8J59 | pdb_00008j59

The structure of a novel thermophilic-like old yellow enzyme from Aspergillus flavus-AfOYE1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.167 (Depositor), 0.172 (DCC) 
  • R-Value Work: 
    0.144 (Depositor) 
  • R-Value Observed: 
    0.145 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8J59

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Structural and functional characterization of a new thermophilic-like OYE from Aspergillus flavus.

Li, N.Wang, Y.Meng, Y.Lv, Y.Zhang, S.Wei, S.Ma, P.Hu, Y.Lin, H.

(2024) Appl Microbiol Biotechnol 108: 134-134

  • DOI: https://doi.org/10.1007/s00253-023-12963-w
  • Primary Citation Related Structures: 
    8J59

  • PubMed Abstract: 

    Old yellow enzymes (OYEs) have been proven as powerful biocatalysts for the asymmetric reduction of activated alkenes. Fungi appear to be valuable sources of OYEs, but most of the fungal OYEs are unexplored. To expand the OYEs toolbox, a new thermophilic-like OYE (AfOYE1) was identified from Aspergillus flavus strain NRRL3357. The thermal stability analysis showed that the T 1/2 of AfOYE1 was 60 °C, and it had the optimal temperature at 45 °C. Moreover, AfOYE1 exhibited high reduction activity in a wide pH range (pH 5.5-8.0). AfOYE1 could accept cyclic enones, acrylamide, nitroalkenes, and α, β-unsaturated aldehydes as substrates and had excellent enantioselectivity toward prochiral alkenes (> 99% ee). Interestingly, an unexpected (S)-stereoselectivity bioreduction toward 2-methylcyclohexenone was observed. The further crystal structure of AfOYE1 revealed that the "cap" region from Ala132 to Thr182, the loop of Ser316 to Gly325, α short helix of Arg371 to Gln375, and the C-terminal "finger" structure endow the catalytic cavity of AfOYE1 quite deep and narrow, and flavin mononucleotide (FMN) heavily buried at the bottom of the active site tunnel. Furthermore, the catalytic mechanism of AfOYE1 was also investigated, and the results confirmed that the residues His211, His214, and Tyr216 compose its catalytic triad. This newly identified thermophilic-like OYE would thus be valuable for asymmetric alkene hydrogenation in industrial processes. KEY POINTS: A new thermophilic-like OYE AfOYE1 was identified from Aspergillus flavus, and the T 1/2 of AfOYE1 was 60 °C AfOYE1 catalyzed the reduction of 2-methylcyclohexenone with (S)-stereoselectivity The crystal structure of AfOYE1 was revealedv.


  • Organizational Affiliation
    • College of Biological Engineering, Henan Unsssiversity of Technology, 100 Lianhua Street, Zhengzhou, 450001, Henan, China.

Macromolecule Content 

  • Total Structure Weight: 86.31 kDa 
  • Atom Count: 6,997 
  • Modeled Residue Count: 774 
  • Deposited Residue Count: 780 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NADPH dehydrogenase afvA
A, B
390Aspergillus flavus NRRL3357Mutation(s): 0 
Gene Names: afvAAFLA_108540
EC: 1.6.99.1
UniProt
Find proteins for B8N8Q9 (Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / IAM 13836 / NRRL 3357 / JCM 12722 / SRRC 167))
Explore B8N8Q9 
Go to UniProtKB:  B8N8Q9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8N8Q9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN
(Subject of Investigation/LOI)

Query on FMN



Download:Ideal Coordinates CCD File
C [auth A],
K [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
M [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO

Query on EDO



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3

Query on NO3



Download:Ideal Coordinates CCD File
E [auth A]NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
D [auth A],
L [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.167 (Depositor), 0.172 (DCC) 
  • R-Value Work:  0.144 (Depositor) 
  • R-Value Observed: 0.145 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.473α = 90
b = 171.422β = 117.6
c = 50.478γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government232102311151
Other government22A180013
National Natural Science Foundation of China (NSFC)China31900876
Other government2019BS020

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Database references, Structure summary