8YZU | pdb_00008yzu

STC truncated SydA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 
    0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Characterization and Engineering of a Bisabolene Synthase Reveal an Unusual Hydride Shift and Key Residues Critical for Mono-, Bi-, and Tricyclic Sesquiterpenes Formation.

Wu, M.Torrence, I.Liu, Y.Wu, J.Ge, R.Ma, K.Liu, D.Ren, J.Fan, S.Ma, M.Siegel, J.B.Tantillo, D.J.Lin, W.Fan, A.

(2025) J Am Chem Soc 147: 10413-10422

  • DOI: https://doi.org/10.1021/jacs.4c17818
  • Primary Citation Related Structures: 
    8YZU, 8YZX, 8YZY

  • PubMed Abstract: 

    Sesquiterpene synthases (STSs) catalyze carbocation cascade reactions with various hydrogen shifts and cyclization patterns that generate structurally diverse sesquiterpene skeletons. However, the molecular basis for hydrogen shifts and cyclizations, which determine STS product distributions, remains enigmatic. In this study, an elusive STS SydA was identified in the biosynthesis of sydonol, which synthesized a new bisabolene-type sesquiterpene 6 with a unique saturated terminal pendant isopentane. Extensive evidence from isotope labeling experiments, crystal structures of SydA and its variant, quantum chemical calculations, and mutagenesis experiments reveal a plausible mechanism for the formation of 6 involving an unusual 1,7-hydride shift, which may be a key branchpoint for monocyclic, bicyclic, and tricyclic products. Structure-based engineering resulted in SydA variants that promote different reaction pathways, leading to the production of bicyclic α-cuprenene and (+)-β-chamigrene and tricyclic 7- epi -β-cedrene and β-microbiotene. These findings not only reveal a new bisabolene and its biosynthesis but also provide insights into the molecular basis of the hydride shifts and cyclizations, which pave the way for engineering STSs to produce complex terpenoid products.


  • Organizational Affiliation
    • State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.

Macromolecule Content 

  • Total Structure Weight: 141.71 kDa 
  • Atom Count: 10,853 
  • Modeled Residue Count: 1,224 
  • Deposited Residue Count: 1,224 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
truncated SydA
A, B, C, D
306Aspergillus versicolorMutation(s): 0 
UniProt
Find proteins for A0A1L9Q3M5 (Aspergillus versicolor CBS 583.65)
Explore A0A1L9Q3M5 
Go to UniProtKB:  A0A1L9Q3M5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1L9Q3M5
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on POP



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B],
M [auth C],
Q [auth D]
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
J [auth B]
K [auth B]
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
N [auth C],
O [auth C],
P [auth C],
R [auth D],
S [auth D],
T [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.151α = 90
b = 125β = 100.65
c = 93.14γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2022YFC2804900
National Natural Science Foundation of China (NSFC)China82173733

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-30
    Type: Initial release
  • Version 1.1: 2026-05-20
    Changes: Database references