7FFH | pdb_00007ffh

Diarylpentanoid-producing polyketide synthase (N199L mutant)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.258 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Identification of a diarylpentanoid-producing polyketide synthase revealing an unusual biosynthetic pathway of 2-(2-phenylethyl)chromones in agarwood.

Wang, X.H.Gao, B.W.Nakashima, Y.Mori, T.Zhang, Z.X.Kodama, T.Lee, Y.E.Zhang, Z.K.Wong, C.P.Liu, Q.Q.Qi, B.W.Wang, J.Li, J.Liu, X.Abe, I.Morita, H.Tu, P.F.Shi, S.P.

(2022) Nat Commun 13: 348-348

  • DOI: https://doi.org/10.1038/s41467-022-27971-z
  • Primary Citation Related Structures: 
    7FFA, 7FFC, 7FFG, 7FFH, 7FFI

  • PubMed Abstract: 

    2-(2-Phenylethyl)chromones (PECs) are the principal constituents contributing to the distinctive fragrance of agarwood. How PECs are biosynthesized is currently unknown. In this work, we describe a diarylpentanoid-producing polyketide synthase (PECPS) identified from Aquilaria sinensis. Through biotransformation experiments using fluorine-labeled substrate, transient expression of PECPS in Nicotiana benthamiana, and knockdown of PECPS expression in A. sinensis calli, we demonstrate that the C 6 -C 5 -C 6 scaffold of diarylpentanoid is the common precursor of PECs, and PECPS plays a crucial role in PECs biosynthesis. Crystal structure (1.98 Å) analyses and site-directed mutagenesis reveal that, due to its small active site cavity (247 Å 3 ), PECPS employs a one-pot formation mechanism including a "diketide-CoA intermediate-released" step for the formation of the C 6 -C 5 -C 6 scaffold. The identification of PECPS, the pivotal enzyme of PECs biosynthesis, provides insight into not only the feasibility of overproduction of pharmaceutically important PECs using metabolic engineering approaches, but also further exploration of how agarwood is formed.


  • Organizational Affiliation
    • Modern Research Center for Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, People's Republic of China.

Macromolecule Content 

  • Total Structure Weight: 93.69 kDa 
  • Atom Count: 5,966 
  • Modeled Residue Count: 771 
  • Deposited Residue Count: 862 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Type III polyketide synthase
A, B
431Aquilaria sinensisMutation(s): 1 
UniProt
Find proteins for A0A385MEG6 (Aquilaria sinensis)
Explore A0A385MEG6 
Go to UniProtKB:  A0A385MEG6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A385MEG6
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.405α = 90
b = 65.196β = 128.109
c = 108.394γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2022-04-06
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description