6KU3

Crystal structure of gibberellin 2-oxidase3 (GA2ox3)in rice


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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Literature

A common allosteric mechanism regulates homeostatic inactivation of auxin and gibberellin.

Takehara, S.Sakuraba, S.Mikami, B.Yoshida, H.Yoshimura, H.Itoh, A.Endo, M.Watanabe, N.Nagae, T.Matsuoka, M.Ueguchi-Tanaka, M.

(2020) Nat Commun 11: 2143-2143

  • DOI: https://doi.org/10.1038/s41467-020-16068-0
  • Primary Citation of Related Structures:  
    6KU3, 6KUN

  • PubMed Abstract: 

    Allosteric regulation is protein activation by effector binding at a site other than the active site. Here, we show via X-ray structural analysis of gibberellin 2-oxidase 3 (GA2ox3), and auxin dioxygenase (DAO), that such a mechanism maintains hormonal homeostasis in plants. Both enzymes form multimers by interacting via GA 4 and indole-3-acetic acid (IAA) at their binding interface. Via further functional analyses we reveal that multimerization of these enzymes gradually proceeds with increasing GA 4 and IAA concentrations; multimerized enzymes have higher specific activities than monomer forms, a system that should favour the maintenance of homeostasis for these phytohormones. Molecular dynamic analysis suggests a possible mechanism underlying increased GA2ox3 activity by multimerization-GA 4 in the interface of oligomerized GA2ox3s may be able to enter the active site with a low energy barrier. In summary, homeostatic systems for maintaining GA and IAA levels, based on a common allosteric mechanism, appear to have developed independently.


  • Organizational Affiliation

    Bioscience and Biotechnology Centre, Nagoya University, Nagoya, 464-8601, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gibberellin 2-beta-dioxygenase 3
A, B, C, D
327Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: GA2OX3Os01g0757200LOC_Os01g55240OJ1414_E05.17
EC: 1.14.11.13
UniProt
Find proteins for Q8S0S6 (Oryza sativa subsp. japonica)
Explore Q8S0S6 
Go to UniProtKB:  Q8S0S6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8S0S6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GA4 (Subject of Investigation/LOI)
Query on GA4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
O [auth B]
U [auth C]
V [auth C]
E [auth A],
F [auth A],
O [auth B],
U [auth C],
V [auth C],
Z [auth D]
GIBBERELLIN A4
C19 H24 O5
RSQSQJNRHICNNH-NFMPGMCNSA-N
AKG
Query on AKG

Download Ideal Coordinates CCD File 
AA [auth D],
G [auth A],
P [auth B],
W [auth C]
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
DA [auth D]
L [auth A]
M [auth A]
N [auth A]
T [auth B]
DA [auth D],
L [auth A],
M [auth A],
N [auth A],
T [auth B],
Y [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
H [auth A]
I [auth A]
J [auth A]
BA [auth D],
CA [auth D],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
Q [auth B],
R [auth B],
S [auth B],
X [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.47α = 90
b = 112.739β = 90
c = 149.51γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
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 ScienceJapan16H06464
Japan Society for the Promotion of ScienceJapan16H06468

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release