1
|
Phi MT, Singer H, Zäh F, Haisch C, Schneider S, Op den Camp HJM, Daumann LJ. Assessing Lanthanide-Dependent Methanol Dehydrogenase Activity: The Assay Matters. Chembiochem 2024; 25:e202300811. [PMID: 38269599 DOI: 10.1002/cbic.202300811] [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: 11/30/2023] [Revised: 12/22/2023] [Indexed: 01/26/2024]
Abstract
Artificial dye-coupled assays have been widely adopted as a rapid and convenient method to assess the activity of methanol dehydrogenases (MDH). Lanthanide(Ln)-dependent XoxF-MDHs are able to incorporate different lanthanides (Lns) in their active site. Dye-coupled assays showed that the earlier Lns exhibit a higher enzyme activity than the late Lns. Despite widespread use, there are limitations: oftentimes a pH of 9 and activators are required for the assay. Moreover, Ln-MDH variants are not obtained by isolation from the cells grown with the respective Ln, but by incubation of an apo-MDH with the Ln. Herein, we report the cultivation of Ln-dependent methanotroph Methylacidiphilum fumariolicum SolV with nine different Lns, the isolation of the respective MDHs and the assessment of the enzyme activity using the dye-coupled assay. We compare these results with a protein-coupled assay using its physiological electron acceptor cytochrome cGJ (cyt cGJ ). Depending on the assay, two distinct trends are observed among the Ln series. The specific enzyme activity of La-, Ce- and Pr-MDH, as measured by the protein-coupled assay, exceeds that measured by the dye-coupled assay. This suggests that early Lns also have a positive effect on the interaction between XoxF-MDH and its cyt cGJ thereby increasing functional efficiency.
Collapse
Affiliation(s)
- Manh Tri Phi
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Helena Singer
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Felix Zäh
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Christoph Haisch
- Faculty of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Sabine Schneider
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Huub J M Op den Camp
- Department of Microbiology, Research Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Lena J Daumann
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
- Chair of Bioinorganic Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| |
Collapse
|
2
|
Xiao Y, Wu K, Batool SS, Wang Q, Chen H, Zhai X, Yu Z, Huang J. Enzymatic properties of alcohol dehydrogenase PedE_M.s. derived from Methylopila sp. M107 and its broad metal selectivity. Front Microbiol 2023; 14:1191436. [PMID: 37560521 PMCID: PMC10409515 DOI: 10.3389/fmicb.2023.1191436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 07/10/2023] [Indexed: 08/11/2023] Open
Abstract
As an important metabolic enzyme in methylotrophs, pyrroloquinoline quinone (PQQ)-dependent alcohol dehydrogenases play significant roles in the global carbon and nitrogen cycles. In this article, a calcium (Ca2+)-dependent alcohol dehydrogenase PedE_M.s., derived from the methylotroph Methylopila sp. M107 was inserted into the modified vector pCM80 and heterologously expressed in the host Methylorubrum extorquens AM1. Based on sequence analysis, PedE_M.s., a PQQ-dependent dehydrogenase belonging to a methanol/ethanol family, was successfully extracted and purified. Showing by biochemical results, its enzymatic activity was detected as 0.72 U/mg while the Km value was 0.028 mM while employing ethanol as optimal substrate. The activity of PedE_M.s. could be enhanced by the presence of potassium (K+) and calcium (Ca2+), while acetonitrile and certain common detergents have been found to decrease the activity of PedE_M.s.. In addition, its optimum temperature and pH were 30°C and pH 9.0, respectively. Chiefly, as a type of Ca2+-dependent alcohol dehydrogenase, PedE_M.s. maintained 60-80% activity in the presence of 10 mM lanthanides and displayed high affinity for ethanol compared to other PedE-type enzymes. The 3D structure of PedE_M.s. was predicted by AlphaFold, and it had an 8-bladed propeller-like super-barrel. Meanwhile, we could speculate that PedE_M.s. contained the conserved residues Glu213, Asn300, and Asp350 through multiple sequence alignment by Clustal and ESpript. The analysis of enzymatic properties of PedE_M.s. enriches our knowledge of the methanol/ethanol family PQQ-dependent dehydrogenase. This study provides new ideas to broaden the application of alcohol dehydrogenase in alcohol concentration calculation, biosensor preparation, and other industries.
Collapse
Affiliation(s)
- Ying Xiao
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Kaijuan Wu
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Syeda Sundas Batool
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Qingqun Wang
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Hao Chen
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Xingyu Zhai
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Zheng Yu
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Jing Huang
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| |
Collapse
|
3
|
Li D, Liang G, Mu P, Lin J, Huang J, Guo C, Li Y, Lin R, Jiang J, Wu J, Deng Y, Wen J. Improvement of catalytic activity of sorbose dehydrogenase for deoxynivalenol degradation by rational design. Food Chem 2023; 423:136274. [PMID: 37159968 DOI: 10.1016/j.foodchem.2023.136274] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 02/27/2023] [Accepted: 04/27/2023] [Indexed: 05/11/2023]
Abstract
Deoxynivalenol (DON) is the most frequently contaminated mycotoxin in food and feed worldwide, causing significant economic losses and health risks. Physical and chemical detoxification methods are widely used, but they cannot efficiently and specifically remove DON. In the study, the combination of bioinformatics screening and experimental verification confirmed that sorbose dehydrogenase (SDH) can effectively convert DON to 3-keto-DON and a substance that removes four hydrogen atoms for DON. Through rational design, the Vmax of the mutants F103L and F103A were increased by 5 and 23 times, respectively. Furthermore, we identified catalytic sites W218 and D281. SDH and its mutants have broad application conditions, including temperature ranges of 10-45 °C and pH levels of 4-9. Additionally, the half-lives of F103A at 90 °C (processing temperature) and 30 °C (storage temperature) were 60.1 min and 100.5 d, respectively. These results suggest that F103A has significant potential in the detoxification application of DON.
Collapse
Affiliation(s)
- Danyang Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| | - Guoqiang Liang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| | - Peiqiang Mu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| | - Jinquan Lin
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| | - Jiarun Huang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| | - Chongwen Guo
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| | - Yang Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| | - Ruqin Lin
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| | - Jun Jiang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| | - Jun Wu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| | - Yiqun Deng
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| | - Jikai Wen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong 510642, PR China.
| |
Collapse
|
4
|
Unusual Cytochrome c552 from Thioalkalivibrio paradoxus: Solution NMR Structure and Interaction with Thiocyanate Dehydrogenase. Int J Mol Sci 2022; 23:ijms23179969. [PMID: 36077365 PMCID: PMC9456337 DOI: 10.3390/ijms23179969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/25/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
The search of a putative physiological electron acceptor for thiocyanate dehydrogenase (TcDH) newly discovered in the thiocyanate-oxidizing bacteria Thioalkalivibrio paradoxus revealed an unusually large, single-heme cytochrome c (CytC552), which was co-purified with TcDH from the periplasm. Recombinant CytC552, produced in Escherichia coli as a mature protein without a signal peptide, has spectral properties similar to the endogenous protein and serves as an in vitro electron acceptor in the TcDH-catalyzed reaction. The CytC552 structure determined by NMR spectroscopy reveals significant differences compared to those of the typical class I bacterial cytochromes c: a high solvent accessible surface area for the heme group and so-called “intrinsically disordered” nature of the histidine-rich N- and C-terminal regions. Comparison of the signal splitting in the heteronuclear NMR spectra of oxidized, reduced, and TcDH-bound CytC552 reveals the heme axial methionine fluxionality. The TcDH binding site on the CytC552 surface was mapped using NMR chemical shift perturbations. Putative TcDH-CytC552 complexes were reconstructed by the information-driven docking approach and used for the analysis of effective electron transfer pathways. The best pathway includes the electron hopping through His528 and Tyr164 of TcDH, and His83 of CytC552 to the heme group in accordance with pH-dependence of TcDH activity with CytC552.
Collapse
|
5
|
Neodymium as Metal Cofactor for Biological Methanol Oxidation: Structure and Kinetics of an XoxF1-Type Methanol Dehydrogenase. mBio 2021; 12:e0170821. [PMID: 34544276 PMCID: PMC8546591 DOI: 10.1128/mbio.01708-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The methane-oxidizing bacterium Methylacidimicrobium thermophilum AP8 thrives in acidic geothermal ecosystems that are characterized by high degassing of methane (CH4), H2, H2S, and by relatively high lanthanide concentrations. Lanthanides (atomic numbers 57 to 71) are essential in a variety of high-tech devices, including mobile phones. Remarkably, the same elements are actively taken up by methanotrophs/methylotrophs in a range of environments, since their XoxF-type methanol dehydrogenases require lanthanides as a metal cofactor. Lanthanide-dependent enzymes seem to prefer the lighter lanthanides (lanthanum, cerium, praseodymium, and neodymium), as slower methanotrophic/methylotrophic growth is observed in medium supplemented with only heavier lanthanides. Here, we purified XoxF1 from the thermoacidophilic methanotroph Methylacidimicrobium thermophilum AP8, which was grown in medium supplemented with neodymium as the sole lanthanide. The neodymium occupancy of the enzyme is 94.5% ± 2.0%, and through X-ray crystallography, we reveal that the structure of the active site shows interesting differences from the active sites of other methanol dehydrogenases, such as an additional aspartate residue in close proximity to the lanthanide. Nd-XoxF1 oxidizes methanol at a maximum rate of metabolism (Vmax) of 0.15 ± 0.01 μmol · min-1 · mg protein-1 and an affinity constant (Km) of 1.4 ± 0.6 μM. The structural analysis of this neodymium-containing XoxF1-type methanol dehydrogenase will expand our knowledge in the exciting new field of lanthanide biochemistry. IMPORTANCE Lanthanides comprise a group of 15 elements with atomic numbers 57 to 71 that are essential in a variety of high-tech devices, such as mobile phones, but were considered biologically inert for a long time. The biological relevance of lanthanides became evident when the acidophilic methanotroph Methylacidiphilum fumariolicum SolV, isolated from a volcanic mud pot, could only grow when lanthanides were supplied to the growth medium. We expanded knowledge in the exciting and rapidly developing field of lanthanide biochemistry by the purification and characterization of a neodymium-containing methanol dehydrogenase from a thermoacidophilic methanotroph.
