2021. [DOI: 10.1246/cl.200774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tomohiro Watanabe
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, Hokkaido 060-0819, Japan
| | - Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
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Shima S, Huang G, Wagner T, Ermler U. Structural Basis of Hydrogenotrophic Methanogenesis. Annu Rev Microbiol 2020; 74:713-733. [DOI: 10.1146/annurev-micro-011720-122807] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Most methanogenic archaea use the rudimentary hydrogenotrophic pathway—from CO2and H2to methane—as the terminal step of microbial biomass degradation in anoxic habitats. The barely exergonic process that just conserves sufficient energy for a modest lifestyle involves chemically challenging reactions catalyzed by complex enzyme machineries with unique metal-containing cofactors. The basic strategy of the methanogenic energy metabolism is to covalently bind C1species to the C1carriers methanofuran, tetrahydromethanopterin, and coenzyme M at different oxidation states. The four reduction reactions from CO2to methane involve one molybdopterin-based two-electron reduction, two coenzyme F420–based hydride transfers, and one coenzyme F430–based radical process. For energy conservation, one ion-gradient-forming methyl transfer reaction is sufficient, albeit supported by a sophisticated energy-coupling process termed flavin-based electron bifurcation for driving the endergonic CO2reduction and fixation. Here, we review the knowledge about the structure-based catalytic mechanism of each enzyme of hydrogenotrophic methanogenesis.
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Affiliation(s)
- Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Gangfeng Huang
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Tristan Wagner
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Ulrich Ermler
- Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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Versantvoort W, Guerrero-Castillo S, Wessels HJCT, van Niftrik L, Jetten MSM, Brandt U, Reimann J, Kartal B. Complexome analysis of the nitrite-dependent methanotroph Methylomirabilis lanthanidiphila. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:734-744. [PMID: 31376363 DOI: 10.1016/j.bbabio.2019.07.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/05/2019] [Accepted: 07/29/2019] [Indexed: 01/31/2023]
Abstract
The atmospheric concentration of the potent greenhouse gases methane and nitrous oxide (N2O) has increased drastically during the last century. Methylomirabilis bacteria can play an important role in controlling the emission of these two gases from natural ecosystems, by oxidizing methane to CO2 and reducing nitrite to N2 without producing N2O. These bacteria have an anaerobic metabolism, but are proposed to possess an oxygen-dependent pathway for methane activation. Methylomirabilis bacteria reduce nitrite to NO, and are proposed to dismutate NO into O2 and N2 by a putative NO dismutase (NO-D). The O2 produced in the cell can then be used to activate methane by a particulate methane monooxygenase. So far, the metabolic model of Methylomirabilis bacteria was based mainly on (meta)genomics and physiological experiments. Here we applied a complexome profiling approach to determine which of the proposed enzymes are actually expressed in Methylomirabilis lanthanidiphila. To validate the proposed metabolic model, we focused on enzymes involved in respiration, as well as nitrogen and carbon transformation. All complexes suggested to be involved in nitrite-dependent methane oxidation, were identified in M. lanthanidiphila, including the putative NO-D. Furthermore, several complexes involved in nitrate reduction/nitrite oxidation and NO reduction were detected, which likely play a role in detoxification and redox homeostasis. In conclusion, complexome profiling validated the expression and composition of enzymes hypothesized to be involved in the energy, methane and nitrogen metabolism of M. lanthanidiphila, thereby further corroborating their unique metabolism involved in the environmentally relevant process of nitrite-dependent methane oxidation.
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Affiliation(s)
- Wouter Versantvoort
- Department of Microbiology, IWWR, Faculty of Science, Radboud University, Nijmegen, the Netherlands.
| | - Sergio Guerrero-Castillo
- Molecular Bioenergetics Group, Radboud Institute for Molecular Life Sciences, Department of Pediatrics, Radboud University Medical Center, Geert-Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Hans J C T Wessels
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Geert-Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Laura van Niftrik
- Department of Microbiology, IWWR, Faculty of Science, Radboud University, Nijmegen, the Netherlands
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Faculty of Science, Radboud University, Nijmegen, the Netherlands
| | - Ulrich Brandt
- Molecular Bioenergetics Group, Radboud Institute for Molecular Life Sciences, Department of Pediatrics, Radboud University Medical Center, Geert-Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands; KPA Aging-Associated Diseases, CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Joachim Reimann
- Department of Microbiology, IWWR, Faculty of Science, Radboud University, Nijmegen, the Netherlands
| | - Boran Kartal
- Microbial Physiology Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.
