Crystal Structure of Cytochrome cL from the Aquatic Methylotrophic Bacterium Methylophaga aminisulfidivorans MPT
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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.
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.
참고문헌 (39)
- Anthony C, "Bacterial oxidation of methane and methanol", Adv. Microb. Physiol, 27, pp.113~210 (1986)
- Pang B, "Eco-friendly phenol-urea-formaldehyde Co-condensed resin adhesives accelerated by resorcinol for plywood manufacturing", ACS Omega, 3, pp.8521~8528 (2018)
- Anderson DJ, "The moxFG region encodes four polypeptides in the methanol-oxidizing bacterium Methylobacterium sp. strain AM1", J. Bacteriol., 170, pp.2254~2262 (1988)
- Anthony C, "Quinoprotein-catalysed reactions", Biochem. J., 320(Pt 3), pp.697~711 (1996)
- Anthony C, "The c-type cytochromes of methylotrophic bacteria", Biochim. Biophys. Acta, 1099, pp.1~15 (1992)
- Nojiri M, "Crystal structures of cytochrome c(L)and methanol dehydrogenase from Hyphomicrobium denitrificans : structural and mechanistic insights into interactions between the two proteins", Biochemistry, 45, pp.3481~3492 (2006)
- Williams P, "The 1.6A X-ray structure of the unusual c-type cytochrome, cytochrome cL, from the methylotrophic bacterium Methylobacterium extorquens", J. Mol. Biol., 357, pp.151~162 (2006)
- Anthony C, "The quinoprotein dehydrogenases for methanol and glucose", Arch. Biochem. Biophys, 428, pp.2~9 (2004)
- Afolabi PR, "Site-directed mutagenesis and X-ray crystallography of the PQQ-containing quinoprotein methanol dehydrogenase and its electron acceptor, cytochrome c(L)", Biochemistry, 40, pp.9799~9809 (2001)
- Dales SL, "The interaction of methanol dehydrogenase and its cytochrome electron acceptor", Biochem. J., 312(Pt 1), pp.261~265 (1995)
- Moser CC, "Tunneling in PSII", Photochem. Photobiol. Sci, 4, pp.933~939 (2005)
- Myung Choi J, "MxaJ structure reveals a periplasmic binding protein-like architecture with unique secondary structural elements", Proteins, 85, pp.1379~1386 (2017)
- Choi JM, "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, 69, pp.902~905 (2013)
- Kim HG, "Methylophaga aminisulfidivorans sp. nov., a restricted facultatively methylotrophic marine bacterium", Int. J. Syst. Evol. Microbiol., 57, pp.2096~2101 (2007)
- Kim HG, "Comparative analysis of two types of methanol dehydrogenase from Methylophaga aminisulfidivorans MPT grown on methanol", J. Basic Microbiol, 52, pp.141~149 (2012)
- Thinh-Phat Cao, "The crystal structure of methanol dehydrogenase, a quinoprotein from the marine methylotrophic bacterium Methylophaga aminisulfidivorans MPT", The Journal of Microbiology, 56(4), pp.246~254 (2018), 한국미생물학회[DOI]
- Choi JM, "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, 67, pp.513~516 (2011)
- Williams PA, "The atomic resolution structure of methanol dehydrogenase from Methylobacterium extorquens", Acta. Crystallogr. D Biol. Crystallogr, 61, pp.75~79 (2005)
- Ghosh M, "The refined structure of the quinoprotein methanol dehydrogenase from Methylobacterium extorquens at 1. 94 A", Structure, 3, pp.177~187 (1995)
- Heldal M, "Mg2+ as an indicator of nutritional status in marine bacteria", ISME J, 6, pp.524~530 (2012)
- Chen L, "Structure of an electron transfer complex : methylamine dehydrogenase, amicyanin, and cytochrome c551i", Science, 264, pp.86~90 (1994)
- Barr I, "Pyridine hemochromagen assay for determining the concentration of heme in purified protein solutions", Bio Protoc, 5, pp.e1594~ (2015)
- Bunkoczi G, "Phaser. MRage: automated molecular replacement", Acta Crystallogr. D Biol. Crystallogr., 69, pp.2276~2286 (2013)
- Emsley P, "Features and development of Coot", Acta Crystallogr. D Biol. Crystallogr, 66, pp.486~501 (2010)
- Emsley P, "Coot : model-building tools for molecular graphics", Acta Crystallogr. D Biol. Crystallogr, 60, pp.2126~2132 (2004)
- Murshudov GN, "REFMAC5 for the refinement of macromolecular crystal structures", Acta Crystallogr. D Biol. Crystallogr, 67, pp.355~367 (2011)
- Headd JJ, "Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution", Acta Crystallogr. D Biol. Crystallogr, 68, pp.381~390 (2012)
- Afonine PV, "Joint X-ray and neutron refinement with phenix.refine", Acta Crystallogr. D Biol. Crystallogr, 66, pp.1153~1163 (2010)
- Davis IW, "MolProbity : all-atom contacts and structure validation for proteins and nucleic acids", Nucleic Acids Res, 35, pp.W375~W383 (2007)
- Almagro Armenteros JJ, "SignalP 5. 0 improves signal peptide predictions using deep neural networks. Nat", Biotechnol, 37, pp.420~423 (2019)
- Schallenberger MA, "Type I signal peptidase and protein secretion in Staphylococcus aureus", J. Bacteriol, 194, pp.2677~2686 (2012)
- Falk JE, "Bond structure in haem compounds", Enzymologia, 32, pp.3~12 (1967)
- Berry EA, "Simultaneous determination of hemes a, b, and c from pyridine hemochrome spectra", Anal. Biochem, 161, pp.1~15 (1987)
- Simonneaux G, "Mechanism of electron transfer in heme proteins and models : the NMR approach", Chem. Rev, 105, pp.2627~2646 (2005)
- Takano T, "Redox conformation changes in refined tuna cytochrome c", Proc. Natl. Acad. Sci. USA, 77, pp.6371~6375 (1980)
- Sigel H, "Metal Ions in Biological Systems: Vol. 17 Calcium and its Role in Biology", pp.89~92 (1984), CRC Press
- Dahlquist FW, "Role of calcium in the thermal stability of thermolysin", Biochemistry, 15, pp.1103~1111 (1976)
- Van Spanning RJ, "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", J. Bacteriol, 173, pp.6948~6961 (1991)
- Chistoserdov AY, "Genetic organization of the mau gene cluster in Methylobacterium extorquens AM1 : complete nucleotide sequence and generation and characteristics of mau mutants", J. Bacteriol, 176, pp.4052~4065 (1994)