7QFX | pdb_00007qfx

Crystal structure of Old Yellow Enzyme AnOYE8 from Aspergillus niger


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.266 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.241 (Depositor), 0.270 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The Family Keeps on Growing: Four Novel Fungal OYEs Characterized.

Robescu, M.S.Loprete, G.Gasparotto, M.Vascon, F.Filippini, F.Cendron, L.Bergantino, E.

(2022) Int J Mol Sci 23

  • DOI: https://doi.org/10.3390/ijms23063050
  • Primary Citation of Related Structures:  
    7QFX

  • PubMed Abstract: 

    Aiming at expanding the portfolio of Old Yellow Enzymes (OYEs), which have been systematically studied to be employed in the chemical and pharmaceutical industries as useful biocatalysts, we decided to explore the immense reservoir of filamentous fungi. We drew from the genome of the two Ascomycetes Aspergillus niger and Botryotinia fuckeliana four new members of the OYE superfamily belonging to the classical and thermophilic-like subfamilies. The two Bf OYEs show wider substrate spectra than the An OYE homologues, which appear as more specialized biocatalysts. According to their mesophilic origins, the new enzymes neither show high thermostability nor extreme pH optimums. The crystal structures of Bf OYE4 and An OYE8 have been determined, revealing the conserved features of the thermophilic-like subclass as well as unique properties, such as a peculiar N-terminal loop involved in dimer surface interactions. For the classical representatives Bf OYE1 and An OYE2, model structures were built and analyzed, showing surprisingly wide open access to the active site cavities due to a shorter β6-loop and a disordered capping subdomain.


  • Organizational Affiliation
    • Synthetic Biology and Biotechnology Unit, Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-dependent flavin oxidoreductaseA [auth B],
B [auth C],
C [auth E],
D [auth G]
422Aspergillus nigerMutation(s): 0 
Gene Names: M747DRAFT_320366
EC: 1
UniProt
Find proteins for A2QBV3 (Aspergillus niger (strain ATCC MYA-4892 / CBS 513.88 / FGSC A1513))
Explore A2QBV3 
Go to UniProtKB:  A2QBV3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2QBV3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
F [auth B],
H [auth C],
J [auth E],
L [auth G]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
I [auth E](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth B],
G [auth C],
K [auth E],
M [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.266 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.241 (Depositor), 0.270 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.533α = 90
b = 65.388β = 107.76
c = 181.417γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-20
    Type: Initial release
  • Version 1.1: 2023-03-08
    Changes: Data collection
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description