Collapse
|
6
|
Sarmiento-Pavía PD, Sosa-Torres ME. Bioinorganic insights of the PQQ-dependent alcohol dehydrogenases. J Biol Inorg Chem 2021; 26:177-203. [PMID: 33606117 DOI: 10.1007/s00775-021-01852-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/07/2021] [Indexed: 12/19/2022]
Abstract
Among the several alcohol dehydrogenases, PQQ-dependent enzymes are mainly found in the α, β, and γ-proteobacteria. These proteins are classified into three main groups. Type I ADHs are localized in the periplasm and contain one Ca2+-PQQ moiety, being the methanol dehydrogenase (MDH) the most representative. In recent years, several lanthanide-dependent MDHs have been discovered exploding the understanding of the natural role of lanthanide ions. Type II ADHs are localized in the periplasm and possess one Ca2+-PQQ moiety and one heme c group. Finally, type III ADHs are complexes of two or three subunits localized in the cytoplasmic membrane and possess one Ca2+-PQQ moiety and four heme c groups, and in one of these proteins, an additional [2Fe-2S] cluster has been discovered recently. From the bioinorganic point of view, PQQ-dependent alcohol dehydrogenases have been revived recently mainly due to the discovery of the lanthanide-dependent enzymes. Here, we review the three types of PQQ-dependent ADHs with special focus on their structural features and electron transfer processes. The PQQ-Alcohol dehydrogenases are classified into three main groups. Type I and type II ADHs are located in the periplasm, while type III ADHs are in the cytoplasmic membrane. ADH-I have a Ca-PQQ or a Ln-PQQ, ADH-II a Ca-PQQ and one heme-c and ADH-III a Ca-PQQ and four hemes-c. This review focuses on their structural features and electron transfer processes.
Collapse
Affiliation(s)
- Pedro D Sarmiento-Pavía
- Facultad de Química, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, 04510, Ciudad de México, Mexico
| | - Martha E Sosa-Torres
- Facultad de Química, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, 04510, Ciudad de México, Mexico.
| |
Collapse
|
7
|
Gutenthaler SM, Phi MT, Singer H, Daumann LJ. Activity assays of methanol dehydrogenases. Methods Enzymol 2021; 650:57-79. [PMID: 33867025 DOI: 10.1016/bs.mie.2021.01.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The field of methanol dehydrogenases (MDHs) has experienced revival in the recent decade due to the observation of lanthanide-dependent MDH, in addition to widely known calcium-MDH. With the advent of lanthanide-dependent alcohol dehydrogenases, the need for reliable assays to evaluate and compare activities between different MDHs is obvious: from extremophilic to neutrophilic organisms, or with different lanthanide ions in the active site. Here we outline four assays that have been reported for Ln-MDH, discussing the advantages and disadvantages of the assays and their components. It should be noted, in 1990Day and Anthony produced a comprehensive summary in Methods in Enzymology on the available methods for Ca-MDH assays at the time (Day & Anthony, 1990). This chapter is an updated appraisal of the most important developments in the last 30years.
Collapse
Affiliation(s)
- Sophie M Gutenthaler
- Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Manh Tri Phi
- Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Helena Singer
- Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Lena J Daumann
- Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany.
| |
Collapse
|
8
|
Chan SI, Chuankhayan P, Reddy Nareddy PK, Tsai IK, Tsai YF, Chen KHC, Yu SSF, Chen CJ. Mechanism of Pyrroloquinoline Quinone-Dependent Hydride Transfer Chemistry from Spectroscopic and High-Resolution X-ray Structural Studies of the Methanol Dehydrogenase from Methylococcus capsulatus (Bath). J Am Chem Soc 2021; 143:3359-3372. [PMID: 33629832 DOI: 10.1021/jacs.0c11414] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The active site of methanol dehydrogenase (MDH) contains a rare disulfide bridge between adjacent cysteine residues. As a vicinal disulfide, the structure is highly strained, suggesting it might work together with the pyrroloquinoline quinone (PQQ) prosthetic group and the Ca2+ ion in the catalytic turnover during methanol (CH3OH) oxidation. We purify MDH from Methylococcus capsulatus (Bath) with the disulfide bridge broken into two thiols. Spectroscopic and high-resolution X-ray crystallographic studies of this form of MDH indicate that the disulfide bridge is redox active. We observe an internal redox process within the holo-MDH that produces a disulfide radical anion concomitant with a companion PQQ radical, as evidenced by an optical absorption at 408 nm and a magnetically dipolar-coupled biradical in the EPR spectrum. These observations are corroborated by electron-density changes between the two cysteine sulfurs of the disulfide bridge as well as between the bound Ca2+ ion and the O5-C5 bond of the PQQ in the high-resolution X-ray structure. On the basis of these findings, we propose a mechanism for the controlled redistribution of the two electrons during hydride transfer from the CH3OH in the alcohol oxidation without formation of the reduced PQQ ethenediol, a biradical mechanism that allows for possible recovery of the hydride for transfer to an external NAD+ oxidant in the regeneration of the PQQ cofactor for multiple catalytic turnovers. In support of this mechanism, a steady-state level of the disulfide radical anion is observed during turnover of the MDH in the presence of CH3OH and NAD+.
Collapse
Affiliation(s)
- Sunney I Chan
- Institute of Chemistry, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - Phimonphan Chuankhayan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | | | - I-Kuen Tsai
- Institute of Chemistry, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - Yi-Fang Tsai
- Institute of Chemistry, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - Kelvin H-C Chen
- Department of Applied Chemistry, National Pingtung University, Pingtung 90003, Taiwan
| | - Steve S-F Yu
- Institute of Chemistry, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - Chun-Jung Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| |
Collapse
|
9
|
Ghosh S, Dhanasingh, I, Ryu J, Kim SW, Lee SH. Crystal Structure of Cytochrome cL from the Aquatic Methylotrophic Bacterium Methylophaga aminisulfidivorans MP T. J Microbiol Biotechnol 2020; 30:1261-1271. [PMID: 32627749 PMCID: PMC9728263 DOI: 10.4014/jmb.2006.06029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 06/29/2020] [Accepted: 07/01/2020] [Indexed: 12/15/2022]
Abstract
Cytochrome cL (CytcL) is an essential protein in the process of methanol oxidation in methylotrophs. It receives an electron from the pyrroloquinoline quinone (PQQ) cofactor of methanol dehydrogenase (MDH) to produce formaldehyde. The direct electron transfer mechanism between CytcL and MDH remains unknown due to the lack of structural information. To help gain a better understanding of the mechanism, we determined the first crystal structure of heme c containing CytcL from the aquatic methylotrophic bacterium Methylophaga aminisulfidivorans MPT at 2.13 Å resolution. The crystal structure of Ma-CytcL revealed its unique features compared to those of the terrestrial homologues. Apart from Fe in heme, three additional metal ion binding sites for Na+ , Ca+ , and Fe2+ were found, wherein the ions mostly formed coordination bonds with the amino acid residues on the loop (G93-Y111) that interacts with heme. Therefore, these ions seemed to enhance the stability of heme insertion by increasing the loop's steadiness. The basic N-terminal end, together with helix α4 and loop (G126 to Y136), contributed positive charge to the region. In contrast, the acidic C-terminal end provided a negatively charged surface, yielding several electrostatic contact points with partner proteins for electron transfer. These exceptional features of Ma-CytcL, along with the structural information of MDH, led us to hypothesize the need for an adapter protein bridging MDH to CytcL within appropriate proximity for electron transfer. With this knowledge in mind, the methanol oxidation complex reconstitution in vitro could be utilized to produce metabolic intermediates at the industry level.
Collapse
Affiliation(s)
- Suparna Ghosh
- Department of Cellular and Molecular Medicine, Chosun University School of Medicine, Gwangju 61452, Republic of Korea,Department of Biomedical Sciences, Graduate School of Chosun University, Gwangju 61452, Republic of Korea
| | - Immanuel Dhanasingh,
- Department of Cellular and Molecular Medicine, Chosun University School of Medicine, Gwangju 61452, Republic of Korea,Department of Biomedical Sciences, Graduate School of Chosun University, Gwangju 61452, Republic of Korea
| | - Jaewon Ryu
- Department of Energy Convergence, Graduate School of Chosun University, Gwangju 61452, Republic of Korea
| | - Si Wouk Kim
- Department of Environmental Engineering, Chosun University, Gwangju 61452, Republic of Korea,Department of Energy Convergence, Graduate School of Chosun University, Gwangju 61452, Republic of Korea
| | - Sung Haeng Lee
- Department of Cellular and Molecular Medicine, Chosun University School of Medicine, Gwangju 61452, Republic of Korea,Department of Biomedical Sciences, Graduate School of Chosun University, Gwangju 61452, Republic of Korea,Corresponding author Phone: +82-62-230-6381 Fax: +82-62-228-7791 E-mail:
| |
Collapse
|
10
|
Featherston ER, Rose HR, McBride MJ, Taylor EM, Boal AK, Cotruvo JA. Biochemical and Structural Characterization of XoxG and XoxJ and Their Roles in Lanthanide-Dependent Methanol Dehydrogenase Activity. Chembiochem 2019; 20:2360-2372. [PMID: 31017712 PMCID: PMC6814260 DOI: 10.1002/cbic.201900184] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Indexed: 12/31/2022]
Abstract
Lanthanide (Ln)-dependent methanol dehydrogenases (MDHs) have recently been shown to be widespread in methylotrophic bacteria. Along with the core MDH protein, XoxF, these systems contain two other proteins, XoxG (a c-type cytochrome) and XoxJ (a periplasmic binding protein of unknown function), about which little is known. In this work, we have biochemically and structurally characterized these proteins from the methyltroph Methylobacterium extorquens AM1. In contrast to results obtained in an artificial assay system, assays of XoxFs metallated with LaIII , CeIII , and NdIII using their physiological electron acceptor, XoxG, display Ln-independent activities, but the Km for XoxG markedly increases from La to Nd. This result suggests that XoxG's redox properties are tuned specifically for lighter Lns in XoxF, an interpretation supported by the unusually low reduction potential of XoxG (+172 mV). The X-ray crystal structure of XoxG provides a structural basis for this reduction potential and insight into the XoxG-XoxF interaction. Finally, the X-ray crystal structure of XoxJ reveals a large hydrophobic cleft and suggests a role in the activation of XoxF. These studies enrich our understanding of the underlying chemical principles that enable the activity of XoxF with multiple lanthanides in vitro and in vivo.
