9RS2 | pdb_00009rs2

Sesterterpene Synthase from Kitasatospora viridis in complex with the surrogate GFSPP

PDB DOI: https://doi.org/10.2210/pdb9RS2/pdb

Classification: LYASE
Organism(s): Kitasatospora viridis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-06-30 Released: 2025-09-24
Deposition Author(s): Li, H., Troycke, P., Yin, Z., Groll, M., Dickschat, J.S.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.238 (Depositor), 0.243 (DCC)
R-Value Work:
0.193 (Depositor), 0.202 (DCC)
R-Value Observed:
0.195 (Depositor)

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

Structure-Guided Engineering of a Bacterial Sesterterpene Synthase for Sesterviridene Diversification.

Li, H., Troycke, P., Yin, Z., Groll, M., Dickschat, J.S.

(2025) J Am Chem Soc 147: 34901-34909

PubMed: 40931719 Search on PubMed
DOI: https://doi.org/10.1021/jacs.5c11309
Primary Citation of Related Structures:
9RRZ, 9RS2, 9RS4, 9RS5

PubMed Abstract:
Terpene synthases produce a remarkable structural diversity from acyclic precursors through complex carbocation cascades. Here, we report the crystal structure of the bacterial sesterterpene synthase StvirS bound to geranylfarnesyl thiopyrophosphate (GFSPP), revealing a preorganized active site that enforces a defined folding of the C25 backbone. Guided by this structure, active-site engineering at 11 positions yielded 23 enzyme variants and 13 new sesterterpenes. Specific substitutions altered reaction trajectories, stereochemistry, or induced premature termination, emphasizing the sensitivity of StvirS to subtle structural changes. Isotopic labeling established the absolute configurations of 11 products and experimentally confirmed a conserved cyclization pathway. These results illustrate how precise noncovalent interactions govern terpene biosynthesis and highlight the promise of structure-based design to reprogram terpene cyclase reactivity.

Organizational Affiliation

Kekulé Institute for Organic Chemistry and Biochemistry,University of Bonn,Gerhard-Domagk-Straße 1,Bonn 53121,Germany.

Macromolecule Content

Total Structure Weight: 81.02 kDa
Atom Count: 5,569
Modeled Residue Count: 678
Deposited Residue Count: 710
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Terpene synthase	A, B	355	Kitasatospora viridis	Mutation(s): 0 Gene Names: FHX73_1760 EC: 4.2.3
UniProt
Find proteins for A0A561SAF2 (Kitasatospora viridis) Explore A0A561SAF2 Go to UniProtKB: A0A561SAF2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A561SAF2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JI6 (Subject of Investigation/LOI) Query on A1JI6 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	[(2~{E},6~{E},10~{E},14~{E})-3,7,11,15,19-pentamethylicosa-2,6,10,14,18-pentaenyl]sulfanyl-phosphonooxy-phosphinic acid C₂₅ H₄₄ O₆ P₂ S GLTFGFJVZBHKFR-GIXZANJISA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], J [auth B], K [auth B], L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B]	M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]