8q3v | pdb_00008q3v
Cryo-EM structure of the methanogenic Na+ translocating N5-methyl-H4MPT:CoM methyltransferase complex
Structural highlights
FunctionMTRA1_METTM Part of a complex that catalyzes the formation of methyl-coenzyme M and tetrahydromethanopterin from coenzyme M and methyl-tetrahydromethanopterin. This is an energy-conserving, sodium-ion translocating step.[HAMAP-Rule:MF_01093][1] Publication Abstract from PubMedMethanogenic 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 N (5)-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(12) derivative (cobamide) as prosthetic group. We present the 2.08 A 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 B(12), 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(12)-carrying domain. Structural and mechanistic basis of the central energy-converting methyltransferase complex of methanogenesis.,Aziz I, Kayastha K, Kaltwasser S, Vonck J, Welsch S, Murphy BJ, Kahnt J, Wu D, Wagner T, Shima S, Ermler U Proc Natl Acad Sci U S A. 2024 Apr 2;121(14):e2315568121. doi: , 10.1073/pnas.2315568121. Epub 2024 Mar 26. PMID:38530900[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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