Collapse
Affiliation(s)
- Emily R. Featherston
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Hannah R. Rose
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Molly J. McBride
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Elle M. Taylor
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Joseph A. Cotruvo
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| |
Collapse
|
11
|
Kalimuthu P, Daumann LJ, Pol A, Op den Camp HJM, Bernhardt PV. Electrocatalysis of a Europium‐Dependent Bacterial Methanol Dehydrogenase with Its Physiological Electron‐Acceptor Cytochrome
c
GJ. Chemistry 2019; 25:8760-8768. [DOI: 10.1002/chem.201900525] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 03/21/2019] [Indexed: 01/27/2023]
Affiliation(s)
- Palraj Kalimuthu
- School of Chemistry and Molecular Biosciences University of Queensland Brisbane 4072 Australia
| | - Lena J. Daumann
- Center for Integrated Protein Science Munich (CIPSM) and Department of Chemistry Ludwig-Maximilians-Universität München Butenandtstr. 5–13, Haus D 81377 München Germany
| | - Arjan Pol
- Department of Microbiology Institute of Wetland and Water Research Radboud University Nijmegen The Netherlands
| | - Huub J. M. Op den Camp
- Department of Microbiology Institute of Wetland and Water Research Radboud University Nijmegen The Netherlands
| | - Paul V. Bernhardt
- School of Chemistry and Molecular Biosciences University of Queensland Brisbane 4072 Australia
| |
Collapse
|
12
|
Picone N, Op den Camp HJM. Role of rare earth elements in methanol oxidation. Curr Opin Chem Biol 2019; 49:39-44. [DOI: 10.1016/j.cbpa.2018.09.019] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/05/2018] [Accepted: 09/21/2018] [Indexed: 11/25/2022]
|
13
|
Contrasting in vitro and in vivo methanol oxidation activities of lanthanide-dependent alcohol dehydrogenases XoxF1 and ExaF from Methylobacterium extorquens AM1. Sci Rep 2019; 9:4248. [PMID: 30862918 PMCID: PMC6414531 DOI: 10.1038/s41598-019-41043-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 02/28/2019] [Indexed: 11/19/2022] Open
Abstract
Lanthanide (Ln) elements are utilized as cofactors for catalysis by XoxF-type methanol dehydrogenases (MDHs). A primary assumption is that XoxF enzymes produce formate from methanol oxidation, which could impact organisms that require formaldehyde for assimilation. We report genetic and phenotypic evidence showing that XoxF1 (MexAM1_1740) from Methylobacterium extorquens AM1 produces formaldehyde, and not formate, during growth with methanol. Enzyme purified with lanthanum or neodymium oxidizes formaldehyde. However, formaldehyde oxidation via 2,6-dichlorophenol-indophenol (DCPIP) reduction is not detected in cell-free extracts from wild-type strain methanol- and lanthanum-grown cultures. Formaldehyde activating enzyme (Fae) is required for Ln methylotrophic growth, demonstrating that XoxF1-mediated production of formaldehyde is essential. Addition of exogenous lanthanum increases growth rate with methanol by 9–12% but does not correlate with changes to methanol consumption or formaldehyde accumulation. Transcriptomics analysis of lanthanum methanol growth shows upregulation of xox1 and downregulation of mxa genes, consistent with the Ln-switch, no differential expression of formaldehyde conversion genes, downregulation of pyrroloquinoline quinone (PQQ) biosynthesis genes, and upregulation of fdh4 formate dehydrogenase (FDH) genes. Additionally, the Ln-dependent ethanol dehydrogenase ExaF reduces methanol sensitivity in the fae mutant strain when lanthanides are present, providing evidence for the capacity of an auxiliary role for ExaF during Ln-dependent methylotrophy.
Collapse
|
14
|
Marino T, Prejanò M, Russo N. How Metal Coordination in the Ca-, Ce-, and Eu-Containing Methanol Dehydrogenase Enzymes Can Influence the Catalysis: A Theoretical Point of View. TRANSITION METALS IN COORDINATION ENVIRONMENTS 2019. [DOI: 10.1007/978-3-030-11714-6_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
15
|
Lumpe H, Pol A, Op den Camp HJM, Daumann LJ. Impact of the lanthanide contraction on the activity of a lanthanide-dependent methanol dehydrogenase - a kinetic and DFT study. Dalton Trans 2018; 47:10463-10472. [PMID: 30020281 PMCID: PMC6085770 DOI: 10.1039/c8dt01238e] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/14/2018] [Indexed: 01/15/2023]
Abstract
Interest in the bioinorganic chemistry of lanthanides is growing rapidly as more and more lanthanide-dependent bacteria are being discovered. Especially the earlier lanthanides have been shown to be preferentially utilized by bacteria that need these Lewis acids as cofactors in their alcohol dehydrogenase enzymes. Here, we investigate the impact of the lanthanide ions lanthanum(iii) to lutetium(iii) (excluding Pm) on the catalytic parameters (vmax, KM, kcat/KM) of a methanol dehydrogenase (MDH) isolated from Methylacidiphilum fumariolicum SolV. Kinetic experiments and DFT calculations were used to discuss why only the earlier lanthanides (La-Gd) promote high MDH activity. Impact of Lewis acidity, coordination number preferences, stability constants and other properties that are a direct result of the lanthanide contraction are discussed in light of the two proposed mechanisms for MDH.
Collapse
Affiliation(s)
- Henning Lumpe
- Ludwig-Maximilians-Universität München
, Department Chemie
,
Butenandtstr. 5-13
, 81377 München
, Germany
.
| | - Arjan Pol
- Department of Microbiology
, Institute of Wetland and Water Research
, Radboud University Nijmegen
,
The Netherlands
| | - Huub J. M. Op den Camp
- Department of Microbiology
, Institute of Wetland and Water Research
, Radboud University Nijmegen
,
The Netherlands
| | - Lena J. Daumann
- Ludwig-Maximilians-Universität München
, Department Chemie
,
Butenandtstr. 5-13
, 81377 München
, Germany
.
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry
, Ludwig-Maximilians-Universität München
,
Germany
| |
Collapse
|
16
|
Yamauchi Y, Nindita Y, Hara K, Umeshiro A, Yabuuchi Y, Suzuki T, Kinashi H, Arakawa K. Quinoprotein dehydrogenase functions at the final oxidation step of lankacidin biosynthesis in Streptomyces rochei 7434AN4. J Biosci Bioeng 2018; 126:145-152. [DOI: 10.1016/j.jbiosc.2018.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 03/05/2018] [Accepted: 03/09/2018] [Indexed: 10/14/2022]
|
17
|
Jahn B, Pol A, Lumpe H, Barends TRM, Dietl A, Hogendoorn C, Op den Camp HJM, Daumann LJ. Similar but Not the Same: First Kinetic and Structural Analyses of a Methanol Dehydrogenase Containing a Europium Ion in the Active Site. Chembiochem 2018; 19:1147-1153. [PMID: 29524328 PMCID: PMC6100108 DOI: 10.1002/cbic.201800130] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Indexed: 01/23/2023]
Abstract
Since the discovery of the biological relevance of rare earth elements (REEs) for numerous different bacteria, questions concerning the advantages of REEs in the active sites of methanol dehydrogenases (MDHs) over calcium(II) and of why bacteria prefer light REEs have been a subject of debate. Here we report the cultivation and purification of the strictly REE-dependent methanotrophic bacterium Methylacidiphilum fumariolicum SolV with europium(III), as well as structural and kinetic analyses of the first methanol dehydrogenase incorporating Eu in the active site. Crystal structure determination of the Eu-MDH demonstrated that overall no major structural changes were induced by conversion to this REE. Circular dichroism (CD) measurements were used to determine optimal conditions for kinetic assays, whereas inductively coupled plasma mass spectrometry (ICP-MS) showed 70 % incorporation of Eu in the enzyme. Our studies explain why bacterial growth of SolV in the presence of Eu3+ is significantly slower than in the presence of La3+ /Ce3+ /Pr3+ : Eu-MDH possesses a decreased catalytic efficiency. Although REEs have similar properties, the differences in ionic radii and coordination numbers across the series significantly impact MDH efficiency.
