Crystal Structure of Cytochrome c(L) from the Aquatic Methylotrophic Bacterium Methylophaga aminisulfidivorans MP(T)

Cytochrome c(L) (Cytc(L)) 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 Cytc(L) 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 Cytc(L) from the aquatic methylotrophic bacterium Methylophaga aminisulfidivorans MP(T) at 2.13 Å resolution. The crystal structure of Ma-Cytc(L) 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 Fe(2+) 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-Cytc(L), along with the structural information of MDH, led us to hypothesize the need for an adapter protein bridging MDH to Cytc(L) 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.