5YBO

Fe(II)/(alpha)ketoglutarate-dependent dioxygenase PrhA in complex with preaustinoid A1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

wwPDB Validation 3D Report Full Report



Literature

Structure function and engineering of multifunctional non-heme iron dependent oxygenases in fungal meroterpenoid biosynthesis.

Nakashima, Y.Mori, T.Nakamura, H.Awakawa, T.Hoshino, S.Senda, M.Senda, T.Abe, I.

(2018) Nat Commun 9: 104-104

  • DOI: 10.1038/s41467-017-02371-w
  • Primary Citation of Related Structures:  
    5YBO, 5YBN, 5YBQ, 5YBP, 5YBS, 5YBR, 5YBT, 5YBM, 5YBL

  • PubMed Abstract: 
  • Non-heme iron and α-ketoglutarate (αKG) oxygenases catalyze remarkably diverse reactions using a single ferrous ion cofactor. A major challenge in studying this versatile family of enzymes is to understand their structure-function relationship. AusE ...

    Non-heme iron and α-ketoglutarate (αKG) oxygenases catalyze remarkably diverse reactions using a single ferrous ion cofactor. A major challenge in studying this versatile family of enzymes is to understand their structure-function relationship. AusE from Aspergillus nidulans and PrhA from Penicillium brasilianum are two highly homologous Fe(II)/αKG oxygenases in fungal meroterpenoid biosynthetic pathways that use preaustinoid A1 as a common substrate to catalyze divergent rearrangement reactions to form the spiro-lactone in austinol and cycloheptadiene moiety in paraherquonin, respectively. Herein, we report the comparative structural study of AusE and PrhA, which led to the identification of three key active site residues that control their reactivity. Structure-guided mutagenesis of these residues results in successful interconversion of AusE and PrhA functions as well as generation of the PrhA double and triple mutants with expanded catalytic repertoire. Manipulation of the multifunctional Fe(II)/αKG oxygenases thus provides an excellent platform for the future development of biocatalysts.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. abei@mol.f.u-tokyo.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PrhAA, B314Penicillium brasilianumMutation(s): 0 
Gene Names: prhA
EC: 1.14.11
Find proteins for A0A1E1FFL0 (Penicillium brasilianum)
Explore A0A1E1FFL0 
Go to UniProtKB:  A0A1E1FFL0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8SX
Query on 8SX

Download CCD File 
B
preaustinoid A1
C26 H36 O7
XBLDTXYFLHSWHN-RFMSQVAGSA-N
 Ligand Interaction
AKG
Query on AKG

Download CCD File 
A, B
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.816α = 90
b = 171.816β = 90
c = 45.665γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata processing
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-01-24
    Type: Initial release