Collapse
Affiliation(s)
- Bérénice Jahn
- Ludwig-Maximilians-Universität MünchenDepartment ChemieButenandtstr. 5–1381377MünchenGermany
| | - Arjan Pol
- Department of Microbiology, Institute of Wetland and Water ResearchRadboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
| | - Henning Lumpe
- Ludwig-Maximilians-Universität MünchenDepartment ChemieButenandtstr. 5–1381377MünchenGermany
| | - Thomas R. M. Barends
- Department of Biomolecular MechanismsMax-Planck Institute for Medical ResearchJahnstrasse 2969120HeidelbergGermany
| | - Andreas Dietl
- Department of Biomolecular MechanismsMax-Planck Institute for Medical ResearchJahnstrasse 2969120HeidelbergGermany
| | - Carmen Hogendoorn
- Department of Microbiology, Institute of Wetland and Water ResearchRadboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
| | - Huub J. M. Op den Camp
- Department of Microbiology, Institute of Wetland and Water ResearchRadboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
| | - Lena J. Daumann
- Ludwig-Maximilians-Universität MünchenDepartment ChemieButenandtstr. 5–1381377MünchenGermany
| |
Collapse
|
18
|
Vemuluri VR, Shaw S, Autenrieth C, Ghosh R. A rapid procedure for the in situ assay of periplasmic, PQQ-dependent methanol dehydrogenase in intact single bacterial colonies. J Microbiol Methods 2017; 137:46-49. [PMID: 28344084 DOI: 10.1016/j.mimet.2017.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 03/22/2017] [Accepted: 03/22/2017] [Indexed: 11/17/2022]
Abstract
Mechanistic details of methanol oxidation catalyzed by the periplasmically-located pyrroloquinoline quinone-dependent methanol dehydrogenase of methylotrophs can be elucidated using site-directed mutants. Here, we present an in situ colony assay of methanol dehydrogenase, which allows robotic screening of large populations of intact small colonies, and regrowth of colonies for subsequent analysis.
Collapse
Affiliation(s)
- Venkata Ramana Vemuluri
- Department of Bioenergetics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany; Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra 411021, India
| | - Shreya Shaw
- Department of Bioenergetics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Caroline Autenrieth
- Department of Bioenergetics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany
| | - Robin Ghosh
- Department of Bioenergetics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany.
| |
Collapse
|
19
|
Rozeboom HJ, Yu S, Mikkelsen R, Nikolaev I, Mulder HJ, Dijkstra BW. Crystal structure of quinone-dependent alcohol dehydrogenase from P
seudogluconobacter saccharoketogenes
. A versatile dehydrogenase oxidizing alcohols and carbohydrates. Protein Sci 2015; 24:2044-54. [DOI: 10.1002/pro.2818] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 09/30/2015] [Accepted: 10/01/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Henriëtte J. Rozeboom
- Laboratory of Biophysical Chemistry; Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen; Groningen The Netherlands
| | - Shukun Yu
- DuPont Industrial Biosciences; Brabrand, Aarhus Denmark
| | | | - Igor Nikolaev
- DuPont Industrial Biosciences; Leiden The Netherlands
| | | | - Bauke W. Dijkstra
- Laboratory of Biophysical Chemistry; Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen; Groningen The Netherlands
| |
Collapse
|
20
|
Leßmeier L, Wendisch VF. Identification of two mutations increasing the methanol tolerance of Corynebacterium glutamicum. BMC Microbiol 2015; 15:216. [PMID: 26474849 PMCID: PMC4609165 DOI: 10.1186/s12866-015-0558-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 10/08/2015] [Indexed: 11/16/2022] Open
Abstract
Background Methanol is present in most ecosystems and may also occur in industrial applications, e.g. as an impurity of carbon sources such as technical glycerol. Methanol often inhibits growth of bacteria, thus, methanol tolerance may limit fermentative production processes. Results The methanol tolerance of the amino acid producing soil bacterium Corynebacterium glutamicum was improved by experimental evolution in the presence of methanol. The resulting strain Tol1 exhibited significantly increased growth rates in the presence of up to 1 M methanol. However, neither transcriptional changes nor increased enzyme activities of the linear methanol oxidation pathway were observed, which was in accordance with the finding that tolerance to the downstream metabolites formaldehyde and formate was not improved. Genome sequence analysis of strain Tol1 revealed two point mutations potentially relevant to enhanced methanol tolerance: one leading to the amino acid exchange A165T of O-acetylhomoserine sulfhydrolase MetY and the other leading to shortened CoA transferase Cat (Q342*). Introduction of either mutation into the genome of C. glutamicum wild type increased methanol tolerance and introduction of both mutations into C. glutamicum was sufficient to achieve methanol tolerance almost indistinguishable from that of strain Tol1. Conclusion The methanol tolerance of C. glutamicum can be increased by two point mutations leading to amino acid exchange of O-acetylhomoserine sulfhydrolase MetY and shortened CoA transferase Cat. Introduction of these mutations into producer strains may be helpful when using carbon sources containing methanol as component or impurity. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0558-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Lennart Leßmeier
- Genetics of Prokaryotes, Faculty of Biology & Center for Biotechnology, Bielefeld University, Bielefeld, 33615, Germany.
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology & Center for Biotechnology, Bielefeld University, Bielefeld, 33615, Germany.
| |
Collapse
|
21
|
Production of carbon-13-labeled cadaverine by engineered Corynebacterium glutamicum using carbon-13-labeled methanol as co-substrate. Appl Microbiol Biotechnol 2015; 99:10163-76. [PMID: 26276544 DOI: 10.1007/s00253-015-6906-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 07/30/2015] [Accepted: 07/31/2015] [Indexed: 10/23/2022]
Abstract
Methanol, a one-carbon compound, can be utilized by a variety of bacteria and other organisms as carbon and energy source and is regarded as a promising substrate for biotechnological production. In this study, a strain of non-methylotrophic Corynebacterium glutamicum, which was able to produce the polyamide building block cadaverine as non-native product, was engineered for co-utilization of methanol. Expression of the gene encoding NAD+-dependent methanol dehydrogenase (Mdh) from the natural methylotroph Bacillus methanolicus increased methanol oxidation. Deletion of the endogenous aldehyde dehydrogenase genes ald and fadH prevented methanol oxidation to carbon dioxide and formaldehyde detoxification via the linear formaldehyde dissimilation pathway. Heterologous expression of genes for the key enzymes hexulose-6-phosphate synthase and 6-phospho-3-hexuloisomerase of the ribulose monophosphate (RuMP) pathway in this strain restored growth in the presence of methanol or formaldehyde, which suggested efficient formaldehyde detoxification involving RuMP key enzymes. While growth with methanol as sole carbon source was not observed, the fate of 13C-methanol added as co-substrate to sugars was followed and the isotopologue distribution indicated incorporation into central metabolites and in vivo activity of the RuMP pathway. In addition, 13C-label from methanol was traced to the secreted product cadaverine. Thus, this synthetic biology approach led to a C. glutamicum strain that converted the non-natural carbon substrate methanol at least partially to the non-native product cadaverine.
Collapse
|
22
|
Takeda K, Ishida T, Igarashi K, Samejima M, Nakamura N, Ohno H. Effect of amines as activators on the alcohol-oxidizing activity of pyrroloquinoline quinone-dependent quinoprotein alcohol dehydrogenase. Biosci Biotechnol Biochem 2014; 78:1195-8. [PMID: 25229857 DOI: 10.1080/09168451.2014.917265] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Pyrroloquinoline quinone-dependent quinoprotein alcohol dehydrogenases (PQQ-ADH) require ammonia or primary amines as activators in in vitro assays with artificial electron acceptors. We found that PQQ-ADH from Pseudomonas putida KT2440 (PpADH) was activated by various primary amines, di-methylamine, and tri-methylamine. The alcohol oxidation activity of PpADH was strongly enhanced and the affinity for substrates was also improved by pentylamine as an activator.
Collapse
Affiliation(s)
- Kouta Takeda
- a Department of Biotechnology and Life Science , Tokyo University of Agriculture and Technology , Koganei , Japan
| | | | | | | | | | | |
Collapse
|
23
|
Keltjens JT, Pol A, Reimann J, Op den Camp HJM. PQQ-dependent methanol dehydrogenases: rare-earth elements make a difference. Appl Microbiol Biotechnol 2014; 98:6163-83. [PMID: 24816778 DOI: 10.1007/s00253-014-5766-8] [Citation(s) in RCA: 245] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 04/07/2014] [Accepted: 04/08/2014] [Indexed: 01/06/2023]
Abstract
Methanol dehydrogenase (MDH) catalyzes the first step in methanol use by methylotrophic bacteria and the second step in methane conversion by methanotrophs. Gram-negative bacteria possess an MDH with pyrroloquinoline quinone (PQQ) as its catalytic center. This MDH belongs to the broad class of eight-bladed β propeller quinoproteins, which comprise a range of other alcohol and aldehyde dehydrogenases. A well-investigated MDH is the heterotetrameric MxaFI-MDH, which is composed of two large catalytic subunits (MxaF) and two small subunits (MxaI). MxaFI-MDHs bind calcium as a cofactor that assists PQQ in catalysis. Genomic analyses indicated the existence of another MDH distantly related to the MxaFI-MDHs. Recently, several of these so-called XoxF-MDHs have been isolated. XoxF-MDHs described thus far are homodimeric proteins lacking the small subunit and possess a rare-earth element (REE) instead of calcium. The presence of such REE may confer XoxF-MDHs a superior catalytic efficiency. Moreover, XoxF-MDHs are able to oxidize methanol to formate, rather than to formaldehyde as MxaFI-MDHs do. While structures of MxaFI- and XoxF-MDH are conserved, also regarding the binding of PQQ, the accommodation of a REE requires the presence of a specific aspartate residue near the catalytic site. XoxF-MDHs containing such REE-binding motif are abundantly present in genomes of methylotrophic and methanotrophic microorganisms and also in organisms that hitherto are not known for such lifestyle. Moreover, sequence analyses suggest that XoxF-MDHs represent only a small part of putative REE-containing quinoproteins, together covering an unexploited potential of metabolic functions.
Collapse
Affiliation(s)
- Jan T Keltjens
- Department of Microbiology, Institute of Wetland and Water Research, Radboud University Nijmegen, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | | | | | | |
Collapse
|
24
|
Nagaoka H. The application of a cytochrome P450 enzyme eluted from encapsulated biomaterials for the catalysis of enantioselective oxidation. RSC Adv 2014. [DOI: 10.1039/c3ra45936e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
|
25
|
Nagaoka H. Application of a Heme-Binding Protein Eluted from Encapsulated Biomaterials to the Catalysis of Enantioselective Oxidation. ACS Catal 2014. [DOI: 10.1021/cs400768x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hiroyuki Nagaoka
- Sanyo Shokuhin Co., Ltd. R & D, 555-4 Asakura, Maebashi, Gunma 371-0811, Japan
| |
Collapse
|
26
|
Gvozdev AR, Tukhvatullin IA, Gvozdev RI. Quinone-dependent alcohol dehydrogenases and FAD-dependent alcohol oxidases. BIOCHEMISTRY (MOSCOW) 2013; 77:843-56. [PMID: 22860906 DOI: 10.1134/s0006297912080056] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This review considers quinone-dependent alcohol dehydrogenases and FAD-dependent alcohol oxidases, enzymes that are present in numerous methylotrophic eu- and prokaryotes and significantly differ in their primary and quaternary structure. The cofactors of the enzymes are bound to the protein polypeptide chain through ionic and hydrophobic interactions. Microorganisms containing these enzymes are described. Methods for purification of the enzymes, their physicochemical properties, and spatial structures are considered. The supposed mechanism of action and practical application of these enzymes as well as their producers are discussed.
Collapse
Affiliation(s)
- A R Gvozdev
- Biosensor AN Ltd., pr. Akademika Semenova 1, 142432 Chernogolovka, Moscow Region, Russia.
| | | | | |
Collapse
|
27
|
Choi JM, Kang JH, Lee DW, Kim SW, Lee SH. Crystallization and preliminary X-ray crystallographic analysis of MxaJ, a component of the methanol-oxidizing system operon from the marine bacterium Methylophaga aminisulfidivorans MPT. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:902-5. [PMID: 23908039 DOI: 10.1107/s1744309113017983] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 06/29/2013] [Indexed: 11/10/2022]
Abstract
The methanol-oxidizing system (mox) is essential for methylotrophic bacteria to extract energy during the oxidoreduction reaction and consists of a series of electron-transfer proteins encoded by the mox operon. One of the key enzymes is the α₂β₂ methanol dehydrogenase complex (type I MDH), which converts methanol to formaldehyde during the 2e⁻ transfer through the prosthetic group pyrroloquinoline quinone. MxaJ, a product of mxaJ of the mox operon, is a component of the MDH complex and enhances the methanol-converting activity of the MDH complex. However, the exact functional mechanism of MxaJ in the complex is not clearly known. To investigate the functional role of MxaJ in MDH activity, an attempt was made to determine its crystal structure. Diffraction data were collected from a selenomethionine-substituted crystal to 1.92 Å resolution at the peak wavelength. The crystal belonged to the orthorhombic space group P2₁2₁2₁, with unit-cell parameters a = 37.127, b = 63.761, c = 99.246 Å. The asymmetric unit contained one MxaJ molecule with a calculated Matthews coefficient of 2.11 Ų Da⁻¹ and a solvent content of 41.7%. Three-dimensional structure determination of the MxaJ protein is currently in progress by the single-wavelength anomalous dispersion technique and model building.
Collapse
Affiliation(s)
- Jin Myung Choi
- Department of Cellular and Molecular Medicine, Chosun University School of Medicine, Gwangju 501-759, Republic of Korea
| | | | | | | | | |
Collapse
|
28
|
Stampolidis P, Kaderbhai NN, Kaderbhai MA. Presence and role of a second disulphide bond in recombinant lupanine hydroxylase using site-directed mutagenesis with 143Cys→Ser and 124,143Cys→Ser mutations in Escherichia coli. FEMS Microbiol Lett 2012; 334:35-43. [DOI: 10.1111/j.1574-6968.2012.02616.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 05/30/2012] [Accepted: 06/02/2012] [Indexed: 11/30/2022] Open
Affiliation(s)
- Pavlos Stampolidis
- Department of Molecular Biology; Max Planck Institute of Biochemistry; Martinsried; Germany
| | - Naheed N. Kaderbhai
- Institute of Biological, Environmental and Rural Sciences; Aberystwyth University; Aberystwyth; UK
| | | |
Collapse
|
29
|
Nagaoka H, Udagawa K, Kirimura K. Cross-linked protein complex exhibiting asymmetric oxidation activities in the absence of added cofactor. Biotechnol Prog 2012; 28:953-61. [PMID: 22736536 DOI: 10.1002/btpr.1580] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 06/13/2012] [Indexed: 11/12/2022]
Abstract
A protein complex (PC) suspension exhibits asymmetric biooxidation activities in the absence of any added cofactor such as NAD(P)(+) or FAD. It can be extracted from pea protein (PP)-gel (PP encapsulated with Ca(2+) alginate gel and aerated in air for several hours) using hot water by rotary shaking and powdered by the following three steps: (1) forming precipitates from the suspension using 30% (w/v) aqueous (NH(4) )(2) SO(4) , (2) crosslinking the precipitates with 0.25% (v/v) GA, and (3) preparing the cross-linked powder by freeze-drying. The cross-linked PC (CLPC) performed asymmetric oxidation of the toward (R)-isomers of rac-1 and rac-2 in 50 mM glycine-NaOH (pH 9.0) buffer/DMSO cosolvent [2.07% (v/v)] with high enantioselectivity; thus, the (S)-isomers can be obtained in greater than 99% ee from the corresponding rac-p-substituted naphthyl methyl carbinol (rac-1 and rac-2). The CLPC activity was not only competitively inhibited by addition of either 1.0 mM ZnCl(2) or a chelating agent such as 1.0 mM EDTA but also denatured by pretreatments: autoclaving at 121°C (20 min) or using 6.0 M guanidine-HCl containing 50 mM DTT. These results indicated that the PC catalytic process may utilize an electron transfer system incorporating a redox cation (e.g., Fe(2+) ⇄ Fe(3+) or Zn). Therefore, the newly introduced CLPC can asymmetrically oxidize the substrates without the addition of any cofactor resulting in a low-cost organic method. Overall, our results show that the CLPC is an easily prepared, low-cost reagent that can function under mild conditions and afford stereoselectivity, regioselectivity, and substrate specificity.
Collapse
Affiliation(s)
- Hiroyuki Nagaoka
- Sanyo Shokuhin Co., Ltd. R & D, 555-4 Asakura, Maebashi, Gunma 371-0811, Japan.
| | | | | |
Collapse
|
30
|
Choi JM, Kim HG, Kim JS, Youn HS, Eom SH, Yu SL, Kim SW, Lee SH. Purification, crystallization and preliminary X-ray crystallographic analysis of a methanol dehydrogenase from the marine bacterium Methylophaga aminisulfidivorans MP(T). Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:513-6. [PMID: 21505255 DOI: 10.1107/s1744309111006713] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 02/22/2011] [Indexed: 11/10/2022]
Abstract
Methylophaga aminisulfidivorans MP(T) is a marine methylotrophic bacterium that utilizes C(1) compounds such as methanol as a carbon and energy source. The released electron from oxidation flows through a methanol-oxidizing system (MOX) consisting of a series of electron-transfer proteins encoded by the mox operon. One of the key enzymes in the pathway is methanol dehydrogenase (MDH), which contains the prosthetic group pyrroloquinoline quinone (PQQ) and converts methanol to formaldehyde in the periplasm by transferring two electrons from the oxidation of one methanol molecule to the electron acceptor cytochrome c(L). In order to obtain molecular insights into the oxidation mechanism, a native heterotetrameric α(2)β(2) MDH complex was directly purified from M. aminisulfidivorans MP(T) grown in the presence of methanol and crystallized. The crystal diffracted to 1.7 Å resolution and belonged to the monoclinic space group P2(1) (unit-cell parameters a = 63.9, b = 109.5, c = 95.6 Å, β = 100.5°). The asymmetric unit of the crystal contained one heterotetrameric complex, with a calculated Matthews coefficient of 2.24 Å(3) Da(-1) and a solvent content of 45.0%.
Collapse
Affiliation(s)
- Jin Myung Choi
- Department of Cellular and Molecular Medicine, Chosun University School of Medicine, Gwangju 501-759, Republic of Korea
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Li J, Gan JH, Mathews FS, Xia ZX. The enzymatic reaction-induced configuration change of the prosthetic group PQQ of methanol dehydrogenase. Biochem Biophys Res Commun 2011; 406:621-6. [DOI: 10.1016/j.bbrc.2011.02.107] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Accepted: 02/21/2011] [Indexed: 10/18/2022]
|
32
|
Abstract
Whole-cell biocatalysis utilizes native or recombinant enzymes produced by cellular metabolism to perform synthetically interesting reactions. Besides hydrolases, oxidoreductases represent the most applied enzyme class in industry. Oxidoreductases are attributed a high future potential, especially for applications in the chemical and pharmaceutical industries, as they enable highly interesting chemistry (e.g., the selective oxyfunctionalization of unactivated C-H bonds). Redox reactions are characterized by electron transfer steps that often depend on redox cofactors as additional substrates. Their regeneration typically is accomplished via the metabolism of whole-cell catalysts. Traditionally, studies towards productive redox biocatalysis focused on the biocatalytic enzyme, its activity, selectivity, and specificity, and several successful examples of such processes are running commercially. However, redox cofactor regeneration by host metabolism was hardly considered for the optimization of biocatalytic rate, yield, and/or titer. This article reviews molecular mechanisms of oxidoreductases with synthetic potential and the host redox metabolism that fuels biocatalytic reactions with redox equivalents. The tools discussed in this review for investigating redox metabolism provide the basis for studies aiming at a deeper understanding of the interplay between synthetically active enzymes and metabolic networks. The ultimate goal of rational whole-cell biocatalyst engineering and use for fine chemical production is discussed.
