9M7E | pdb_00009m7e

Crystal structure of AsDMS D333N mutant in complex with drimenyl phosphate

PDB DOI: https://doi.org/10.2210/pdb9M7E/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Aquimarina spongiae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-03-10 Released: 2025-09-10
Deposition Author(s): Fujiyama, K., Vo, N.N.Q., Takahashi, S.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.243 (Depositor), 0.217 (DCC)
R-Value Work:
0.202 (Depositor)
R-Value Observed:
0.204 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structural insights into a bacterial terpene cyclase fused with haloacid Dehalogenase-like phosphatase.

Fujiyama, K., Takagi, H., Vo, N.N.Q., Morita, N., Nogawa, T., Takahashi, S.

(2025) Chem Sci 16: 15310-15319

PubMed: 40852458 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1039/d5sc04719f
Primary Citation Related Structures:
9M7D, 9M7E, 9M7F

PubMed Abstract:
Terpene cyclases (TCs), consisting of various combinations of α, β, and γ domains, have been extensively studied. Recently, non-canonical enzymes comprising a TCβ domain and a haloacid dehalogenase (HAD)-like domain (referred to as HAD-TCβ) have been discovered. However, their overall structure remains unclear. In this study, we determined the co-crystal structures of drimenol synthase from Aquimarina spongiae (AsDMS), which catalyzes the conversion of farnesyl pyrophosphate (1) into drimenol (2). Crystallographic analyses of the enzyme bound to substrates 1 and drimenyl monophosphate (3) demonstrated that the TCβ domain catalyzes a class II cyclization reaction initiated by protonation, whereas the HAD domain catalyzes a phosphatase-like dephosphorylation reaction dependent on a divalent metal. Crystallographic and gel filtration analyses revealed that AsDMS adopts a dimeric assembly. This dimerization positioned the TCβ and HAD domains to facilitate efficient substrate transfer via electrostatic substrate channeling. Furthermore, to investigate the structure-function relationship of the AsDMS TCβ domain, we used AlphaFold2 to model the structure of the fungal albicanol (4) synthase. Comparative analysis of active-site residues between AsDMS and fungal 4-synthase enabled rational protein engineering, converting AsDMS activity from 2-synthase to 4-synthase. This study provides insights into the biosynthesis of valuable drimane-type sesquiterpenes via targeted mutagenesis.

Organizational Affiliation

Natural Product Biosynthesis Research Unit, RIKEN Center for Sustainable Resource Science Wako Saitama 351-0198 Japan shunjitaka@riken.jp.

Macromolecule Content

Total Structure Weight: 123.15 kDa
Atom Count: 8,521
Modeled Residue Count: 1,023
Deposited Residue Count: 1,042
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED	A, B	521	Aquimarina spongiae	Mutation(s): 1 Gene Names: SAMN04488508_102320
UniProt
Find proteins for A0A1M6CXF0 (Aquimarina spongiae) Explore A0A1M6CXF0 Go to UniProtKB: A0A1M6CXF0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1M6CXF0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FPP (Subject of Investigation/LOI) Query on FPP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain P [auth B] MOL2 format, chain C [auth A] MOL2 format, chain P [auth B] mmCIF format, chain C [auth A] mmCIF format, chain P [auth B]	C [auth A], P [auth B]	FARNESYL DIPHOSPHATE C₁₅ H₂₈ O₇ P₂ VWFJDQUYCIWHTN-YFVJMOTDSA-N		Interactions Focus chain C [auth A] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain P [auth B]
A1MAK (Subject of Investigation/LOI) Query on A1MAK Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain Y [auth B] MOL2 format, chain O [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain O [auth A] mmCIF format, chain Y [auth B]	O [auth A], Y [auth B]	drimenyl phosphate C₁₅ H₂₇ O₄ P SUUFHHSNBZAZJL-KCQAQPDRSA-N		Interactions Focus chain O [auth A] Focus chain Y [auth B] Interactions & Density Focus chain O [auth A] Focus chain Y [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], R [auth B], S [auth B], T [auth B], U [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain Q [auth B] MOL2 format, chain D [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain D [auth A] mmCIF format, chain Q [auth B]	D [auth A], Q [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain Q [auth B] Interactions & Density Focus chain D [auth A] Focus chain Q [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	L [auth A] M [auth A] N [auth A] V [auth B] W [auth B] L [auth A], M [auth A], N [auth A], V [auth B], W [auth B], X [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]