8RI6 | pdb_00008ri6

Beta-galactosidase (LacZ) purified from E. coli.

  • Classification: HYDROLASE
  • Organism(s): Escherichia coli
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-12-18 Released: 2025-01-01 
  • Deposition Author(s): Hardenbrook, N.J., Sheng, Y., Zhang, P.
  • Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), European Research Council (ERC), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Wellcome Trust

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: other
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Bacterial pathogen deploys the iminosugar glycosyrin to manipulate plant glycobiology.

Sanguankiattichai, N.Chandrasekar, B.Sheng, Y.Hardenbrook, N.Tabak, W.W.A.Drapal, M.Kaschani, F.Grunwald-Gruber, C.Krahn, D.Buscaill, P.Yamamoto, S.Kato, A.Nash, R.Fleet, G.Strasser, R.Fraser, P.D.Kaiser, M.Zhang, P.Preston, G.M.van der Hoorn, R.A.L.

(2025) Science 388: 297-303

  • DOI: https://doi.org/10.1126/science.adp2433
  • Primary Citation of Related Structures:  
    8RI6, 8RI7, 8RI8

  • PubMed Abstract: 

    The extracellular space (apoplast) in plants is a key battleground during microbial infections. To avoid recognition, the bacterial model phytopathogen Pseudomonas syringae pv. tomato DC3000 produces glycosyrin. Glycosyrin inhibits the plant-secreted β-galactosidase BGAL1, which would otherwise initiate the release of immunogenic peptides from bacterial flagellin. Here, we report the structure, biosynthesis, and multifunctional roles of glycosyrin. High-resolution cryo-electron microscopy and chemical synthesis revealed that glycosyrin is an iminosugar with a five-membered pyrrolidine ring and a hydrated aldehyde that mimics monosaccharides. Glycosyrin biosynthesis was controlled by virulence regulators, and its production is common in bacteria and prevents flagellin recognition and alters the extracellular glycoproteome and metabolome of infected plants. These findings highlight a potentially wider role for glycobiology manipulation by plant pathogens across the plant kingdom.


  • Organizational Affiliation
    • Department of Biology, University of Oxford, Oxford, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-galactosidase
A, B, C, D
1,030Escherichia coliMutation(s): 0 
Gene Names: lacZb0344JW0335
EC: 3.2.1.23
UniProt
Find proteins for P00722 (Escherichia coli (strain K12))
Explore P00722 
Go to UniProtKB:  P00722
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00722
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
I [auth B]
J [auth B]
M [auth C]
E [auth A],
F [auth A],
I [auth B],
J [auth B],
M [auth C],
N [auth C],
Q [auth D],
R [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
K [auth B]
L [auth B]
O [auth C]
G [auth A],
H [auth A],
K [auth B],
L [auth B],
O [auth C],
P [auth C],
S [auth D],
T [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/T015128/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/R017913/1
European Research Council (ERC)European Union101021133
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU54 AI170791-7522
Wellcome TrustUnited Kingdom206422/Z/17/Z

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-01
    Type: Initial release
  • Version 1.1: 2026-03-25
    Changes: Data collection, Database references