8RQH | pdb_00008rqh

Crystal Structure of the flavoprotein monooxygenase TrlE from Streptomyces cyaneofuscatus Soc7

PDB DOI: https://doi.org/10.2210/pdb8RQH/pdb

Classification: FLAVOPROTEIN
Organism(s): Streptomyces cyaneofuscatus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-01-18 Released: 2024-05-15
Deposition Author(s): Sowa, S.T., Hoeing, L.S., Jakob, R.P., Maier, T., Teufel, R.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.238 (Depositor), 0.242 (DCC)
R-Value Work:
0.191 (Depositor), 0.198 (DCC)

Starting Model: in silico
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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

Biosynthesis of the bacterial antibiotic 3,7-dihydroxytropolone through enzymatic salvaging of catabolic shunt products.

Hoing, L., Sowa, S.T., Toplak, M., Reinhardt, J.K., Jakob, R., Maier, T., Lill, M.A., Teufel, R.

(2024) Chem Sci 15: 7749-7756

PubMed: 38784727 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1039/d4sc01715c
Primary Citation Related Structures:
8RQH

PubMed Abstract:
The non-benzenoid aromatic tropone ring is a structural motif of numerous microbial and plant natural products with potent bioactivities. In bacteria, tropone biosynthesis involves early steps of the widespread CoA-dependent phenylacetic acid (paa) catabolon, from which a shunt product is sequestered and surprisingly further utilized as a universal precursor for structurally and functionally diverse tropone derivatives such as tropodithietic acid or (hydroxy)tropolones. Here, we elucidate the biosynthesis of the antibiotic 3,7-dihydroxytropolone in Actinobacteria by in vitro pathway reconstitution using paa catabolic enzymes as well as dedicated downstream tailoring enzymes, including a thioesterase (TrlF) and two flavoprotein monooxygenases (TrlCD and TrlE). We furthermore mechanistically and structurally characterize the multifunctional key enzyme TrlE, which mediates an unanticipated ipso -substitution involving a hydroxylation and subsequent decarboxylation of the CoA-freed side chain, followed by ring oxidation to afford tropolone. This study showcases a remarkably efficient strategy for 3,7-dihydroxytropolone biosynthesis and illuminates the functions of the involved biosynthetic enzymes.

Organizational Affiliation

Pharmaceutical Biology, Department of Pharmaceutical Sciences, University of Basel Klingelbergstrasse 50 4056 Basel Switzerland robin.teufel@unibas.ch.

Macromolecule Content

Total Structure Weight: 94.31 kDa
Atom Count: 6,060
Modeled Residue Count: 763
Deposited Residue Count: 852
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tropone 2-monooxygenase	A, B	426	Streptomyces cyaneofuscatus	Mutation(s): 0 Gene Names: trlE
UniProt
Find proteins for A0A2S1JZI9 (Streptomyces cyaneofuscatus) Explore A0A2S1JZI9 Go to UniProtKB: A0A2S1JZI9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2S1JZI9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B]	D [auth A], G [auth B], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]