8HW8 | pdb_00008hw8

Crystal structure of Heterodera glycines chitinase 2 D129A/E131A mutant in complex with nodulation factor SmNF-V (C16:2, S)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 
    0.187 (Depositor), 0.191 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

A soybean cyst nematode suppresses microbial plant symbionts using a lipochitooligosaccharide-hydrolysing enzyme.

Chen, W.Wang, D.Ke, S.Cao, Y.Xiang, W.Guo, X.Yang, Q.

(2024) Nat Microbiol 9: 1993-2005

  • DOI: https://doi.org/10.1038/s41564-024-01727-5
  • Primary Citation Related Structures: 
    8HW6, 8HW7, 8HW8

  • PubMed Abstract: 

    Cyst nematodes are the most damaging species of plant-parasitic nematodes. They antagonize the colonization of beneficial microbial symbionts that are important for nutrient acquisition of plants. The molecular mechanism of the antagonism, however, remains elusive. Here, through biochemical combined with structural analysis, we reveal that Heterodera glycines, the most notorious soybean cyst nematode, suppresses symbiosis by secreting an enzyme named HgCht2 to hydrolyse the key symbiotic signalling molecules, lipochitooligosaccharides (LCOs). We solved the three-dimensional structures of apo HgCht2, as well as its chitooligosaccharide-bound and LCO-bound forms. These structures elucidated the substrate binding and hydrolysing mechanism of the enzyme. We designed an HgCht2 inhibitor, 1516b, which successfully suppresses the antagonism of cyst nematodes towards nitrogen-fixing rhizobia and phosphorus-absorbing arbuscular mycorrhizal symbioses. As HgCht2 is phylogenetically conserved across all cyst nematodes, our study revealed a molecular mechanism by which parasitic cyst nematodes antagonize the establishment of microbial symbiosis and provided a small-molecule solution.


  • Organizational Affiliation
    • State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 41.13 kDa 
  • Atom Count: 2,924 
  • Modeled Residue Count: 326 
  • Deposited Residue Count: 356 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chitinase356Heterodera glycinesMutation(s): 2 
EC: 3.2.1.14
UniProt
Find proteins for Q8I6X8 (Heterodera glycines)
Explore Q8I6X8 
Go to UniProtKB:  Q8I6X8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8I6X8
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranoseB [auth D]4N/A
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
68X
(Subject of Investigation/LOI)

Query on 68X



Download:Ideal Coordinates CCD File
D [auth A](2~{Z},9~{E})-~{N}-[(2~{R},3~{S},4~{R},5~{S},6~{S})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]hexadeca-2,9-dienamide
C22 H39 N O6
BQDHAOHXPSOCQH-OQVMBZPUSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
E [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free:  0.187 (Depositor), 0.191 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.005α = 90
b = 69.384β = 105.2
c = 50.818γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

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)China31830076
National Natural Science Foundation of China (NSFC)China32161133010
National Natural Science Foundation of China (NSFC)China32272595

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-05
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Structure summary
  • Version 1.2: 2024-12-18
    Changes: Database references