6KUN | pdb_00006kun

Crystal structure of dioxygenase for auxin oxidation (DAO) in rice

PDB DOI: https://doi.org/10.2210/pdb6KUN/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Oryza sativa Indica Group
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-09-02 Released: 2020-05-13
Deposition Author(s): Takehara, S., Mikami, B., Sakuraba, S., Matsuoka, M., Ueguchi-Tanaka, M.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.243 (Depositor), 0.254 (DCC)
R-Value Work:
0.188 (Depositor), 0.205 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

PubMed: 32358569 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-020-16068-0
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 65.29 kDa
Atom Count: 4,839
Modeled Residue Count: 588
Deposited Residue Count: 600
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-oxoglutarate-dependent dioxygenase DAO	A, B	300	Oryza sativa Indica Group	Mutation(s): 0 Gene Names: DAO, OsI_16300, OSIGBa0106G07.8 EC: 1.14.11
UniProt
Find proteins for Q01IX6 (Oryza sativa subsp. indica) Explore Q01IX6 Go to UniProtKB: Q01IX6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q01IX6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IAC (Subject of Investigation/LOI) Query on IAC Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B]	1H-INDOL-3-YLACETIC ACID C₁₀ H₉ N O₂ SEOVTRFCIGRIMH-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
AKG Query on AKG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], I [auth B], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.243 (Depositor), 0.254 (DCC)
R-Value Work: 0.188 (Depositor), 0.205 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.247	α = 90
b = 78.304	β = 90
c = 94.003	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-05-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	16H06468
Japan Society for the Promotion of Science (JSPS)	Japan	16H06464

Revision History (Full details and data files)

Version 1.0: 2020-05-13
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary