8G3H

Structure of cobalamin-dependent methionine synthase (MetH) in a resting state

Summary for 8G3H

• Entry DOI: 10.2210/pdb8g3h/pdb
• EMDB information: 29699
• Descriptor: Methionine synthase, ZINC ION, COBALAMIN (3 entities in total)
• Functional Keywords: methyltransferase, transferase, amino-acid biosynthesis, methionine biosynthesis
• Biological source: Thermus filiformis
• Total number of polymer chains: 1
• Total formula weight: 132708.03

Authors

Watkins, M.B.,Ando, N. (deposition date: 2023-02-07, release date: 2023-06-28, Last modification date: 2024-06-19)

Primary citation

Watkins, M.B.,Wang, H.,Burnim, A.,Ando, N.
Conformational switching and flexibility in cobalamin-dependent methionine synthase studied by small-angle X-ray scattering and cryoelectron microscopy.
Proc.Natl.Acad.Sci.USA, 120:e2302531120-e2302531120, 2023

PubMed Abstract: Cobalamin-dependent methionine synthase (MetH) catalyzes the synthesis of methionine from homocysteine and 5-methyltetrahydrofolate (CH-Hfolate) using the unique chemistry of its cofactor. In doing so, MetH links the cycling of -adenosylmethionine with the folate cycle in one-carbon metabolism. Extensive biochemical and structural studies on  MetH have shown that this flexible, multidomain enzyme adopts two major conformations to prevent a futile cycle of methionine production and consumption. However, as MetH is highly dynamic as well as both a photosensitive and oxygen-sensitive metalloenzyme, it poses special challenges for structural studies, and existing structures have necessarily come from a "divide and conquer" approach. In this study, we investigate MetH and a thermophilic homolog from using small-angle X-ray scattering (SAXS), single-particle cryoelectron microscopy (cryo-EM), and extensive analysis of the AlphaFold2 database to present a structural description of the full-length MetH in its entirety. Using SAXS, we describe a common resting-state conformation shared by both active and inactive oxidation states of MetH and the roles of CH-Hfolate and flavodoxin in initiating turnover and reactivation. By combining SAXS with a 3.6-Å cryo-EM structure of the MetH, we show that the resting-state conformation consists of a stable arrangement of the catalytic domains that is linked to a highly mobile reactivation domain. Finally, by combining AlphaFold2-guided sequence analysis and our experimental findings, we propose a general model for functional switching in MetH.

PubMed: 37339208
DOI: 10.1073/pnas.2302531120

Experimental method

ELECTRON MICROSCOPY (3.6 Å)