8AGQ | pdb_00008agq

Crystal structure of anthocyanin-related GSTF8 from Populus trichocarpa in complex with (-)-catechin and glutathione

PDB DOI: https://doi.org/10.2210/pdb8AGQ/pdb

Classification: TRANSFERASE
Organism(s): Populus trichocarpa
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-07-20 Released: 2023-08-30
Deposition Author(s): Eichenberger, M., Hueppi, S., Schwander, T., Mittl, P., Buller, M.R.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.09 Å
R-Value Free:
0.149 (Depositor), 0.149 (DCC)
R-Value Work:
0.132 (Depositor), 0.133 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The catalytic role of glutathione transferases in heterologous anthocyanin biosynthesis.

Eichenberger, M., Schwander, T., Huppi, S., Kreuzer, J., Mittl, P.R.E., Peccati, F., Jimenez-Oses, G., Naesby, M., Buller, R.M.

(2023) Nat Catal 6: 927-938

PubMed: 37881531 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41929-023-01018-y
Primary Citation Related Structures:
8AGQ

PubMed Abstract:
Anthocyanins are ubiquitous plant pigments used in a variety of technological applications. Yet, after over a century of research, the penultimate biosynthetic step to anthocyanidins attributed to the action of leucoanthocyanidin dioxygenase has never been efficiently reconstituted outside plants, preventing the construction of heterologous cell factories. Through biochemical and structural analysis, here we show that anthocyanin-related glutathione transferases, currently implicated only in anthocyanin transport, catalyse an essential dehydration of the leucoanthocyanidin dioxygenase product, flavan-3,3,4-triol, to generate cyanidin. Building on this knowledge, introduction of anthocyanin-related glutathione transferases into a heterologous biosynthetic pathway in baker's yeast results in >35-fold increased anthocyanin production. In addition to unravelling the long-elusive anthocyanin biosynthesis, our findings pave the way for the colourants' heterologous microbial production and could impact the breeding of industrial and ornamental plants.

Organizational Affiliation

Competence Center for Biocatalysis, Zurich University of Applied Sciences, Wädenswil, Switzerland.

Macromolecule Content

Total Structure Weight: 25.17 kDa
Atom Count: 2,269
Modeled Residue Count: 213
Deposited Residue Count: 214
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione transferase	A	214	Populus trichocarpa	Mutation(s): 0 Gene Names: POPTR_017G138800 EC: 2.5.1.18
UniProt
Find proteins for B9MWW0 (Populus trichocarpa) Explore B9MWW0 Go to UniProtKB: B9MWW0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B9MWW0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH (Subject of Investigation/LOI) Query on GSH Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	Glutathione C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
M5O (Subject of Investigation/LOI) Query on M5O Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(2~{S},3~{R})-2-[3,4-bis(oxidanyl)phenyl]-3,4-dihydro-2~{H}-chromene-3,5,7-triol C₁₅ H₁₄ O₆ PFTAWBLQPZVEMU-HIFRSBDPSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH) Query on PRD_002593	B [auth A]	Glutathione	Peptide-like / Oxidation-reduction		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]