Structural and Mechanistic Basis of the Central Energy-Converting Methyltransferase Complex of Methanogenesis

Methanogenic archaea inhabiting anaerobic environments play a crucial role in the global biogeochemical material cycle. The most universal electrogenic reaction of their methane- producing energy metabolism is catalyzed byN5- methyl- tetrahydromethanopterin: coenzyme M methyltransferase (MtrABCDEFGH), which couples the vectorial Na+ transport with a methyl transfer between the one- carbon carriers tetrahydromethanopterin and coenzyme M via a vitamin B12 derivative (cobamide) as prosthetic group. We present the 2.08 & Aring; cryo-EM structure of Mtr(ABCDEFG)3 composed of the central Mtr(ABFG)3 stalk symmetrically flanked by three membrane- spanning MtrCDE globes. Tetraether glycolipids visible in the map fill gaps inside the multisubunit complex. Putative coenzyme M and Na+ were identified inside or in a side- pocket of a cytoplasmic cavity formed within MtrCDE. Its bottom marks the gate of the transmembrane pore occluded in the cryo-EM map. By integrating Alphafold2 information, functionally competent MtrA-MtrH and MtrA-MtrCDE subcomplexes could be modeled and thus the methyl- tetrahydromethanopterin demethylation and coenzyme M methylation half- reactions structurally described. Methyl- transfer- driven Na+ transport is proposed to be based on a strong and weak complex between MtrCDE and MtrA carrying vitamin B12, the latter being placed at the entrance of the cytoplasmic MtrCDE cavity. Hypothetically, strongly attached methyl- cob(III)amide (His - on) carrying MtrA induces an inward- facing conformation, Na+ flux into the membrane protein center and finally coenzyme M methylation while the generated loosely attached (or detached) MtrA carrying cob(I)amide (His - off) induces an outward- facing conformation and an extracellular Na+ outflux. Methyl- cob(III)amide (His - on) is regenerated in the distant active site of the methyl- tetrahydromethanopterin binding MtrH implicating a large - scale shuttling movement of the vitamin B12 - carrying domain.