7EKD

Crystal structure of gibberellin 3-oxidase 2 (GA3ox2) in rice


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Evolutionary alterations in gene expression and enzymatic activities of gibberellin 3-oxidase 1 in Oryza.

Kawai, K.Takehara, S.Kashio, T.Morii, M.Sugihara, A.Yoshimura, H.Ito, A.Hattori, M.Toda, Y.Kojima, M.Takebayashi, Y.Furuumi, H.Nonomura, K.I.Mikami, B.Akagi, T.Sakakibara, H.Kitano, H.Matsuoka, M.Ueguchi-Tanaka, M.

(2022) Commun Biol 5: 67-67

  • DOI: https://doi.org/10.1038/s42003-022-03008-5
  • Primary Citation of Related Structures:  
    7EKD

  • PubMed Abstract: 

    Proper anther and pollen development are important for plant reproduction. The plant hormone gibberellin is important for anther development in rice, but its gametophytic functions remain largely unknown. Here, we report the functional and evolutionary analyses of rice gibberellin 3-oxidase 1 (OsGA3ox1), a gibberellin synthetic enzyme specifically expressed in the late developmental stages of anthers. Enzymatic and X-ray crystallography analyses reveal that OsGA3ox1 has a higher GA 7 synthesis ratio than OsGA3ox2. In addition, we generate an osga3ox1 knockout mutant by genome editing and demonstrate the bioactive gibberellic acid synthesis by the OsGA3ox1 action during starch accumulation in pollen via invertase regulation. Furthermore, we analyze the evolution of Oryza GA3ox1s and reveal that their enzyme activity and gene expression have evolved in a way that is characteristic of the Oryza genus and contribute to their male reproduction ability.


  • Organizational Affiliation

    Bioscience and Biotechnology Center, Nagoya University, Chikusa, Nagoya, 464-8601, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gibberellin 3-beta-dioxygenase 2373Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: GA3OX2D18Os01g0177400LOC_Os01g08220OsJ_00594P0013F10.29
EC: 1.14.11.15
UniProt
Find proteins for Q9FU53 (Oryza sativa subsp. japonica)
Explore Q9FU53 
Go to UniProtKB:  Q9FU53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FU53
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J5X (Subject of Investigation/LOI)
Query on J5X

Download Ideal Coordinates CCD File 
H [auth A]Gibberellin A9
C19 H24 O4
MHVYWTXXZIFXDT-YGNOGLJPSA-N
AKG (Subject of Investigation/LOI)
Query on AKG

Download Ideal Coordinates CCD File 
F [auth A]2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
G [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.838α = 90
b = 45.594β = 102.26
c = 68.538γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

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)Japan16H06464
Japan Society for the Promotion of Science (JSPS)Japan16H06468
Japan Society for the Promotion of Science (JSPS)Japan16H04907
Japan Society for the Promotion of Science (JSPS)Japan20H03272

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-16
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description