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      KCI등재 SCIE SCOPUS

      The crystal structure of methanol dehydrogenase, a quinoprotein from the marine methylotrophic bacterium Methylophaga aminisulfidivorans MPT

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      https://www.riss.kr/link?id=A106056283

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      다국어 초록 (Multilingual 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...

      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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      참고문헌 (Reference)

      1 Marion, G.M., "pH of seawater" 126 : 89-96, 2011

      2 Suplatov, D., "Zebra: A web server for bioinformatic analysis of diverse protein families" 32 : 1752-1758, 2013

      3 Xia, Z.X., "X-ray structure of methanol dehydrogenase from Paracoccus denitrificans and molecular modeling of its interactions with cytochrome c-551i" 8 : 843-854, 2003

      4 Anthony, C., "The structure and function of methanol dehydrogenase and related quinoproteins containing pyrrolo-quinoline quinone" 304 : 665-674, 1994

      5 Ghosh, M., "The refined structure of the quinoprotein methanol dehydrogenase from Methylobacterium extorquens at 1.94 A" 15 : 177-187, 1995

      6 Culkin, F., "The major constituents of sea water;Chemical oceanography" First Academic Press 121-161, 1965

      7 Halevy, I., "The geologic history of seawater pH" 355 : 1069-1071, 2017

      8 Li, J., "The enzymatic reaction-induced configuration change of the prosthetic group PQQ of methanol dehydrogenase" 406 : 621-626, 2011

      9 Williams, P.A., "The atomic resolution structure of methanol dehydrogenase from Methylobacterium extorquens" 61 : 75-79, 2004

      10 Blake, C.C.F., "The active site of methanol dehydrogenase contains a disulphide bridge between adjacent cysteine residues" 1 : 102-105, 1994

      1 Marion, G.M., "pH of seawater" 126 : 89-96, 2011

      2 Suplatov, D., "Zebra: A web server for bioinformatic analysis of diverse protein families" 32 : 1752-1758, 2013

      3 Xia, Z.X., "X-ray structure of methanol dehydrogenase from Paracoccus denitrificans and molecular modeling of its interactions with cytochrome c-551i" 8 : 843-854, 2003

      4 Anthony, C., "The structure and function of methanol dehydrogenase and related quinoproteins containing pyrrolo-quinoline quinone" 304 : 665-674, 1994

      5 Ghosh, M., "The refined structure of the quinoprotein methanol dehydrogenase from Methylobacterium extorquens at 1.94 A" 15 : 177-187, 1995

      6 Culkin, F., "The major constituents of sea water;Chemical oceanography" First Academic Press 121-161, 1965

      7 Halevy, I., "The geologic history of seawater pH" 355 : 1069-1071, 2017

      8 Li, J., "The enzymatic reaction-induced configuration change of the prosthetic group PQQ of methanol dehydrogenase" 406 : 621-626, 2011

      9 Williams, P.A., "The atomic resolution structure of methanol dehydrogenase from Methylobacterium extorquens" 61 : 75-79, 2004

      10 Blake, C.C.F., "The active site of methanol dehydrogenase contains a disulphide bridge between adjacent cysteine residues" 1 : 102-105, 1994

      11 Culpepper, M.A., "Structure and protein-protein interactions of methanol dehydrogenase from Methylococcus capsulatus (Bath)" 53 : 6211-6219, 2014

      12 Haynes, C.A., "Rethinking biological activation of methane and conversion to liquid fuels" 10 : 331-339, 2014

      13 Harris, T.K., "Replacement of enzymebound calcium with strontium alters the kinetic properties of methanol dehydrogenase" 300 : 175-182, 1994

      14 Murshudov, G.N., "Refinement of macromolecular structures by the maximum-likelihood method" 53 : 240-255, 1997

      15 Pol, A., "Rare earth metals are essential for methanotrophic life in volcanic mudpots" 16 : 255-264, 2014

      16 Anthony, C., "Quinoprotein-catalysed reactions" 320 : 697-711, 1996

      17 Choi, J.M., "Purification, crystallization and preliminary X-ray crystallographic analysis of a methanol dehydrogenase from the marine bacterium Methylophaga aminisulfidivorans MPT" 67 : 513-516, 2011

      18 Kester, D.R., "Preparation of artificial seawater" 12 : 176-179, 1967

      19 Olsson, M.H.M., "PROPKA3 consistent treatment of internal and surface residues in empirical pKa predictions" 7 : 525-537, 2011

      20 Archer, D., "Ocean methane hydrates as a slow tipping point in the global carbon cycle" 106 : 20596-20601, 2008

      21 Choi, J.M., "MxaJ structure reveals a periplasmic binding protein-like architecture with unique secondary structural elements" 85 : 1379-1386, 2017

      22 Edgar, R.C, "Muscle multiple sequence alignment with high accuracy and high throughput" 32 : 1792-1797, 2004

      23 Chen, V.B., "Molprobity: All-atom structure validation for macromolecular crystallography" 66 : 12-21, 2009

      24 Abergel, C., "Molecular replacement: Tricks and treats" 69 : 2167-2173, 2013

      25 Kim, H.G., "Methylophaga aminisulfidivorans sp. nov., a restricted facultatively methylotrophic marine bacterium" 57 : 2096-2101, 2007

      26 Spanning, R.J.M.V., "Isolation and characterization of the moxJ, moxG, moxI, and moxR genes of Paracoccus denitrificans: Inactivation of moxJ, moxG, and moxR and the resultant effect on methylotrophic growth" 173 : 6948-6961, 1991

      27 Altschul, S.F., "Gapped BLAST and PSIBLAST: A new generation of protein database search programs" 25 : 3389-3402, 1997

      28 Emsley, P., "Features and development of Coot" 66 : 486-501, 2010

      29 Baker, N.A., "Electrostatics of nanosystems: Application to microtubules and the ribosome" 98 : 10037-10041, 2001

      30 Xia, Z.X., "Determination of the gene sequence and the three-dimensional structure at 2.4 angstroms resolution of methanol dehydrogenase from Methylophilus W3A1" 259 : 480-501, 1996

      31 Nojiri, M., "Crystal structures of cytochrome cL and methanol dehydrogenase from Hyphomicrobium denitrificans: Structural and mechanistic insights into interactions between the two proteins" 45 : 3481-3492, 2006

      32 Zheng, Y.J., "Conformation of coenzyme pyrroloquinoline quinone and role of $Ca^{2+}$ in the catalytic mechanism of quinoprotein methanol dehydrogenase" 94 : 11881-11886, 1997

      33 Kim, H.G., "Comparative analysis of two types of methanol dehydrogenase from Methylophaga aminisulfidivorans MPT grown on methanol" 52 : 141-149, 2012

      34 Suplatov, D., "Bioinformatic analysis of protein families for identification of variable amino acid residues responsible for functional diversity" 32 : 75-87, 2013

      35 Anthony, C., "Bacterial oxidation of methane and methanol" 27 : 113-210, 1986

      36 Echols, N., "Automating crystallographic structure solution and refinement of protein-ligand complexes" 70 : 144-154, 2013

      37 Knittel, K., "Anaerobic oxidation of methane: Progress with an unknown process" 63 : 311-334, 2009

      38 Heldal, M., "$Mg^{2+}$ as an indicator of nutritional status in marine bacteria" 6 : 524-530, 2011

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