8HAR | pdb_00008har

SAH-bound C-Methyltransferase Fur6 from Streptomyces sp. KO-3988

PDB DOI: https://doi.org/10.2210/pdb8HAR/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Streptomyces sp. KO-3988
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-10-26 Released: 2023-11-01
Deposition Author(s): Noguchi, T., Nagata, R., Tomita, T., Kuzuyama, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.256 (Depositor), 0.258 (DCC)
R-Value Work:
0.211 (Depositor), 0.215 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Biosynthesis of the tetrahydroxynaphthalene-derived meroterpenoid furaquinocin via reductive deamination and intramolecular hydroalkoxylation of an alkene.

Noguchi, T., Zhao, F., Moriwaki, Y., Yamamoto, H., Kudo, K., Nagata, R., Tomita, T., Terada, T., Shimizu, K., Nishiyama, M., Kuzuyama, T.

(2025) Chem Sci

PubMed: 40191119 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1039/d4sc08319a
Primary Citation Related Structures:
8HAR

PubMed Abstract:
Hybrid isoprenoid-polyketides, known as meroterpenoids, are a family of natural products that exhibit various bioactivities and are promising drug scaffolds. Despite the structural diversity of 1,3,6,8-tetrahydroxynaphthalene (THN)-derived meroterpenoids, such as furaquinocin, naphterpin, and furanonaphthoquinone, several biosynthetic genes for these compounds are conserved, suggesting a shared biosynthetic mechanism. However, the common biosynthetic mechanism and pathway-specific structural diversification mechanisms of these meroterpenoids are not yet fully understood. This study reveals the biosynthetic pathway for furaquinocin, demonstrating that it involves reductive deamination to form a key hydroquinone intermediate essential for subsequent reactions, including a unique cyclization step. We identified the mechanism of reductive deamination of the biosynthetic intermediate 8-amino-flaviolin through transient diazotization, leading to the formation of the hydroquinone intermediate 1,2,4,5,7-pentahydroxynaphthalene (PHN). Structural and computational studies confirmed that PHN is a key substrate for the subsequent methylation. We also showed that the hydroquinone intermediates are prerequisites for the subsequent pathway-specific reactions, including prenylation and novel intramolecular hydroalkoxylation of an alkene. This hydroalkoxylation reaction is notable in that a methyltransferase homolog catalyzes it in an S -adenosylmethionine-independent manner. Our findings provide a new model for furaquinocin biosynthesis, offering insights into the biosynthetic strategies for THN-derived meroterpenoids.

Organizational Affiliation

Graduate School of Agricultural and Life Sciences, The University of Tokyo 1-1-1 Yayoi, Bunkyo-ku Tokyo 113-8657 Japan utkuz@g.ecc.u-tokyo.ac.jp.

Macromolecule Content

Total Structure Weight: 77.79 kDa
Atom Count: 5,483
Modeled Residue Count: 714
Deposited Residue Count: 714
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fur6	A, B	357	Streptomyces sp. KO-3988	Mutation(s): 0
UniProt
Find proteins for Q2L6E4 (Streptomyces sp. (strain KO-3988)) Explore Q2L6E4 Go to UniProtKB: Q2L6E4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2L6E4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH (Subject of Investigation/LOI) Query on SAH Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]