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- The crystal structure of methanol dehydrogenase, a quinoprotein from the marine methylotrophic bacterium Methylophaga aminisulfidivorans MPT
- Thinh-Phat Cao , Jin Myung Choi , Si Wouk Kim , Sung Haeng Lee
- J. Microbiol. 2018;56(4):246-254. Published online February 28, 2018
- DOI: https://doi.org/10.1007/s12275-018-7483-y
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- 13 Crossref
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Abstract
- The first crystal structure of a pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH) from a marine methylotrophic bacterium, Methylophaga aminisulfidivorans MPT (MDHMas), was determined at 1.7 Å resolution. The active form of MDHMas (or MDHIMas) is a heterotetrameric α2β2, where each β-subunit assembles on one side of each of the α-subunits, in a symmetrical fashion, so that two β-subunits surround the two PQQ-binding pockets on the α-subunits. The active site consists of a PQQ molecule surrounded by a β-propeller fold for each α-subunit. Interestingly, the PQQ molecules are coordinated by a Mg2+ ion, instead of the Ca2+ ion that is commonly found in the terrestrial MDHI, indicating the efficiency of osmotic balance regulation in the high salt environment. The overall interaction of the β-subunits with the α-subunits appears tighter than that of terrestrial homologues, suggesting the efficient maintenance of MDHIMas integrity in the sea water environment to provide a firm basis for complex formation with MxaJMas or Cyt cL. With the help of the features mentioned above, our research may enable the elucidation of the full molecular mechanism of methanol oxidation by taking advantage of marine bacterium-originated proteins in the methanol oxidizing system (mox), including MxaJ, as the attainment of these proteins from terrestrial bacteria for structural studies has not been successful.
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Citations
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- Computational insights into the molecular dynamics of the binding of ligands in the methanol dehydrogenase
One-Sun Lee, Sung Haeng Lee
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Emily R. Featherston, Joseph A. Cotruvo
Biochimica et Biophysica Acta (BBA) - Molecular Cell Research.2021; 1868(1): 118864. CrossRef - Bioinorganic insights of the PQQ-dependent alcohol dehydrogenases
Pedro D. Sarmiento-Pavía, Martha E. Sosa-Torres
JBIC Journal of Biological Inorganic Chemistry.2021; 26(2-3): 177. CrossRef - Bioinformatic analysis of subfamily-specific regions in 3D-structures of homologs to study functional diversity and conformational plasticity in protein superfamilies
Daria Timonina, Yana Sharapova, Vytas Švedas, Dmitry Suplatov
Computational and Structural Biotechnology Journal.2021; 19: 1302. CrossRef - Methanol Dehydrogenases as a Key Biocatalysts for Synthetic Methylotrophy
Thien-Kim Le, Yu-Jin Lee, Gui Hwan Han, Soo-Jin Yeom
Frontiers in Bioengineering and Biotechnology.2021;[Epub] CrossRef - Lanthanide-dependent alcohol dehydrogenases require an essential aspartate residue for metal coordination and enzymatic function
Nathan M. Good, Matthias Fellner, Kemal Demirer, Jian Hu, Robert P. Hausinger, N. Cecilia Martinez-Gomez
Journal of Biological Chemistry.2020; 295(24): 8272. CrossRef - Zebra2: advanced and easy-to-use web-server for bioinformatic analysis of subfamily-specific and conserved positions in diverse protein superfamilies
Dmitry Suplatov, Yana Sharapova, Elizaveta Geraseva, Vytas Švedas
Nucleic Acids Research.2020; 48(W1): W65. CrossRef - Biological Pincer Complexes
Jorge L. Nevarez, Aiko Turmo, Jian Hu, Robert P. Hausinger
ChemCatChem.2020; 12(17): 4242. CrossRef - Crystal structure of Cytochrome cL from the aquatic methylotrophic bacterium Methylophaga aminisulfidivorans MPT
Suparna Ghosh, Immanuel Dhanasingh, Jaewon Ryu, Si Wouk Kim, Sung Haeng Lee
Journal of Microbiology and Biotechnology.2020; 30(8): 1261. CrossRef - New metal cofactors and recent metallocofactor insights
Robert P Hausinger
Current Opinion in Structural Biology.2019; 59: 1. CrossRef - Lanthanides‐based catalysis in eukaryotes
Giovanna De Simone, Fabio Polticelli, Silvio Aime, Paolo Ascenzi
IUBMB Life.2018; 70(11): 1067. CrossRef
- Computational insights into the molecular dynamics of the binding of ligands in the methanol dehydrogenase
Research Support, Non-U.S. Gov't
- Characterization of Methylophaga sp. strain SK1 Cytochrome cL Expressed in Escherichia coli
- Hee Gon Kim , Trong Nhat Phan , Tae Sa Jang , Moonjoo Koh , Si Wouk Kim
- J. Microbiol. 2005;43(6):499-502.
