RnDmpX in complex with DMSP

Experimental Data Snapshot

  • Resolution: 2.05 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

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Ubiquitous occurrence of a dimethylsulfoniopropionate ABC transporter in abundant marine bacteria.

Li, C.Y.Mausz, M.A.Murphy, A.Zhang, N.Chen, X.L.Wang, S.Y.Gao, C.Aguilo-Ferretjans, M.M.Silvano, E.Lidbury, I.D.E.A.Fu, H.H.Todd, J.D.Chen, Y.Zhang, Y.Z.

(2023) ISME J 17: 579-587

  • DOI: https://doi.org/10.1038/s41396-023-01375-3
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Dimethylsulfoniopropionate (DMSP) is a ubiquitous organosulfur compound in marine environments with important functions in both microorganisms and global biogeochemical carbon and sulfur cycling. The SAR11 clade and marine Roseobacter group (MRG) represent two major groups of heterotrophic bacteria in Earth's surface oceans, which can accumulate DMSP to high millimolar intracellular concentrations. However, few studies have investigated how SAR11 and MRG bacteria import DMSP. Here, through comparative genomics analyses, genetic manipulations, and biochemical analyses, we identified an ABC (ATP-binding cassette)-type DMSP-specific transporter, DmpXWV, in Ruegeria pomeroyi DSS-3, a model strain of the MRG. Mutagenesis suggested that DmpXWV is a key transporter responsible for DMSP uptake in strain DSS-3. DmpX, the substrate binding protein of DmpXWV, had high specificity and binding affinity towards DMSP. Furthermore, the DmpX DMSP-binding mechanism was elucidated from structural analysis. DmpX proteins are prevalent in the numerous cosmopolitan marine bacteria outside the SAR11 clade and the MRG, and dmpX transcription was consistently high across Earth's entire global ocean. Therefore, DmpXWV likely enables pelagic marine bacteria to efficiently import DMSP from seawater. This study offers a new understanding of DMSP transport into marine bacteria and provides novel insights into the environmental adaption of marine bacteria.

  • Organizational Affiliation

    Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China. Lcy@ouc.edu.cn.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycine betaine/proline ABC transporter, periplasmic glycinebetaine/proline-binding protein322Roseovarius nubinhibens ISMMutation(s): 0 
Gene Names: ISM_12265
Find proteins for A3SME7 (Roseovarius nubinhibens (strain ATCC BAA-591 / DSM 15170 / ISM))
Explore A3SME7 
Go to UniProtKB:  A3SME7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3SME7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DQY (Subject of Investigation/LOI)
Query on DQY

Download Ideal Coordinates CCD File 
B [auth A]3-(dimethyl-lambda~4~-sulfanyl)propanoic acid
C5 H12 O2 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.05 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.332α = 90
b = 74.332β = 90
c = 87.788γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

  • Released Date: 2023-01-25 
  • Deposition Author(s): Li, C.Y.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2023-02-22
    Changes: Database references
  • Version 1.2: 2023-04-05
    Changes: Database references