6KU3 | pdb_00006ku3

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

PDB DOI: https://doi.org/10.2210/pdb6KU3/pdb

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

Deposited: 2019-08-30 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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.243 (Depositor), 0.246 (DCC)
R-Value Work:
0.197 (Depositor), 0.208 (DCC)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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: 145.54 kDa
Atom Count: 10,323
Modeled Residue Count: 1,262
Deposited Residue Count: 1,308
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gibberellin 2-beta-dioxygenase 3	A, B, C, D	327	Oryza sativa Japonica Group	Mutation(s): 0 Gene Names: GA2OX3, Os01g0757200, LOC_Os01g55240, OJ1414_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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8S0S6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GA4 (Subject of Investigation/LOI) Query on GA4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain O [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain Z [auth D] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain O [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain Z [auth D] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain O [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D]
AKG Query on AKG Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain P [auth B] SDF format, chain G [auth A] SDF format, chain AA [auth D] MOL2 format, chain W [auth C] MOL2 format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain AA [auth D] mmCIF format, chain W [auth C] mmCIF format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain AA [auth D]	AA [auth D], G [auth A], P [auth B], W [auth C]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain G [auth A] Focus chain P [auth B] Focus chain W [auth C] Interactions & Density Focus chain AA [auth D] Focus chain G [auth A] Focus chain P [auth B] Focus chain W [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain T [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain DA [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain T [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain DA [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain T [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain DA [auth D]	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		Interactions Focus chain DA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain T [auth B] Focus chain Y [auth C] Interactions & Density Focus chain DA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain T [auth B] Focus chain Y [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain CA [auth D] SDF format, chain BA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain CA [auth D] MOL2 format, chain BA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain CA [auth D] mmCIF format, chain BA [auth D]	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		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth C]