9OU1 | pdb_00009ou1

Crystal structure of maize AKR4C13 in P21 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.183 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.159 (Depositor), 0.169 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Functional genomics and structural insights into maize aldo-keto reductase-4 family: Stress metabolism and substrate specificity in embryos.

Morais de Sousa, S.Oliveira de Giuseppe, P.Murakami, M.T.Guan, J.C.Saunders, J.W.Kiyota, E.Santos, M.L.Schmelz, E.A.Yunes, J.A.Koch, K.E.

(2025) J Biological Chem 301: 110404-110404

  • DOI: https://doi.org/10.1016/j.jbc.2025.110404
  • Primary Citation of Related Structures:  
    9OU1

  • PubMed Abstract: 

    Aldo-keto reductases (AKRs) are ubiquitous in nature and are able to reduce a wide range of substrates, from simple sugars to potentially toxic aldehydes. In plants, AKRs are involved in key metabolic processes including reactive aldehyde detoxification. This study aimed to i) delineate a maize gene family encoding Aldo Keto Reductase-4s (AKR4s) ii) help bridge sequence-to-function gaps among them, and iii) focus on a family member implicated in embryo specific stress metabolism. We employed a genome-wide analysis approach to identify maize genes encoding AKR4s, defining and annotating a 15-member gene family that clustered into three subgroups. Expression profiling, validated through wet lab experiments, revealed distinct functional roles: i) AKR4C Zm-1 functions in aldehyde detoxification during stress, ii) AKR4C Zm-2 includes stress-responsive AKRs with diverse substrate affinities, and iii) AKR4A/B Zm-3 contributes to specialized metabolites like phytosiderophores for iron transport. To investigate the impact of sequence variation on function, we characterized ZmAKR4C13, a representative of AKR4C Zm-1. Its mRNA and protein were predominantly localized in embryos, suggesting a specialized role. Recombinant ZmAKR4C13 efficiently reduced methylglyoxal and small aldehydes but showed poor activity toward aldoses larger than four carbons. Crystallographic analysis identified a size constraint at the active site, attributed to the bulkier LEU residue at position 294. Collectively, our results emphasize how subtle modifications in active-site architecture influence AKR substrate specificity. They also demonstrate a potential role of maize ZmAKR4C13 in detoxifying methylglyoxal and other small metabolites that could contribute to stress signaling in embryos.


  • Organizational Affiliation
    • Embrapa Maize and Sorghum, Sete Lagoas, MG, Brazil, 35701-970. Electronic address: sylvia.sousa@embrapa.br.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldose reductase, AKR4C13
A, B
327Zea maysMutation(s): 0 
Gene Names: AR3
UniProt
Find proteins for E9JVD4 (Zea mays)
Explore E9JVD4 
Go to UniProtKB:  E9JVD4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9JVD4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A, B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.183 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.159 (Depositor), 0.169 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.823α = 90
b = 115.37β = 104.247
c = 56.532γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
BALBESphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institute of Food and Agriculture (NIFA, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2025-07-30
    Changes: Database references