Collapse
|
33
|
Schmidt S, Christen P, Kiefer P, Vorholt JA. Functional investigation of methanol dehydrogenase-like protein XoxF in Methylobacterium extorquens AM1. Microbiology (Reading) 2010; 156:2575-2586. [DOI: 10.1099/mic.0.038570-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Methanol dehydrogenase-like protein XoxF of Methylobacterium extorquens AM1 exhibits a sequence identity of 50 % to the catalytic subunit MxaF of periplasmic methanol dehydrogenase in the same organism. The latter has been characterized in detail, identified as a pyrroloquinoline quinone (PQQ)-dependent protein, and shown to be essential for growth in the presence of methanol in this methylotrophic model bacterium. In contrast, the function of XoxF in M. extorquens AM1 has not yet been elucidated, and a phenotype remained to be described for a xoxF mutant. Here, we found that a xoxF mutant is less competitive than the wild-type during colonization of the phyllosphere of Arabidopsis thaliana, indicating a function for XoxF during plant colonization. A comparison of the growth parameters of the M. extorquens AM1 xoxF mutant with those of the wild-type during exponential growth revealed a reduced methanol uptake rate and a reduced growth rate for the xoxF mutant of about 30 %. Experiments with cells starved for carbon revealed that methanol oxidation in the xoxF mutant occurs less rapidly compared with the wild-type, especially in the first minutes after methanol addition. A distinct phenotype for the xoxF mutant was also observed when formate and CO2 production were measured after the addition of methanol or formaldehyde to starved cells. The wild-type, but not the xoxF mutant, accumulated formate upon substrate addition and had a 1 h lag in CO2 production under the experimental conditions. Determination of the kinetic properties of the purified enzyme showed a conversion capacity for both formaldehyde and methanol. The results suggest that XoxF is involved in one-carbon metabolism in M. extorquens AM1.
Collapse
Affiliation(s)
- Sabrina Schmidt
- Institute of Microbiology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Philipp Christen
- Institute of Microbiology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Patrick Kiefer
- Institute of Microbiology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Julia A. Vorholt
- Institute of Microbiology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| |
Collapse
|
34
|
Idupulapati NB, Mainardi DS. Quantum Chemical Modeling of Methanol Oxidation Mechanisms by Methanol Dehydrogenase Enzyme: Effect of Substitution of Calcium by Barium in the Active Site. J Phys Chem A 2010; 114:1887-96. [DOI: 10.1021/jp9083025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nagesh B. Idupulapati
- Institute for Micromanufacturing, Chemical Engineering Program, Louisiana Tech University, Ruston, Louisiana 71272
| | - Daniela S. Mainardi
- Institute for Micromanufacturing, Chemical Engineering Program, Louisiana Tech University, Ruston, Louisiana 71272
| |
Collapse
|
35
|
Hothi P, Sutcliffe M, Scrutton N. Kinetic isotope effects and ligand binding in PQQ-dependent methanol dehydrogenase. Biochem J 2009; 388:123-33. [PMID: 15617516 PMCID: PMC1186700 DOI: 10.1042/bj20041731] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The reaction of PQQ (2,7,9-tricarboxypyrroloquinoline quinone)-dependent MDH (methanol dehydrogenase) from Methylophilus methylotrophus has been studied under steady-state conditions in the presence of an alternative activator [GEE (glycine ethyl ester)] and compared with similar reactions performed with ammonium (used more generally as an activator in steady-state analysis of MDH). Studies of initial velocity with methanol (protiated methanol, C1H3O1H) and [2H]methanol (deuteriated methanol, C2H3O2H) as substrate, performed with different concentrations of GEE and PES (phenazine ethosulphate), indicate competitive binding effects for substrate and PES on the stimulation and inhibition of enzyme activity by GEE. GEE is more effective at stimulating activity than ammonium at low concentrations, suggesting tighter binding of GEE to the active site. Inhibition of activity at high GEE concentration is less pronounced than at high ammonium concentration. This suggests a close spatial relationship between the stimulatory (KS) and inhibitory (KI) binding sites in that binding of GEE to the KS site sterically impairs the binding of GEE to the KI site. The binding of GEE is also competitive with the binding of PES, and GEE is more effective than ammonium in competing with PES. This competitive binding of GEE and PES lowers the effective concentration of PES at the site competent for electron transfer. Accordingly, the oxidative half-reaction, which is second-order with respect to PES concentration, is more rate-limiting in steady-state turnover with GEE than with ammonium. The smaller methanol C-1H/C-2H kinetic isotope effects observed with GEE are consistent with a larger contribution made by the oxidative half-reaction to rate limitation. Cyanide is much less effective at suppressing 'endogenous' activity in the presence of GEE than with ammonium, which is attributed to impaired binding of cyanide to the catalytic site through steric interaction with GEE bound at the KS site. The kinetic model developed previously for reactions of MDH with ammonium [Hothi, Basran, Sutcliffe and Scrutton (2003) Biochemistry 42, 3966-3978] is consistent with data obtained with GEE, although a more detailed structural interpretation is given here. Molecular-modelling studies rationalize the kinetic observations in terms of a complex binding scenario at the molecular level involving two spatially distinct inhibitory sites (KI and KI'). The KI' site caps the entrance to the active site and is interpreted as the PES binding site. The KI site is adjacent to, and, for GEE, overlaps with, the KS site, and is located in the active-site cavity close to the PQQ cofactor and the catalytic site for methanol oxidation.
Collapse
Affiliation(s)
- Parvinder Hothi
- *Department of Biochemistry, University of Leicester, University Road, Leicester LE1 7RH, U.K
| | - Michael J. Sutcliffe
- *Department of Biochemistry, University of Leicester, University Road, Leicester LE1 7RH, U.K
- †Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, U.K
| | - Nigel S. Scrutton
- *Department of Biochemistry, University of Leicester, University Road, Leicester LE1 7RH, U.K
- To whom correspondence should be addressed (email )
| |
Collapse
|
36
|
Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources. PLoS One 2009; 4:e5584. [PMID: 19440302 PMCID: PMC2680597 DOI: 10.1371/journal.pone.0005584] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2009] [Accepted: 03/30/2009] [Indexed: 11/22/2022] Open
Abstract
Background Methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes of two pink-pigmented facultative methylotrophic bacteria of the Alpha-proteobacterial genus Methylobacterium, the reference species Methylobacterium extorquens strain AM1 and the dichloromethane-degrading strain DM4, were compared. Methodology/Principal Findings The 6.88 Mb genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid and three plasmids, while the 6.12 Mb genome of strain DM4 features a 5.94 Mb chromosome and two plasmids. The chromosomes are highly syntenic and share a large majority of genes, while plasmids are mostly strain-specific, with the exception of a 130 kb region of the strain AM1 megaplasmid which is syntenic to a chromosomal region of strain DM4. Both genomes contain large sets of insertion elements, many of them strain-specific, suggesting an important potential for genomic plasticity. Most of the genomic determinants associated with methylotrophy are nearly identical, with two exceptions that illustrate the metabolic and genomic versatility of Methylobacterium. A 126 kb dichloromethane utilization (dcm) gene cluster is essential for the ability of strain DM4 to use DCM as the sole carbon and energy source for growth and is unique to strain DM4. The methylamine utilization (mau) gene cluster is only found in strain AM1, indicating that strain DM4 employs an alternative system for growth with methylamine. The dcm and mau clusters represent two of the chromosomal genomic islands (AM1: 28; DM4: 17) that were defined. The mau cluster is flanked by mobile elements, but the dcm cluster disrupts a gene annotated as chelatase and for which we propose the name “island integration determinant” (iid). Conclusion/Significance These two genome sequences provide a platform for intra- and interspecies genomic comparisons in the genus Methylobacterium, and for investigations of the adaptive mechanisms which allow bacterial lineages to acquire methylotrophic lifestyles.
