21FJ | pdb_000021fj

Cryo-EM structure of DddT in closed substrate-free conformation in the presence of potassium ions and dimethylsulfoniopropionate

PDB DOI: https://doi.org/10.2210/pdb21FJ/pdb
EM Map EMD-67627: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Psychrobacter sp. D2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-12-11 Released: 2026-05-20
Deposition Author(s): Zhu, W.J., Wang, P.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.18 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural insights into bacterial dimethylsulfoniopropionate import by BCCT-family transporters.

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.

(2026) EMBO J

PubMed: 42104083 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s44318-026-00798-w
Primary Citation Related Structures:
21FF, 21FH, 21FI, 21FJ, 21FK

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.

Organizational Affiliation

MOE Key Laboratory of Evolution and Marine Biodiversity, State Key Laboratory of Marine Food Processing and Safety Control, College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China. zhangyz@sdu.edu.cn.

Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China. zhangyz@sdu.edu.cn.

Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center & Laoshan Laboratory, Qingdao, China. zhangyz@sdu.edu.cn.

MOE Key Laboratory of Evolution and Marine Biodiversity, State Key Laboratory of Marine Food Processing and Safety Control, College of Marine Life Sciences & Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.

Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.

Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center & Laoshan Laboratory, Qingdao, China.

Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Ministry of Natural Resources, Shanghai, China.

State Key Laboratory of Genetics and Development of Complex Phenotypes, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Neurobiology, School of Life Sciences, Fudan University, Shanghai, China.

School of Life Sciences, Department of Chemical Biology, Southern University of Science and Technology, Shenzhen, China.

School of Biological Sciences, University of East Anglia, Norwich, UK.

Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.

Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK. luning.liu@liverpool.ac.uk.

Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center & Laoshan Laboratory, Qingdao, China. wangpeng3331@ouc.edu.cn.