21FH

Cryo-EM structure of DddT G101D in substrate-free outward open conformation

Summary for 21FH

• Entry DOI: 10.2210/pdb21fh/pdb
• EMDB information: 67625
• Descriptor: DddT, SODIUM ION (3 entities in total)
• Functional Keywords: trimer, psychrobacter sp. d2, dimethylsulfoniopropionate transporter, substrate-free outward open conformation, transport protein
• Biological source: Psychrobacter sp. D2
• Total number of polymer chains: 1
• Total formula weight: 57835.63

Authors

Zhu, W.J.,Wang, P. (deposition date: 2025-12-11, release date: 2026-05-20)

Primary citation

Zhang, Y.Z.,Zhu, W.J.,Li, K.,Ding, H.T.,Hattori, M.,Liu, S.,Ge, C.,Qin, Q.L.,Teng, Z.J.,Liu, N.H.,Cao, H.Y.,Li, C.Y.,Chen, X.L.,Shen, Q.T.,Todd, J.D.,Liu, L.N.,Wang, P.
Structural insights into bacterial dimethylsulfoniopropionate import by BCCT-family transporters.
Embo J., 2026

PubMed Abstract: Dimethylsulfoniopropionate (DMSP) is a ubiquitous marine organosulfur compound central to microbial stress responses, chemotaxis, and nutrient cycling. Its catabolism produces dimethylsulfide (DMS), a climate-active gas, and plays a key role in the global sulfur cycle. However, the molecular basis of DMSP import, underpinning its microbial metabolism, remains poorly understood. Here, we identify and characterize the BCCT-family transporter DddT from Psychrobacter sp. D2, a marine gamma-proteobacterium that utilizes DMSP as a carbon source. DddT is essential for DMSP uptake and functions as a Na-coupled symporter driven by the transmembrane sodium gradient. Using cryo-electron microscopy, we determined DddT structures in multiple conformational states, revealing its Na-dependent transport mechanism involving two sodium ions, one coordinated by a previously uncharacterized binding site. Sequence analysis shows that DddT-like proteins with conserved sodium-binding features are widespread in marine bacteria, suggesting this Na-coupled transport mechanism represents a broadly conserved feature of the BCCT family. Our findings provide mechanistic insights into sodium-driven substrate uptake and marine sulfur cycling.

PubMed: 42104083
DOI: 10.1038/s44318-026-00798-w

Experimental method

ELECTRON MICROSCOPY (2.66 Å)