8Q3V
Cryo-EM structure of the methanogenic Na+ translocating N5-methyl-H4MPT:CoM methyltransferase complex
Summary for 8Q3V
| Entry DOI | 10.2210/pdb8q3v/pdb |
| EMDB information | 18135 |
| Descriptor | Tetrahydromethanopterin S-methyltransferase subunit A 1, SODIUM ION, Tetrahydromethanopterin S-methyltransferase subunit B, ... (11 entities in total) |
| Functional Keywords | methanogenesis, tetrahydromethanopterin, coenzyme m, vitamin b12, na+ transport, transferase |
| Biological source | Methanothermobacter marburgensis More |
| Total number of polymer chains | 21 |
| Total formula weight | 423829.90 |
| Authors | |
| Primary citation | Aziz, I.,Kayastha, K.,Kaltwasser, S.,Vonck, J.,Welsch, S.,Murphy, B.J.,Kahnt, J.,Wu, D.,Wagner, T.,Shima, S.,Ermler, U. Structural and mechanistic basis of the central energy-converting methyltransferase complex of methanogenesis. Proc.Natl.Acad.Sci.USA, 121:e2315568121-e2315568121, 2024 Cited by PubMed Abstract: 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 by -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 B derivative (cobamide) as prosthetic group. We present the 2.08 Å cryo-EM structure of Mtr(ABCDEFG) composed of the central Mtr(ABFG) 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 B, 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 B-carrying domain. PubMed: 38530900DOI: 10.1073/pnas.2315568121 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.08 Å) |
Structure validation
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