4Y5T

Structure of FtmOx1 apo with metal Iron


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Endoperoxide formation by an alpha-ketoglutarate-dependent mononuclear non-haem iron enzyme.

Yan, W.Song, H.Song, F.Guo, Y.Wu, C.H.Sae Her, A.Pu, Y.Wang, S.Naowarojna, N.Weitz, A.Hendrich, M.P.Costello, C.E.Zhang, L.Liu, P.Jessie Zhang, Y.

(2015) Nature 527: 539-543

  • DOI: 10.1038/nature15519
  • Primary Citation of Related Structures:  
    4Y5S, 4Y5T

  • PubMed Abstract: 
  • Many peroxy-containing secondary metabolites have been isolated and shown to provide beneficial effects to human health. Yet, the mechanisms of most endoperoxide biosyntheses are not well understood. Although endoperoxides have been suggested as key reaction intermediates in several cases, the only well-characterized endoperoxide biosynthetic enzyme is prostaglandin H synthase, a haem-containing enzyme ...

    Many peroxy-containing secondary metabolites have been isolated and shown to provide beneficial effects to human health. Yet, the mechanisms of most endoperoxide biosyntheses are not well understood. Although endoperoxides have been suggested as key reaction intermediates in several cases, the only well-characterized endoperoxide biosynthetic enzyme is prostaglandin H synthase, a haem-containing enzyme. Fumitremorgin B endoperoxidase (FtmOx1) from Aspergillus fumigatus is the first reported α-ketoglutarate-dependent mononuclear non-haem iron enzyme that can catalyse an endoperoxide formation reaction. To elucidate the mechanistic details for this unique chemical transformation, we report the X-ray crystal structures of FtmOx1 and the binary complexes it forms with either the co-substrate (α-ketoglutarate) or the substrate (fumitremorgin B). Uniquely, after α-ketoglutarate has bound to the mononuclear iron centre in a bidentate fashion, the remaining open site for oxygen binding and activation is shielded from the substrate or the solvent by a tyrosine residue (Y224). Upon replacing Y224 with alanine or phenylalanine, the FtmOx1 catalysis diverts from endoperoxide formation to the more commonly observed hydroxylation. Subsequent characterizations by a combination of stopped-flow optical absorption spectroscopy and freeze-quench electron paramagnetic resonance spectroscopy support the presence of transient radical species in FtmOx1 catalysis. Our results help to unravel the novel mechanism for this endoperoxide formation reaction.


    Organizational Affiliation

    Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Verruculogen synthaseA, B315Aspergillus fumigatus Af293Mutation(s): 0 
Gene Names: ftmOx1ftmFAFUA_8G00230
EC: 1.14.11.38
UniProt
Find proteins for Q4WAW9 (Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100))
Explore Q4WAW9 
Go to UniProtKB:  Q4WAW9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
H [auth B]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A], E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CO
Query on CO

Download Ideal Coordinates CCD File 
G [auth B]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.445α = 90
b = 45.561β = 99.74
c = 105.409γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-02-12 
  • Released Date: 2015-11-04 
  • Deposition Author(s): Yan, W., Zhang, Y.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM093903

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2015-11-18
    Changes: Database references
  • Version 1.2: 2015-12-09
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence