7F14

Crystal structure of isomerase Dcr3 complex with substrate analogue 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.212 

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This is version 1.1 of the entry. See complete history


Literature

Structural Basis for Isomerization Reactions in Fungal Tetrahydroxanthone Biosynthesis and Diversification.

Yang, J.Mori, T.Wei, X.Matsuda, Y.Abe, I.

(2021) Angew Chem Int Ed Engl 60: 19458-19465

  • DOI: https://doi.org/10.1002/anie.202107884
  • Primary Citation of Related Structures:  
    7F0O, 7F0Y, 7F0Z, 7F10, 7F11, 7F13, 7F14

  • PubMed Abstract: 

    The novel isomerase NsrQ, from Aspergillus novofumigatus, is a key enzyme in the biosynthesis of fungal tetrahydroxanthones and is responsible for dearomatizing cyclization to provide a tetrahydroxanthone scaffold. NsrQ catalyzes a two-step isomerization reaction, involving the isomerization of allylic alcohol and subsequent inversion of configuration at the methyl group. We report on the biochemical and structural characterizations of NsrQ, and its homologue Dcr3, from Diaporthe longicolla. The crystal structures of NsrQ and Dcr3 revealed their similar overall structures, with a cone-shaped α+β barrel fold, to those of the nuclear transport factor 2-like superfamily enzymes. Furthermore, the structures of Dcr3 and NsrQ variants complexed with substrate analogues and the site-directed mutagenesis studies identified the catalytic residues and the important hydrophobic residues in shaping the active site pocket for substrate binding. These enzymes thus utilize Glu and His residues as acid-base catalysts. Based on these observations, we proposed a detailed reaction mechanism for NsrQ-catalyzed isomerization reactions.


  • Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dcr3
A, B
172Diaporthe longicollaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0BJ (Subject of Investigation/LOI)
Query on 0BJ

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
methyl 2-[2,6-bis(oxidanyl)phenyl]carbonyl-5-methyl-3-oxidanyl-benzoate
C16 H14 O6
HZZOIPFDIKYDFZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.212 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.094α = 90
b = 104.094β = 90
c = 138.681γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-20
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description