9FVT | pdb_00009fvt

Crystal structure of marine sulfatase (OpSulf1) from Ochrovirga pacifica

• PDB DOI: https://doi.org/10.2210/pdb9FVT/pdb

• Classification: HYDROLASE
• Organism(s): Ochrovirga pacifica
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-06-28 Released: 2024-07-17 
• Deposition Author(s): Solanki, V.A., Krull, J., Hehemann, J.H.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.175 (DCC) 

Starting Model: in silico

Literature

Sulfated mannan of diatoms selects host-specific microbiota in the sunlit ocean.

Krull, J., Sidhu, C., Solanki, V., Bligh, M., Rossler, L., Singh, R.K., Huang, G., Robb, C.S., Teeling, H., Seeberger, P.H., Schweder, T., Crawford, C.J., Hehemann, J.H.

(2026) Microbiome 14

• PubMed: 41888912 
• DOI: https://doi.org/10.1186/s40168-026-02379-9
• Primary Citation Related Structures: 
  9FVT


• PubMed Abstract: 
  

  Diatoms, a keystone phylum in Earth's ecosystems, are responsible for substantial oxygen production and the fixation of carbon dioxide in the form of carbohydrates that fuel global food webs. They host diverse prokaryotes, yet how diatoms preferentially recruit those with complementary metabolic traits remains unknown. We discovered that diatoms exude a C6-sulfated α-1,3-mannan that serves as a selective carbon source for adapted Polaribacter. Its structure was resolved using NMR spectroscopy, chromatography, chemical synthesis, and enzymatic dissection. Biochemical, physiological, and structural analyses demonstrated, that specialized Bacteroidota employ a four-enzyme pathway to metabolize this glycan. Metagenomic and transcriptomic data revealed that sulfated mannan utilization loci are globally abundant and actively expressed in surface ocean bacterioplankton. Because this mannan provides only carbon, oxygen, sulfur, and hydrogen, bacteria must obtain other essential elements elsewhere, reinforcing metabolic interdependence. Together, these results define a chemically specific interaction between diatoms and specialized bacteria that is mediated by a single sulfated polysaccharide and a dedicated four-enzyme degradation pathway. Presence of this pathway in marine metagenomes and transcriptomes indicates that a sulfated mannan from diatoms exerts selection pressure in the sunlit ocean microbiome. Video Abstract.

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Organizational Affiliation: 
• Faculty of Chemistry & Biology, BIOM, University of Bremen, Bremen, Germany.
MARUM, University of Bremen, Bremen, Germany.
Max Planck Institute for Marine Microbiology, Bremen, Germany.
Institute of Pharmacy, University of Greifswald, Greifswald, Germany.
Institute of Marine Biotechnology, Greifswald, Germany.
Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl Von Ossietzky Universität Oldenburg, Oldenburg, Germany.
Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.
Max Planck Institute of Colloids and Interfaces, Potsdam, Germany. [e-mail].
School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland. [e-mail].
Faculty of Chemistry & Biology, BIOM, University of Bremen, Bremen, Germany. [e-mail].
MARUM, University of Bremen, Bremen, Germany. [e-mail].
Max Planck Institute for Marine Microbiology, Bremen, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 238.33 kDa 
• Atom Count: 18,258 
• Modeled Residue Count: 2,076 
• Deposited Residue Count: 2,076 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfatase	A, B, C, D	519	Ochrovirga pacifica	Mutation(s): 0  Gene Names: Sulfatase
UniProt
Find proteins for A0AAX7FM35 (Ochrovirga pacifica) Explore A0AAX7FM35  Go to UniProtKB:  A0AAX7FM35

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.175 (DCC) 

Diffraction Data: https://doi.org/10.18430/M39FVT

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.268	α = 90
b = 115.268	β = 90
c = 169.831	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-07-17 
Deposition Author(s): Solanki, V.A., Krull, J., Hehemann, J.H.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	HE 7217/2-3

Revision History  

• Version 1.0: 2024-07-17
  Type: Initial release
  
• Version 1.1: 2025-03-05
  Changes: Derived calculations, Structure summary
• Version 1.2: 2026-01-28
  Changes: Database references
• Version 1.3: 2026-04-15
  Changes: Database references
• Version 1.4: 2026-04-22
  Changes: Database references