9L4T

The crystal structure of BurB-Met complex

Summary for 9L4T

• Entry DOI: 10.2210/pdb9l4t/pdb
• Descriptor: BurB, METHIONINE (3 entities in total)
• Functional Keywords: dmsp synthesis; s-methyltransferase; set domain; global sulfur cycle, transferase
• Biological source: Burkholderia thailandensis
• Total number of polymer chains: 2
• Total formula weight: 40578.47

Authors

Li, C.Y.,Cao, H.Y. (deposition date: 2024-12-21, release date: 2025-08-20, Last modification date: 2025-12-24)

Primary citation

Zhang, N.,Lin, Y.,Wang, N.,Cao, H.-.Y.,Zhang, B.,Gao, Y.-.N.,Zhang, Y.-.Z.,Li, C.-.Y.
Mechanistic insights into the dimethylsulfoniopropionate synthesis enzyme BurB.
Appl.Environ.Microbiol., 91:e0135425-e0135425, 2025

PubMed Abstract: Dimethylsulfoniopropionate (DMSP) is one of the most abundant organosulfur molecules on Earth. It possesses various physiological functions in microorganisms and plays key roles in the global climate regulation. BurB, a SET (Suppressor of variegation, Enhancer of zeste and Trithorax) domain-containing enzyme identified from , initiates DMSP synthesis by methylating methionine (Met) to -methyl-methionine (SMM), with -adenosyl methionine (SAM) as a methyl donor. Here, the crystal structures of BurB-Met and BurB-SMM-SAM were determined, and the catalytic mechanism of BurB was proposed based on structural and biochemical analyses. BurB is a specific -methyltransferase involved in the DMSP methylation synthesis pathway. The Met molecule is bound in the substrate binding pocket mainly via hydrogen bonding interactions with the main chains of the BurB residues. With the binding of SAM, the loop (Gln37-Ala44) possessing a gating function generates a conformational change and seals the substrate binding pocket, which may promote the subsequent nucleophilic attack of the Met molecule on the methyl group of SAM via the proximity and desolvation mechanism. Our results offer a better understanding of the catalytic mechanisms of SET domain-containing methyltransferases and provide novel insights into DMSP synthesis and the global sulfur cycling.

PubMed: 40905665
DOI: 10.1128/aem.01354-25

Experimental method

X-RAY DIFFRACTION (2.16 Å)