8WWD

Crystal structure of (S)-DHPS dehydrogenase HpsP from Dinoroseobacter shibae DFL 12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Enantioselective transformation of phytoplankton-derived dihydroxypropanesulfonate by marine bacteria.

Liu, L.Gao, X.Dong, C.Wang, H.Chen, X.Ma, X.Liu, S.Chen, Q.Lin, D.Jiao, N.Tang, K.

(2024) ISME J 18

  • DOI: https://doi.org/10.1093/ismejo/wrae084
  • Primary Citation of Related Structures:  
    8WWD, 8WWE, 8WWF

  • PubMed Abstract: 

    Chirality, a fundamental property of matter, is often overlooked in the studies of marine organic matter cycles. Dihydroxypropanesulfonate (DHPS), a globally abundant organosulfur compound, serves as an ecologically important currency for nutrient and energy transfer from phytoplankton to bacteria in the ocean. However, the chirality of DHPS in nature and its transformation remain unclear. Here, we developed a novel approach using chiral phosphorus-reagent labeling to separate DHPS enantiomers. Our findings demonstrated that at least one enantiomer of DHPS is present in marine diatoms and coccolithophores, and that both enantiomers are widespread in marine environments. A novel chiral-selective DHPS catabolic pathway was identified in marine Roseobacteraceae strains, where HpsO and HpsP dehydrogenases at the gateway to DHPS catabolism act specifically on R-DHPS and S-DHPS, respectively. R-DHPS is also a substrate for the dehydrogenase HpsN. All three dehydrogenases generate stable hydrogen bonds between the chirality-center hydroxyls of DHPS and highly conserved residues, and HpsP also form coordinate-covalent bonds between the chirality-center hydroxyls and Zn2+, which determines the mechanistic basis of strict stereoselectivity. We further illustrated the role of enzymatic promiscuity in the evolution of DHPS metabolism in Roseobacteraceae and SAR11. This study provides the first evidence of chirality's involvement in phytoplankton-bacteria metabolic currencies, opening a new avenue for understanding the ocean organosulfur cycle.


  • Organizational Affiliation

    State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiang'an South Road, Xiamen 361102, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc-containing alcohol dehydrogenase
A, B, C, D
337Dinoroseobacter shibae DFL 12 = DSM 16493Mutation(s): 0 
Gene Names: Dshi_2036
UniProt
Find proteins for A8LPS1 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12))
Explore A8LPS1 
Go to UniProtKB:  A8LPS1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8LPS1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth B]
I [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth C],
L [auth C],
M [auth D],
N [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.183α = 90
b = 290.538β = 98.38
c = 54.277γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China92251306
Other government2020YFA0608300
National Natural Science Foundation of China (NSFC)China42188102
National Natural Science Foundation of China (NSFC)China42276120
Other government121311KYSB20190029

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release
  • Version 1.1: 2024-09-11
    Changes: Database references
  • Version 1.2: 2024-09-18
    Changes: Derived calculations