5Y7T

Quaternary complex of AsqJ-Fe3+-2OG-D-cyclopeptin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Insights into the Desaturation of Cyclopeptin and its C3 Epimer Catalyzed by a non-Heme Iron Enzyme: Structural Characterization and Mechanism Elucidation.

Liao, H.J.Li, J.Huang, J.L.Davidson, M.Kurnikov, I.Lin, T.S.Lee, J.L.Kurnikova, M.Guo, Y.Chan, N.L.Chang, W.C.

(2018) Angew. Chem. Int. Ed. Engl. 57: 1831-1835

  • DOI: 10.1002/anie.201710567
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • AsqJ, an iron(II)- and 2-oxoglutarate-dependent enzyme found in viridicatin-type alkaloid biosynthetic pathways, catalyzes sequential desaturation and epoxidation to produce cyclopenins. Crystal structures of AsqJ bound to cyclopeptin and its C3 epim ...

    AsqJ, an iron(II)- and 2-oxoglutarate-dependent enzyme found in viridicatin-type alkaloid biosynthetic pathways, catalyzes sequential desaturation and epoxidation to produce cyclopenins. Crystal structures of AsqJ bound to cyclopeptin and its C3 epimer are reported. Meanwhile, a detailed mechanistic study was carried out to decipher the desaturation mechanism. These findings suggest that a pathway involving hydrogen atom abstraction at the C10 position of the substrate by a short-lived FeIV -oxo species and the subsequent formation of a carbocation or a hydroxylated intermediate is preferred during AsqJ-catalyzed desaturation.


    Organizational Affiliation

    Institute of Biochemistry and Molecular Biology, College of Medicine, National (Taiwan) University, Taipei, 100, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Iron/alpha-ketoglutarate-dependent dioxygenase asqJ
B
315Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139)Mutation(s): 0 
Gene Names: asqJ
EC: 1.14.-.-
Find proteins for Q5AR53 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Go to UniProtKB:  Q5AR53
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AKG
Query on AKG

Download SDF File 
Download CCD File 
B
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
8R0
Query on 8R0

Download SDF File 
Download CCD File 
B
(3R)-4-methyl-3-(phenylmethyl)-1,3-dihydro-1,4-benzodiazepine-2,5-dione
C17 H16 N2 O2
KSQNKZMAMGACTL-OAHLLOKOSA-N
 Ligand Interaction
FE
Query on FE

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.199 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 73.471α = 90.00
b = 118.619β = 90.00
c = 66.427γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-08-18 
  • Released Date: 2018-01-24 
  • Deposition Author(s): Liao, H.J.

Revision History 

  • Version 1.0: 2018-01-24
    Type: Initial release
  • Version 1.1: 2018-01-31
    Type: Database references
  • Version 1.2: 2018-02-07
    Type: Database references
  • Version 1.3: 2018-02-21
    Type: Database references