9X0I | pdb_00009x0i

Glyoxysomal Citrate Synthase 3 from Arabidopsis thaliana in complex with OAA and CoA

PDB DOI: https://doi.org/10.2210/pdb9X0I/pdb

Classification: TRANSFERASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-09-30 Released: 2026-02-04
Deposition Author(s): Nishio, K., Takagi, K., Mizushima, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.197 (Depositor), 0.206 (DCC)
R-Value Work:
0.166 (Depositor), 0.172 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of glyoxysomal citrate synthase 3 from Arabidopsis thaliana reveals a novel oligomeric state.

Nishio, K., Takagi, K., Mizushima, T.

(2026) J Struct Biol 218: 108293-108293

PubMed: 41580056 Search on PubMed
DOI: https://doi.org/10.1016/j.jsb.2026.108293
Primary Citation Related Structures:
9X0I, 9XAU, 9XDG

PubMed Abstract:
Citrate synthase (CS) is a pivotal enzyme in carbohydrate and energy metabolism, with distinct isoforms present in various eukaryotic compartments, including mitochondria and glyoxysomes in plants. While CSs exhibit diverse oligomeric states, detailed structural information on higher plant non-mitochondrial Type II CSs has been limited. We herein determined the crystal structures of CS 3 from Arabidopsis thaliana (AtCSY3) in complex with oxaloacetate (OAA) and acetyl-coenzyme A (CoA)-OAA at resolutions of 2.0 and 1.7 Å, respectively. These structures revealed that AtCSY3 can form a homo-tetrameric assembly that is distinct from the hexameric Escherichia coli CS and the octameric Ananas comosus CS. The tetrameric arrangement observed in the crystal structure is mediated by hydrogen-bonding and hydrophobic interactions between subunits. Gel filtration chromatography further suggests the presence of a tetrameric species in solution under the purification conditions. Ligand density was observed near the interface between the two dimers in the tetrameric structure; however, no experimental evidence is currently available to determine whether ligand binding affects the oligomeric state or enzymatic activity of AtCSY3. These structures illustrate the structural diversity of CS oligomerization and provide a structural basis for studies of plant glyoxysomal CSs.

Organizational Affiliation

Department of Science, Graduate School of Science, University of Hyogo, 2167, Shosha, Himeji 671-2280, Japan.

Macromolecule Content

Total Structure Weight: 108 kDa
Atom Count: 7,902
Modeled Residue Count: 881
Deposited Residue Count: 958
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Citrate synthase 3, peroxisomal	A, B	479	Arabidopsis thaliana	Mutation(s): 0 Gene Names: CSY3, At2g42790, F7D19.21 EC: 2.3.3.16
UniProt
Find proteins for Q9SJH7 (Arabidopsis thaliana) Explore Q9SJH7 Go to UniProtKB: Q9SJH7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9SJH7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B]	D [auth A], K [auth B]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]
OAA Query on OAA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	OXALOACETATE ION C₄ H₃ O₅ KHPXUQMNIQBQEV-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth A], M [auth B], N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B]