- DOI: https://doi.org/2299 [pii]
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Abstract
- Methylophaga sp. strain SK1 is a new restricted facultative methanol-oxidizing bacterium that was isolated from seawater. The aim of this study was to characterize the electron carriers involved in the methanol oxidation process in Methylophaga sp. strain SK1. The gene encoding cytochrome cL (mxaG) was cloned and the recombinant gene was expressed in Escherichia coli DH5 under strict anaerobic conditions. The recombinant cytochrome cL had the same molecular weight and absorption spectra as the wild-type cytochrome cL both in the reduced and oxidized forms. The electron flow rate from methanol dehydrogenase (MDH) to the recombinant cytochrome cL was similar to that from MDH to the wild-type cytochrome cL. These results suggest that recombinant cytochrome cL acts as a physiological primary electron acceptor for MDH.
- Effect of copper on the growth and methanol dehydrogenase activity of methylobacillusd sp. strain SK1 DSM 8269
- Kim, Si W. , Kim, Young M.
- J. Microbiol. 1996;34(2):172-178.
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Abstract
- Methylobacillus sp. strain SK1, which grows only on methanol, was found to grow in the absence of added copper. The doubling time (t_d = 1.3 h) of the bacterium growing at the exponential growth phase at 30℃ in the absence of copper was the same as that of the cell growing in the presence of copper. The bacterium growing after the exponential phase in the absence of copper, however, grew faster than the cell growing in the presence of copper. Cells harvested after thee early stationary phase in the presence of copper were found to exhibit no methanol dehydrogenase (MDH) activity, but the amount and subunit structure of the enzyme in the cells were almost the same as that in cells harboring active MDH. Pellets of the cells harvested after the early stationary phase in the presence of copper were pale green. Cell-free extracts prepared from cells harvested at the early stationary phase in the presence of copper were pink and exhibited MDH activity, but it turned dark-green rapidly from the surface under air. The green-colored portions of the extracts showed no MDH activity and contained c-type cytochromes that were oxidized completely. The inactive MDH activity and contained c-type cytochromes that were oxidized completely. The inactive MDH proteins in the green portions were found to have antigenic sites identical to those of the active one as the inactive MDHs in cells grown in the presence of copper. The bacterium was found to accumulate copper actively during the exponential growth phase. MDH prepared from cells grown in the presence or absence of copper was found to be more stable under nitrogen gas than under air. Methanol at 10 mM was found to enhance the stability of the MDH under air.
- Kinetic and spectral investigations on Ca^2+ and Sr^2+ containing methanol dehydrogenases
- Kim, Si Wouk , Kim, Chung, Sung , Lee, Jung Sup , Koh, Moon Joo , Yang, Song Suk , Duine, Johannis A. , Kim, Young Min
- J. Microbiol. 1997;35(3):200-205.
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Abstract
- Both Ca^2+ and Sr^2+ containing methanol dehydrogenases (MDH) were purified to homogeneity with yields of 48% and 42%, respectively, from Methylabacillus methanolovorus sp. strain SK5. Most of the biochemical and structural properties were similar to each other. However, some differences were found: (1) although the overall shape of the absorption spectrum of Sr^2+ MDH was very similar to that of Ca^2+ MDH, the absorption intensity originating from the cofactor in Sr^2+. MDH was higher than that in Ca^2+-MDH. Small blue shift of the maximum was also observed. These are probably due to a difference in redox state of the cofactors in Ca^2+ and Sr^2+ -MDH; (2)Sr^2+ -MDH was more heat-stable than Ca^2+-MDH above 56℃; (3) the V_max values for the methanol-dependent activities of Sr^2+ Ca^2+ -MDH in the presence of 3 mM KCN were 2.038 and 808 nmol/mg protein/min, respectively. In addition, the K_m values of Sr^2+ and Ca^2+ MDH for methanol were 12 and 21 uM, respectively; (4) the endogenous activity of Ca^2+ -MDH was more sensitive than that of Sr^2+ -MDH in the presence of cyanide; (5) Diethyl pyrocarbonate treatment increased the enzyme activities of Ca^2+ and Sr^2+ MDH 4.2 and 1.4 folds, respectively. These results indicate that Sr^2+ stabilizes the structural conformation and enhances the activity of MDH more than Ca^2+.
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