Collapse
|
37
|
Idupulapati N, Mainardi D. Coordination and binding of ions in Ca2+- and Ba2+-containing methanol dehydrogenase and interactions with methanol. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.01.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
38
|
Mennenga B, Kay CWM, Görisch H. Quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa: the unusual disulfide ring formed by adjacent cysteine residues is essential for efficient electron transfer to cytochrome c 550. Arch Microbiol 2009; 191:361-7. [DOI: 10.1007/s00203-009-0460-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 01/21/2009] [Accepted: 01/26/2009] [Indexed: 10/21/2022]
|
39
|
Idupulapati N, Mainardi D. A DMol3study of the methanol addition–elimination oxidation mechanism by methanol dehydrogenase enzyme. MOLECULAR SIMULATION 2008. [DOI: 10.1080/08927020802235656] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- N.B. Idupulapati
- a Institute for Micromanufacturing, Louisiana Tech University , Ruston, USA
| | - D.S. Mainardi
- b Chemical Engineering Program, Institute for Micromanufacturing, Louisiana Tech University , Ruston, USA
| |
Collapse
|
40
|
Weber S, Bittl R. Studies of Organic Protein Cofactors Using Electron Paramagnetic Resonance. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.2270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
41
|
Kane SR, Chakicherla AY, Chain PSG, Schmidt R, Shin MW, Legler TC, Scow KM, Larimer FW, Lucas SM, Richardson PM, Hristova KR. Whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1. J Bacteriol 2007; 189:1931-45. [PMID: 17158667 PMCID: PMC1855728 DOI: 10.1128/jb.01259-06] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Accepted: 11/29/2006] [Indexed: 11/20/2022] Open
Abstract
Methylibium petroleiphilum PM1 is a methylotroph distinguished by its ability to completely metabolize the fuel oxygenate methyl tert-butyl ether (MTBE). Strain PM1 also degrades aromatic (benzene, toluene, and xylene) and straight-chain (C(5) to C(12)) hydrocarbons present in petroleum products. Whole-genome analysis of PM1 revealed an approximately 4-Mb circular chromosome and an approximately 600-kb megaplasmid, containing 3,831 and 646 genes, respectively. Aromatic hydrocarbon and alkane degradation, metal resistance, and methylotrophy are encoded on the chromosome. The megaplasmid contains an unusual t-RNA island, numerous insertion sequences, and large repeated elements, including a 40-kb region also present on the chromosome and a 29-kb tandem repeat encoding phosphonate transport and cobalamin biosynthesis. The megaplasmid also codes for alkane degradation and was shown to play an essential role in MTBE degradation through plasmid-curing experiments. Discrepancies between the insertion sequence element distribution patterns, the distributions of best BLASTP hits among major phylogenetic groups, and the G+C contents of the chromosome (69.2%) and plasmid (66%), together with comparative genome hybridization experiments, suggest that the plasmid was recently acquired and apparently carries the genetic information responsible for PM1's ability to degrade MTBE. Comparative genomic hybridization analysis with two PM1-like MTBE-degrading environmental isolates (approximately 99% identical 16S rRNA gene sequences) showed that the plasmid was highly conserved (ca. 99% identical), whereas the chromosomes were too diverse to conduct resequencing analysis. PM1's genome sequence provides a foundation for investigating MTBE biodegradation and exploring the genetic regulation of multiple biodegradation pathways in M. petroleiphilum and other MTBE-degrading beta-proteobacteria.
Collapse
Affiliation(s)
- Staci R Kane
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Kay CWM, Mennenga B, Görisch H, Bittl R. Substrate binding in quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa studied by electron-nuclear double resonance. Proc Natl Acad Sci U S A 2006; 103:5267-72. [PMID: 16567634 PMCID: PMC1459345 DOI: 10.1073/pnas.0509667103] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Binding of methanol to the quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa has been studied by pulsed electron-nuclear double resonance at 9 GHz. Shifts in the hyperfine couplings of the pyrroloquinoline quinone radical provide direct evidence for a change in the environment of the cofactor when substrate is present. By performing experiments with deuteriated methanol, we confirmed that methanol was the cause of the effect. Density functional theory calculations show that these shifts can be understood if a water molecule, which is often found in x-ray structures of the active site of quinoprotein alcohol dehydrogenases, is displaced by the substrate. The difference between the binding of water and methanol is that the water molecule forms a hydrogen bond to O5 of pyrroloquinoline quinone, which the methanol, by virtue of its methyl group, does not. The results support the proposal that aspartate rather than glutamate is the catalytically active base for a hydride transfer mechanism in quinoprotein alcohol dehydrogenases.
Collapse
Affiliation(s)
- Christopher W. M. Kay
- *Institut für Experimentalphysik, Fachbereich Physik, Freie Universität, 14195 Berlin, Germany; and
| | - Bina Mennenga
- Fachgebiet Technische Biochemie, Institut für Biotechnologie, Technische Universität, 13353 Berlin, Germany
| | - Helmut Görisch
- Fachgebiet Technische Biochemie, Institut für Biotechnologie, Technische Universität, 13353 Berlin, Germany
| | - Robert Bittl
- *Institut für Experimentalphysik, Fachbereich Physik, Freie Universität, 14195 Berlin, Germany; and
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
43
|
Williams P, Coates L, Mohammed F, Gill R, Erskine P, Bourgeois D, Wood SP, Anthony C, Cooper JB. The 1.6Å X-ray Structure of the Unusual c-type Cytochrome, Cytochrome cL, from the Methylotrophic Bacterium Methylobacterium extorquens. J Mol Biol 2006; 357:151-62. [PMID: 16414073 DOI: 10.1016/j.jmb.2005.12.055] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2005] [Revised: 12/12/2005] [Accepted: 12/14/2005] [Indexed: 10/25/2022]
Abstract
The structure of cytochrome cL from Methylobacterium extorquens has been determined by X-ray crystallography to a resolution of 1.6 A. This unusually large, acidic cytochrome is the physiological electron acceptor for the quinoprotein methanol dehydrogenase in the periplasm of methylotrophic bacteria. Its amino acid sequence is completely different from that of other cytochromes but its X-ray structure reveals a core that is typical of class I cytochromes c, having alpha-helices folded into a compact structure enclosing the single haem c prosthetic group and leaving one edge of the haem exposed. The haem is bound through thioether bonds to Cys65 and Cys68, and the fifth ligand to the haem iron is provided by His69. Remarkably, the sixth ligand is provided by His112, and not by Met109, which had been shown to be the sixth ligand in solution. Cytochrome cL is unusual in having a disulphide bridge that tethers the long C-terminal extension to the body of the structure. The crystal structure reveals that, close to the inner haem propionate, there is tightly bound calcium ion that is likely to be involved in stabilization of the redox potential, and that may be important in the flow of electrons from reduced pyrroloquinoline quinone in methanol dehydrogenase to the haem of cytochrome cL. As predicted, both haem propionates are exposed to solvent, accounting for the unusual influence of pH on the redox potential of this cytochrome.
Collapse
Affiliation(s)
- Paul Williams
- School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Kay CWM, Mennenga B, Görisch H, Bittl R. Structure of the Pyrroloquinoline Quinone Radical in Quinoprotein Ethanol Dehydrogenase. J Biol Chem 2006; 281:1470-6. [PMID: 16267040 DOI: 10.1074/jbc.m511132200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Quinoprotein alcohol dehydrogenases use the pyrroloquinoline quinone (PQQ) cofactor to catalyze the oxidation of alcohols. The catalytic cycle is thought to involve a hydride transfer from the alcohol to the oxidized PQQ, resulting in the generation of aldehyde and reduced PQQ. Reoxidation of the cofactor by cytochrome proceeds in two sequential steps via the PQQ radical. We have used a combination of electron nuclear double resonance and density functional theory to show that the PQQ radical is not protonated at either O-4 or O-5, a result that is at variance with the general presumption of a singly protonated radical. The quantum mechanical calculations also show that reduced PQQ is unlikely to be protonated at O-5; rather, it is either singly protonated at O-4 or not protonated at either O-4 or O-5, a result that also challenges the common assumption of a reduced PQQ protonated at both O-4 and O-5. The reaction cycle of PQQ-dependent alcohol dehydrogenases is revised in light of these findings.
Collapse
Affiliation(s)
- Christopher W M Kay
- Institut für Experimentalphysik, Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany.
| | | | | | | |
Collapse
|
45
|
Toyama H, Chen ZW, Fukumoto M, Adachi O, Matsushita K, Mathews FS. Molecular Cloning and Structural Analysis of Quinohemoprotein Alcohol Dehydrogenase ADH-IIG from Pseudomonas putida HK5. J Mol Biol 2005; 352:91-104. [PMID: 16061256 DOI: 10.1016/j.jmb.2005.06.078] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2005] [Revised: 06/28/2005] [Accepted: 06/28/2005] [Indexed: 11/26/2022]
Abstract
Depending on the alcohols used as growth substrates, Pseudomonas putida HK5 produces two distinct quinohemoprotein alcohol dehydrogenases, ADH-IIB and ADH-IIG, both of which contain pyrroloquinoline quinone (PQQ) and heme c as the prosthetic groups but show different substrate specificities, especially for diol substrates. Molecular cloning of the gene of ADH-IIB and its crystal structure are already reported. Here, molecular cloning of the gene, qgdA, and solution of the three-dimensional structure of ADH-IIG are reported. The enzyme consists of 718 amino acid residues including a signal sequence of 29 amino acid residues. The PQQ domain is highly homologous to other quinoproteins, especially to quinohemoproteins. The crystal structure of ADH-IIG, determined at 2.2A resolution, shows that the overall structure and the amino acid residues involved in PQQ binding are quite similar to ADH-IIB and to another quinohemoprotein ADH, qhEDH from Comamonas testosteroni. However, the lengths of the linker regions connecting the PQQ and the cytochrome domains are different from each other, leading to a significant difference in orientation of the cytochrome domain with respect to the PQQ domain. Apart from ADH-IIB and qhEDH, ADH-IIG has an extra 12-residue helix within loop 3 in the PQQ domain and an extra 3(10) helix in the C terminus of the cytochrome domain, and both helices appear parallel and linked by a hydrogen bond. The amino acid residues contacting substrate/product in the crystal structures are also different among them. In the crystal structure of ADH-IIG with 1,2-propanediol, one of the hydroxyl groups of the substrate forms a hydrogen bond with O5 of PQQ and OD1 of Asp300, and the other interacts with a water molecule and with NE2 of Trp386, the corresponding residue of which is not found in ADH-IIB and qhEDH, and might be the residue responsible for making ADH-IIG prefer diol substrates.
