9M53 | pdb_00009m53

Crystal structure of 1L-myo-inositol 1-phosphate synthase 1 from Oryza sativa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 
    0.188 (Depositor), 0.197 (DCC) 
  • R-Value Work: 
    0.148 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 
    0.150 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Chemical inhibition of INO1 reduces phytic acid in rice and wheat grains for enhanced micronutrient bioavailability.

Akabane, T.Kamino, S.Okamura, T.Sugaya, A.Nakamura, M.Ikeda, K.Yonezawa, T.Fukushima, A.Kojima, S.Aoki, Y.Chujo, S.Yamauchi, Y.Shibusawa, R.Ishimaru, K.Nagasaka, S.Katoh, E.Hirotsu, N.

(2026) Nat Food 7: 163-173

  • DOI: https://doi.org/10.1038/s43016-026-01295-3
  • Primary Citation Related Structures: 
    9M53

  • PubMed Abstract: 

    Phytic acid (PA), the major phosphorus storage compound in cereal grains, chelates essential minerals such as iron and zinc, thereby preventing their absorption in the human intestine and contributing to micronutrient deficiencies. Myo-inositol 3-phosphate synthase 1 (INO1) is a key enzyme in PA biosynthesis, catalysing the pathway's first step and determining PA contents in cereal grains. Although the genetic modification of PA biosynthesis enzymes can reduce PA levels in grains by disrupting enzyme function, it often impairs germination and seedling growth. Here we used a plant chemical biology approach targeting INO1 to reduce PA levels in rice (Oryza sativa L.) and wheat (Triticum aestivum L.) through chemical intervention. From over 1,000 molecules, candidate compounds were identified on the basis of biophysical or biochemical screening. When applied to developing seeds in panicles or spikes, these selected compounds reduced the PA content in grains of rice and wheat. This study presents a strategy for developing low-PA crops and contributes to global efforts to reduce malnutrition.


  • Organizational Affiliation
    • Graduate School of Life Sciences, Toyo University, Asaka, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inositol-3-phosphate synthase 1
A, B, C, D
516Oryza sativaMutation(s): 0 
Gene Names: RINO1INO1INO1-1Os03g0192700LOC_Os03g09250
EC: 5.5.1.4
UniProt
Find proteins for O64437 (Oryza sativa subsp. japonica)
Explore O64437 
Go to UniProtKB:  O64437
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO64437
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAI
Query on NAI

Download Ideal Coordinates CCD File 
AA [auth C],
F [auth A],
IA [auth D],
M [auth B]
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
KPG
Query on KPG

Download Ideal Coordinates CCD File 
E [auth A],
HA [auth D],
L [auth B],
Z [auth C]
[(3S,4R,5S)-3,4,5,6,6-pentahydroxy-2-oxo-hexyl] dihydrogen phosphate
C6 H13 O10 P
GGBBRMAUDBKNLU-WISUUJSJSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
FA [auth C]
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
JA [auth D],
KA [auth D],
LA [auth D],
MA [auth D],
N [auth B],
NA [auth D],
O [auth B],
OA [auth D],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
GA [auth C],
K [auth A],
PA [auth D],
Y [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free:  0.188 (Depositor), 0.197 (DCC) 
  • R-Value Work:  0.148 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 0.150 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.301α = 90
b = 137.079β = 90
c = 217.966γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
BUCCANEERmodel building
Cootmodel building
MOLREPphasing
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan23K05066
Japan Society for the Promotion of Science (JSPS)Japan23KJ1979
Japan Science and TechnologyJapanJPMJSP2159

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-04
    Type: Initial release
  • Version 1.1: 2026-03-25
    Changes: Database references