8ZN9 | pdb_00008zn9

A vast marine sulfonate-based carbon cycle fueled by novel sulfoquinovosidases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.238 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 8ZN9

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Cosmopolitan marine bacteria facilitate a vast phytoplankton-derived sulfonate-based carbon flow through sulfoquinovosidases.

Ma, X.Wang, H.Dong, C.Liu, L.Qiu, X.Chen, X.Chen, Q.Wang, L.Zhang, Y.Jiao, N.Williams, S.J.Tang, K.

(2025) Nat Commun 17: 209-209

  • DOI: https://doi.org/10.1038/s41467-025-66898-z
  • Primary Citation Related Structures: 
    8ZN9

  • PubMed Abstract: 

    Sulfoquinovose (SQ) and sulfoquinovosyl glycerol (SQGro) are derived from abundant membrane sulfolipids termed sulfoquinovosyl diacylglycerols (SQDG) and produced by photosynthetic organisms, serving as sources of carbon and sulfur for bacteria. The conversion processes of these sulfoquinovosyl compounds within marine ecosystems, and their quantitative contributions to the marine organic matter pool, are poorly understood. Here, we identify Alteromonas macleodii, a marine bacterium capable of metabolizing SQ and SQGro through a sulfoquinovosidase. This enzyme converts SQGro to SQ and is a member of a clade within glycoside hydrolase family 31, distinct from other sulfoquinovosidases. The ubiquitous presence of sulfoquinovosidases and their transcripts throughout marine environments implicates active metabolism of sulfoquinovose glycosides, particularly in the sunlit surface ocean. We further demonstrate that marine algae produce significant quantities of cellular SQGro, and we estimate the annual turnover of SQGro using field samples from coastal and open ocean environments. Together with SQDG and SQ, these sulfoquinovosyl compounds constitute a substantial portion of the marine organic carbon turnover, estimated at around 1.5 petagrams of carbon per annum. These findings reveal a vast, previously unappreciated pool of organosulfonates within the microbial food web that contributes significantly to the marine carbon and sulfur cycles.


  • Organizational Affiliation
    • State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Science, Xiamen University, Xiamen, China.

Macromolecule Content 

  • Total Structure Weight: 272.57 kDa 
  • Atom Count: 19,937 
  • Modeled Residue Count: 2,203 
  • Deposited Residue Count: 2,400 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Oxidoreductase, putative
A, B, C, D, E
A, B, C, D, E, F
400Roseobacter denitrificans OCh 114Mutation(s): 0 
Gene Names: RD1_2308
UniProt
Find proteins for Q167F5 (Roseobacter denitrificans (strain ATCC 33942 / OCh 114))
Explore Q167F5 
Go to UniProtKB:  Q167F5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ167F5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD

Query on NAD



Download:Ideal Coordinates CCD File
G [auth A]
IB [auth E]
JA [auth C]
T [auth B]
TB [auth F]
G [auth A],
IB [auth E],
JA [auth C],
T [auth B],
TB [auth F],
VA [auth D]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
AA [auth B]
AB [auth D]
AC [auth F]
BA [auth B]
BB [auth D]
AA [auth B],
AB [auth D],
AC [auth F],
BA [auth B],
BB [auth D],
BC [auth F],
CA [auth B],
CB [auth D],
CC [auth F],
DA [auth B],
DB [auth D],
DC [auth F],
EA [auth B],
EB [auth D],
EC [auth F],
FA [auth B],
FB [auth D],
GA [auth B],
GB [auth D],
H [auth A],
HA [auth B],
HB [auth D],
I [auth A],
IA [auth B],
J [auth A],
JB [auth E],
K [auth A],
KA [auth C],
KB [auth E],
L [auth A],
LA [auth C],
LB [auth E],
M [auth A],
MA [auth C],
MB [auth E],
N [auth A],
NA [auth C],
NB [auth E],
O [auth A],
OA [auth C],
OB [auth E],
P [auth A],
PA [auth C],
PB [auth E],
Q [auth A],
QA [auth C],
QB [auth E],
R [auth A],
RA [auth C],
RB [auth E],
S [auth A],
SA [auth C],
SB [auth E],
TA [auth C],
U [auth B],
UA [auth C],
UB [auth F],
V [auth B],
VB [auth F],
W [auth B],
WA [auth D],
WB [auth F],
X [auth B],
XA [auth D],
XB [auth F],
Y [auth B],
YA [auth D],
YB [auth F],
Z [auth B],
ZA [auth D],
ZB [auth F]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.238 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.92α = 90
b = 56.69β = 96.1
c = 217.3γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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: 2025-08-27
    Type: Initial release
  • Version 1.1: 2026-03-11
    Changes: Database references