Collapse
Affiliation(s)
- Hirohide Toyama
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi 753-8515, Japan.
| | | | | | | | | | | |
Collapse
|
46
|
Kay CWM, Mennenga B, Görisch H, Bittl R. Substrate-Binding in Quinoprotein Ethanol Dehydrogenase from Pseudomonas aeruginosa Studied by Electron Paramagnetic Resonance at 94 GHz. J Am Chem Soc 2005; 127:7974-5. [PMID: 15926796 DOI: 10.1021/ja050972c] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pyrroloquinoline quinone (2,7,9-tricarboxypyrroloquinoline quinone, PQQ) is one of several quinone cofactors that is utilized in a class of dehydrogenases known as quinoproteins. In this contribution, we have used continuous-wave high-field/high-frequency electron paramagnetic resonance (EPR) at 94 GHz (W-band) to study substrate binding in ethanol dehydrogenase (QEDH) from Pseudomonas aeruginosa, taking advantage of the fact that the enzyme is isolated with a substantial proportion of the PQQ cofactor in the paramagnetic semiquinone form. In the substrate-free enzyme, the principal values of the g-tensor, obtained by spectral simulation are: gx = 2.00585(2), gy = 2.00518(2), and gz = 2.00212(2), giving giso = 2.00438(2). All three principal values of the g-tensor decrease when ethanol is bound to the protein: gx = 2.00574(2), gy = 2.00511(2), and gz = 2.00207(2), giving giso = 2.00431(2). The results represent the first direct evidence for the tight binding of an alcohol to a PQQ-dependent alcohol dehydrogenase and show that ethanol also binds to the enzyme even when the PQQ cofactor is in the semiquinone form. The decrease in g is consistent with an increase in polarity in the immediate vicinity of the PQQ cofactor and probably reflects a changed geometry of the PQQ-Ca2+ complex when ethanol binds.
Collapse
Affiliation(s)
- Christopher W M Kay
- Institut für Experimentalphysik, Fachbereich Physik, Freie Universität Berlin, 14195 Berlin, Germany
| | | | | | | |
Collapse
|
47
|
Reddy SY, Bruice TC. Determination of enzyme mechanisms by molecular dynamics: studies on quinoproteins, methanol dehydrogenase, and soluble glucose dehydrogenase. Protein Sci 2005; 13:1965-78. [PMID: 15273299 PMCID: PMC2279812 DOI: 10.1110/ps.04673404] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Molecular dynamics (MD) simulations have been carried out to study the enzymatic mechanisms of quinoproteins, methanol dehydrogenase (MDH), and soluble glucose dehydrogenase (sGDH). The mechanisms of reduction of the orthoquinone cofactor (PQQ) of MDH and sGDH involve concerted base-catalyzed proton abstraction from the hydroxyl moiety of methanol or from the 1-hydroxyl of glucose, and hydride equivalent transfer from the substrate to the quinone carbonyl carbon C5 of PQQ. The products of methanol and glucose oxidation are formaldehyde and glucolactone, respectively. The immediate product of PQQ reduction, PQQH- [-HC5(O-)-C4(=O)-] and PQQH [-HC5(OH)-C4(=O)-] converts to the hydroquinone PQQH2 [-C5(OH)=C4(OH)-]. The main focus is on MD structures of MDH * PQQ * methanol, MDH * PQQH-, MDH * PQQH, sGDH * PQQ * glucose, sGDH * PQQH- (glucolactone, and sGDH * PQQH. The reaction PQQ-->PQQH- occurs with Glu 171-CO2- and His 144-Im as the base species in MDH and sGDH, respectively. The general-base-catalyzed hydroxyl proton abstraction from substrate concerted with hydride transfer to the C5 of PQQ is assisted by hydrogen-bonding to the C5=O by Wat1 and Arg 324 in MDH and by Wat89 and Arg 228 in sGDH. Asp 297-COOH would act as a proton donor for the reaction PQQH(-)-->PQQH, if formed by transfer of the proton from Glu 171-COOH to Asp 297-CO2- in MDH. For PQQH-->PQQH2, migration of H5 to the C4 oxygen may be assisted by a weak base like water (either by crystal water Wat97 or bulk solvent, hydrogen-bonded to Glu 171-CO2- in MDH and by Wat89 in sGDH).
Collapse
Affiliation(s)
- Swarnalatha Y Reddy
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| | | |
Collapse
|
48
|
Reddy SY, Bruice TC. Mechanisms of ammonia activation and ammonium ion inhibition of quinoprotein methanol dehydrogenase: a computational approach. Proc Natl Acad Sci U S A 2004; 101:15887-92. [PMID: 15520392 PMCID: PMC528780 DOI: 10.1073/pnas.0407209101] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mechanism of methanol oxidation by quinoprotein methanol dehydrogenase (MDH.PQQ) in combination with methanol (MDH.PQQ.methanol) involves Glu-171--CO2(-) general base removal of the hydroxyl proton of methanol in concert with hydride equivalent transfer to the >C5=O quinone carbon of pyrroloquinoline quinone (PQQ) and rearrangement to hydroquinone (PQQH2) with release of formaldehyde. Molecular dynamics (MD) studies of the structures of MDH.PQQ.methanol in the presence of activator NH3 and inhibitor NH4(+) have been carried out. In the MD structure of MDH.PQQ.methanol.NH3, the hydrated NH3 resides at a distance of approximately 24 A away from methanol and the ortho-quinone portion of PQQ. As such, influence of NH3 on the oxidation reaction is not probable. We find that NH4(+) competes with the substrate by hydrogen-bonding to Glu-171CO2(-) such that the MDH.PQQ.methanol.NH4(+) complex is not reactive. Ammonia readily forms imines with quinone. Imines are present in solution as neutral (>C5=NH) and protonated (>C5=NH2(+)) species. MD simulations establish that the >C5=NH2(+) derivative of MDH.PQQ(NH2(+).methanol structure is unreactive because of the nonproductive means of methanol binding. The structure obtained by the MD simulations with the neutral >C5=NH imine of MDH.PQQ(NH).methanol structure is similar to the reactive MDH.PQQ.methanol complex. This active site geometry allows for catalysis of hydride equivalent transfer to the >C5=NH of PQQ(NH) by concerted Glu-171CO(2)(-) general-base removal of the H-OCH3 proton and Arg-324H+ general-acid proton transfer to the imine nitrogen. Enzyme-bound <C5(H)NH2 derivative of PQQ [PQQ(NH)] and CH(2)O product are formed.
Collapse
Affiliation(s)
- Swarnalatha Y Reddy
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA
| | | |
Collapse
|
49
|
Anthony C. The quinoprotein dehydrogenases for methanol and glucose. Arch Biochem Biophys 2004; 428:2-9. [PMID: 15234264 DOI: 10.1016/j.abb.2004.03.038] [Citation(s) in RCA: 135] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2004] [Revised: 03/19/2004] [Indexed: 11/29/2022]
Abstract
This review summarises our current understanding of two of the main types of quinoprotein dehydrogenase in which pyrroloquinoline quinone (PQQ) is the only prosthetic group. These are the soluble methanol dehydrogenase and the membrane glucose dehydrogenase (mGDH). The membrane GDH has an additional N-terminal domain by which it is tightly anchored to the membrane, and a periplasmic domain whose structure has been modelled on the X-ray structure of the alpha-subunit of MDH which contains PQQ in the active site. This review discusses their structures and mechanisms, concentrating particularly on the pathways for electron transfer from the reduced PQQ, through the protein, to their electron acceptors. In MDH, this is the specific cytochrome c(L), the electron transfer pathway probably involving the unique disulphide ring in the active site. By contrast, mGDH contains a permanently bound ubiquinone, which acts as a single electron carrier, mediating electron transfer through the protein to the membrane ubiquinone.
Collapse
Affiliation(s)
- Christopher Anthony
- School of Biological Sciences, University of Southampton, Southampton SO16 7PX, UK.
| |
Collapse
|
50
|
Miyanaga A, Koseki T, Matsuzawa H, Wakagi T, Shoun H, Fushinobu S. Crystal structure of a family 54 alpha-L-arabinofuranosidase reveals a novel carbohydrate-binding module that can bind arabinose. J Biol Chem 2004; 279:44907-14. [PMID: 15292273 DOI: 10.1074/jbc.m405390200] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
As the first known structures of a glycoside hydrolase family 54 (GH54) enzyme, we determined the crystal structures of free and arabinose-complex forms of Aspergillus kawachii IFO4308 alpha-l-arabinofuranosidase (AkAbfB). AkAbfB comprises two domains: a catalytic domain and an arabinose-binding domain (ABD). The catalytic domain has a beta-sandwich fold similar to those of clan-B glycoside hydrolases. ABD has a beta-trefoil fold similar to that of carbohydrate-binding module (CBM) family 13. However, ABD shows a number of characteristics distinctive from those of CBM family 13, suggesting that it could be classified into a new CBM family. In the arabinose-complex structure, one of three arabinofuranose molecules is bound to the catalytic domain through many interactions. Interestingly, a disulfide bond formed between two adjacent cysteine residues recognized the arabinofuranose molecule in the active site. From the location of this arabinofuranose and the results of a mutational study, the nucleophile and acid/base residues were determined to be Glu(221) and Asp(297), respectively. The other two arabinofuranose molecules are bound to ABD. The O-1 atoms of the two arabinofuranose molecules bound at ABD are both pointed toward the solvent, indicating that these sites can both accommodate an arabinofuranose side-chain moiety linked to decorated arabinoxylans.
Collapse
Affiliation(s)
- Akimasa Miyanaga
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | | | | | | | | | | |
Collapse
|