9WLV | pdb_00009wlv

The Crystal Structure of Alpha-Beta-fold_hydrolase from Microlunatus sagamiharensis.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.179 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.144 (Depositor), 0.157 (DCC) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Independent horizontal transfer of genes encoding alpha / beta-hydrolases with strigolactone binding and hydrolytic activities from bacteria to fungi and plants.

Wang, Q.Ye, Y.Wang, L.Guan, Y.Wang, S.Wang, Z.Sun, H.Smith, S.M.Huang, J.

(2025) Mol Plant 18: 1949-1961

  • DOI: https://doi.org/10.1016/j.molp.2025.09.021
  • Primary Citation of Related Structures:  
    9WLV

  • PubMed Abstract: 

    Strigolactones (SLs) are not only phytohormones that influence multiple aspects of plant growth and development but also signaling molecules for interactions between plants and certain fungi or bacteria. In plants, the SL receptor is an α/β-hydrolase (ABH) encoded by the DWARF14 (D14)/KARRIKIN INSENSITIVE2 (KAI2) gene family, which is known to be derived from proteobacterial RsbQ through horizontal gene transfer (HGT). In the phytopathogenic fungus Cryphonectria parasitica, another ABH named CpD14 was found to possess SL binding and hydrolytic activities and mediate SL responses, exhibiting potential SL perception functions. Here, we demonstrate that CpD14 and its homologs in Leotiomyceta fungi were derived from Actinobacteria through an independent HGT event, forming a distinct CpD14-like (CDL) family across fungi and bacteria. X-ray crystallography and structural analyses reveal that actinobacterial and fungal CDL proteins share a conserved core "α/β fold" domain with D14/KAI2/RsbQ but possess a unique lid domain. Biochemical assays show that both actinobacterial CDL and proteobacterial RsbQ can recognize and hydrolyze SLs, suggesting that they are pre-adapted for SL responses and potential perception. Both plant D14/KAI2 and fungal CDL proteins retained these functional activities, whereas they evolved distinct ligand specificities for SL structural variants. Collectively, this work reveals that independent HGT events from two bacterial groups provided plants and their interacting fungi with pre-adapted ABH proteins, which were deployed for SL perception or responses.


  • Organizational Affiliation
    • State Key Laboratory of Plant Diversity and Specialty Crops & Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pimeloyl-ACP methyl ester carboxylesteraseA [auth AAA],
B [auth BBB]
290Microlunatus sagamiharensisMutation(s): 0 
Gene Names: SAMN04488544_1883
UniProt
Find proteins for A0A1H2MDS2 (Microlunatus sagamiharensis)
Explore A0A1H2MDS2 
Go to UniProtKB:  A0A1H2MDS2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1H2MDS2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4HP
Query on 4HP

Download Ideal Coordinates CCD File 
F [auth AAA],
M [auth BBB]
4-HYDROXYPHENYLACETATE
C8 H8 O3
XQXPVVBIMDBYFF-UHFFFAOYSA-N
3HR
Query on 3HR

Download Ideal Coordinates CCD File 
O [auth BBB](3R)-3-hydroxybutanoic acid
C4 H8 O3
WHBMMWSBFZVSSR-GSVOUGTGSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth AAA],
D [auth AAA]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth AAA]
H [auth AAA]
I [auth AAA]
J [auth AAA]
K [auth AAA]
G [auth AAA],
H [auth AAA],
I [auth AAA],
J [auth AAA],
K [auth AAA],
L [auth AAA],
N [auth BBB],
P [auth BBB]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth AAA]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.179 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.144 (Depositor), 0.157 (DCC) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.212α = 90
b = 125.212β = 90
c = 79.73γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata 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)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release
  • Version 1.1: 2026-02-11
    Changes: Database references