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Reimann J, Jetten MSM, Keltjens JT. Metal enzymes in "impossible" microorganisms catalyzing the anaerobic oxidation of ammonium and methane. Met Ions Life Sci 2015; 15:257-313. [PMID: 25707470 DOI: 10.1007/978-3-319-12415-5_7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ammonium and methane are inert molecules and dedicated enzymes are required to break up the N-H and C-H bonds. Until recently, only aerobic microorganisms were known to grow by the oxidation of ammonium or methane. Apart from respiration, oxygen was specifically utilized to activate the inert substrates. The presumed obligatory need for oxygen may have resisted the search for microorganisms that are capable of the anaerobic oxidation of ammonium and of methane. However extremely slowly growing, these "impossible" organisms exist and they found other means to tackle ammonium and methane. Anaerobic ammonium-oxidizing (anammox) bacteria use the oxidative power of nitric oxide (NO) by forging this molecule to ammonium, thereby making hydrazine (N2H4). Nitrite-dependent anaerobic methane oxidizers (N-DAMO) again take advantage of NO, but now apparently disproportionating the compound into dinitrogen and dioxygen gas. This intracellularly produced dioxygen enables N-DAMO bacteria to adopt an aerobic mechanism for methane oxidation.Although our understanding is only emerging how hydrazine synthase and the NO dismutase act, it seems clear that reactions fully rely on metal-based catalyses known from other enzymes. Metal-dependent conversions not only hold for these key enzymes, but for most other reactions in the central catabolic pathways, again supported by well-studied enzymes from model organisms, but adapted to own specific needs. Remarkably, those accessory catabolic enzymes are not unique for anammox bacteria and N-DAMO. Close homologs are found in protein databases where those homologs derive from (partly) known, but in most cases unknown species that together comprise an only poorly comprehended microbial world.
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Affiliation(s)
- Joachim Reimann
- Department of Microbiology, Institute of Wetland and Water Research (IWWR), Radboud University of Nijmegen, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands,
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Angelucci F, Morea V, Angelaccio S, Saccoccia F, Contestabile R, Ilari A. The crystal structure of archaeal serine hydroxymethyltransferase reveals idiosyncratic features likely required to withstand high temperatures. Proteins 2014; 82:3437-49. [PMID: 25257552 DOI: 10.1002/prot.24697] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 09/09/2014] [Accepted: 09/10/2014] [Indexed: 01/19/2023]
Abstract
Serine hydroxymethyltransferases (SHMTs) play an essential role in one-carbon unit metabolism and are used in biomimetic reactions. We determined the crystal structure of free (apo) and pyridoxal-5'-phosphate-bound (holo) SHMT from Methanocaldococcus jannaschii, the first from a hyperthermophile, from the archaea domain of life and that uses H₄MPT as a cofactor, at 2.83 and 3.0 Å resolution, respectively. Idiosyncratic features were observed that are likely to contribute to structure stabilization. At the dimer interface, the C-terminal region folds in a unique fashion with respect to SHMTs from eubacteria and eukarya. At the active site, the conserved tyrosine does not make a cation-π interaction with an arginine like that observed in all other SHMT structures, but establishes an amide-aromatic interaction with Asn257, at a different sequence position. This asparagine residue is conserved and occurs almost exclusively in (hyper)thermophile SHMTs. This led us to formulate the hypothesis that removal of frustrated interactions (such as the Arg-Tyr cation-π interaction occurring in mesophile SHMTs) is an additional strategy of adaptation to high temperature. Both peculiar features may be tested by designing enzyme variants potentially endowed with improved stability for applications in biomimetic processes.
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Affiliation(s)
- Francesco Angelucci
- Department of Life, Health and Environmental Sciences, University of L'Aquila, P.le Salvatore Tommasi 1, L'Aquila, Italy
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Carbone V, Schofield LR, Beattie AK, Sutherland-Smith AJ, Ronimus RS. The crystal structure of methenyltetrahydromethanopterin cyclohydrolase from Methanobrevibacter ruminantium. Proteins 2013; 81:2064-70. [DOI: 10.1002/prot.24372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 07/09/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Vincenzo Carbone
- AgResearch Limited, Grasslands Research Centre; Tennent Drive, Private Bag 11008 Palmerston North 4442 New Zealand
| | - Linley R. Schofield
- AgResearch Limited, Grasslands Research Centre; Tennent Drive, Private Bag 11008 Palmerston North 4442 New Zealand
| | - Amy K. Beattie
- AgResearch Limited, Lincoln Research Centre; Cnr Springs Road and Gerald Street, Private Bag 4749 Christchurch 8140 New Zealand
| | | | - Ron S. Ronimus
- AgResearch Limited, Grasslands Research Centre; Tennent Drive, Private Bag 11008 Palmerston North 4442 New Zealand
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Wang K, Chen Y. Analysis of a novel protein in human colorectal adenocarcinoma. Mol Med Rep 2013; 8:529-34. [PMID: 23778839 DOI: 10.3892/mmr.2013.1526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 05/29/2013] [Indexed: 11/05/2022] Open
Abstract
Colorectal adenocarcinoma (CRC) is the third most common type of cancer worldwide with a low 5‑year survival rate. The present study aimed to investigate the structure and function of a novel protein identified from human colorectal adenocarcinoma (CRC). A differentially expressed sequence tag (GenBank accession number, ES274081) was collected from GenBank. Bioinformatics tools were employed to obtain the sequence of the full‑length cDNA in order to localize the open reading frame and to predict the protein sequence. Mass spectro-metry was used to analyze the structure of this novel protein and western blot analysis was used to confirm the expression of this protein in human CRC tissue samples. The full‑length cDNA was composed of 4,283‑bp nucleotides and the sequence information was obtained (GenBank accession number, NM_001013649). The corresponding protein molecule contained 165 amino acids, with a monoisotopic molecular weight of 18.6033 kDa and an isoelectric point of 8.43, determined by mass spectrometry. The protein structure and its function in adenocarcinoma were further explored. In the present study, a novel protein, which may be involved in nuclear signal transduction, was identified using bioinformatics, mass spectrometry and western blot analysis.
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Affiliation(s)
- Kaicheng Wang
- Department of Anatomy, Premedical and Forensic Medical Institute, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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