8HLE

Structure of DddY-DMSOP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

DMSOP-cleaving enzymes are diverse and widely distributed in marine microorganisms.

Carrion, O.Li, C.Y.Peng, M.Wang, J.Pohnert, G.Azizah, M.Zhu, X.Y.Curson, A.R.J.Wang, Q.Walsham, K.S.Zhang, X.H.Monaco, S.Harvey, J.M.Chen, X.L.Gao, C.Wang, N.Wang, X.J.Wang, P.Giovanonni, S.J.Lee, C.P.Suffridge, C.P.Zhang, Y.Luo, Z.Wang, D.Todd, J.D.Zhang, Y.Z.

(2023) Nat Microbiol 8: 2326-2337

  • DOI: https://doi.org/10.1038/s41564-023-01526-4
  • Primary Citation of Related Structures:  
    8HLE, 8HLF

  • PubMed Abstract: 

    Dimethylsulfoxonium propionate (DMSOP) is a recently identified and abundant marine organosulfur compound with roles in oxidative stress protection, global carbon and sulfur cycling and, as shown here, potentially in osmotolerance. Microbial DMSOP cleavage yields dimethyl sulfoxide, a ubiquitous marine metabolite, and acrylate, but the enzymes responsible, and their environmental importance, were unknown. Here we report DMSOP cleavage mechanisms in diverse heterotrophic bacteria, fungi and phototrophic algae not previously known to have this activity, and highlight the unappreciated importance of this process in marine sediment environments. These diverse organisms, including Roseobacter, SAR11 bacteria and Emiliania huxleyi, utilized their dimethylsulfoniopropionate lyase 'Ddd' or 'Alma' enzymes to cleave DMSOP via similar catalytic mechanisms to those for dimethylsulfoniopropionate. Given the annual teragram predictions for DMSOP production and its prevalence in marine sediments, our results highlight that DMSOP cleavage is likely a globally significant process influencing carbon and sulfur fluxes and ecological interactions.


  • Organizational Affiliation

    MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China. O.Carrion-Fonseca@uea.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DMSP lyase DddY
A, B
407Acinetobacter bereziniae NIPH 3Mutation(s): 1 
Gene Names: F963_02809
UniProt
Find proteins for N8X9V6 (Acinetobacter bereziniae NIPH 3)
Explore N8X9V6 
Go to UniProtKB:  N8X9V6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupN8X9V6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.803α = 90
b = 73.387β = 91.14
c = 87.368γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-04
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Structure summary