8ZAE | pdb_00008zae

Crystal structure of RuABA3 from Rutstroemia sp. NJR-2017a WRK4 in complex with FsPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 
    0.250 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Molecular insights into a distinct class of terpenoid cyclases.

Li, S.Huang, J.W.Min, J.Li, H.Ning, M.Zhou, S.Yang, Y.Chen, C.C.Guo, R.T.

(2025) Nat Commun 16: 207-207

  • DOI: https://doi.org/10.1038/s41467-024-55717-6
  • Primary Citation of Related Structures:  
    8ZAC, 8ZAD, 8ZAE, 8ZAF, 8ZAG

  • PubMed Abstract: 

    Terpenoid cyclases (TCs) account for the synthesis of the most widespread and diverse natural compounds. A sesquiterpene cyclase termed BcABA3 from an abscisic acid-producing fungus Botrytis cinerea that yields (2Z,4E)-α-ionylideneethane but lacks signature feature of canonical TCs represents a distinct type of TCs. Here, we report the crystal structures of BcABA3, a closely related RuABA3 from Rutstroemia sp. and a bacterial SkABA3 from Shimazuella kribbensis. These ABA3 proteins adopt an all-α-helix fold and bind pyrophosphate moiety of farnesyl pyrophosphate by Glu-chelated Mg 2+ ion cluster. We conduct mutagenesis experiments to validate the role of the substrate-binding residues. SkABA3 appears to yield compounds that are distinct from (2Z,4E)-α-ionylideneethane. These results not only provide the molecular insight into ABA3 proteins that serve as an important basis to the future investigation of this class of TCs, but also reveal the existence of more uncharacterized terpenoids synthesized via dedicated machineries.


  • Organizational Affiliation
    • State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aba 3 protein
A, B
405Rutstroemia sp. NJR-2017a WRK4Mutation(s): 0 
Gene Names: CJF32_00009727
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FPS (Subject of Investigation/LOI)
Query on FPS

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE
C15 H28 O6 P2 S
MYMLCRQRXFRQGP-YFVJMOTDSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free:  0.250 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.765α = 90
b = 89.475β = 90
c = 142.712γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SAINTdata scaling
SAINTdata reduction
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: 2024-12-11
    Type: Initial release
  • Version 1.1: 2025-01-22
    Changes: Database references, Refinement description