8YP2 | pdb_00008yp2

the crystal structure of inactive Magnaporthe grisea oxidoreductase in complex with NADP and Glycerol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 
    0.248 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of an Aldo-keto Reductase MGG_00097 from Magnaporthe grisea.

Huang, X.Jiang, H.Lin, Y.Li, X.Bi, C.Qi, S.Tang, D.Wang, Z.Lin, S.

(2025) Plant Pathol J 41: 167-178

  • DOI: https://doi.org/10.5423/PPJ.OA.07.2024.0115
  • Primary Citation Related Structures: 
    8YP2, 8YP9

  • PubMed Abstract: 

    The enzyme MGG_00097 from rice blast fungus (Magnaporthe grisea) is a NADPH-dependent oxidoreductase, involved in synthesizing glycerol from dihydroxyacetone phosphate and dihydroxyacetone. The 35.5-kDa monomer belongs to the aldo-keto reductase superfamily, characterized by a highly conserved catalytic tetrad. This study, elucidates the expression, purification, and kinetic properties of recombinant MGG_00097. The ternary complex of MGG_00097 with NADP+ and glycerol was refined to a 2.9 Å resolution, revealing critical insights into substrate binding and catalysis. NADP+ binds within the active site, with residues Ser221, Leu223, Ser225, Lys271, Ser272, Ser273, Thr274, Arg277, and Asn281 forming the substrate and cofactor-binding pockets. A Y56A mutation reveals the open conformation of the cofactor-binding pocket, with Glu29 and Gln226 functioning as hinge residues for the conformational changes upon cofactor binding. These findings contribute to the understanding of MGG_00097's catalytic mechanism and offer a basis for further biochemical and potential biotechnological applications.


  • Organizational Affiliation
    • Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, 610041 Chengdu, China.

Macromolecule Content 

  • Total Structure Weight: 114.98 kDa 
  • Atom Count: 7,780 
  • Modeled Residue Count: 960 
  • Deposited Residue Count: 996 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NADP-dependent oxidoreductase domain-containing protein
A, B, C
332Pyricularia griseaMutation(s): 0 
Gene Names: PgNI_11595
EC: 1.1.1.156
UniProt
Find proteins for Q0GYU4 (Hypocrea jecorina)
Explore Q0GYU4 
Go to UniProtKB:  Q0GYU4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0GYU4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free:  0.248 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.761α = 90
b = 110.78β = 90
c = 171.508γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release
  • Version 1.1: 2025-04-23
    Changes: Database references