2ONG | pdb_00002ong

Crystal Structure of of limonene synthase with 2-fluorogeranyl diphosphate (FGPP) ezymatically converted to 2-fluorolinalyl diphosphate (FLPP)

PDB DOI: https://doi.org/10.2210/pdb2ONG/pdb

Classification: LYASE
Organism(s): Mentha spicata
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-01-23 Released: 2007-03-06
Deposition Author(s): Hyatt, D.C., Youn, B., Croteau, R., Kang, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.241 (Depositor), 0.230 (DCC)
R-Value Work:
0.208 (Depositor), 0.220 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Structure of limonene synthase, a simple model for terpenoid cyclase catalysis.

Hyatt, D.C., Youn, B., Zhao, Y., Santhamma, B., Coates, R.M., Croteau, R.B., Kang, C.

(2007) Proc Natl Acad Sci U S A 104: 5360-5365

PubMed: 17372193 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.0700915104
Primary Citation Related Structures:
2ONG, 2ONH

PubMed Abstract:
The crystal structure of (4S)-limonene synthase from Mentha spic ata, a metal ion-dependent monoterpene cyclase that catalyzes the coupled isomerization and cyclization of geranyl diphosphate, is reported at 2.7-A; resolution in two forms liganded to the substrate and intermediate analogs, 2-fluorogeranyl diphosphate and 2-fluorolinalyl diphosphate, respectively. The implications of these findings are described for domain interactions in the homodimer and for changes in diphosphate-metal ion coordination and substrate binding conformation in the course of the multistep reaction.

Organizational Affiliation

Institute of Biological Chemistry, Washingston State University, Pullman, WA 99164-6340, USA.

Macromolecule Content

Total Structure Weight: 129.62 kDa
Atom Count: 9,181
Modeled Residue Count: 1,086
Deposited Residue Count: 1,086
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4S-limonene synthase	A, B	543	Mentha spicata	Mutation(s): 1
UniProt
Find proteins for Q40322 (Mentha spicata) Explore Q40322 Go to UniProtKB: Q40322
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q40322
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F3P Query on F3P Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B]	F [auth A], L [auth B]	(3S)-2-fluoro-3,7-dimethylocta-1,6-dien-3-yl trihydrogen diphosphate C₁₀ H₁₉ F O₇ P₂ UEWCETXFDYIXPA-JTQLQIEISA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B]
BTB Query on BTB Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	G [auth A], H [auth A], M [auth B], N [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A] D [auth A] E [auth A] I [auth B] J [auth B] C [auth A], D [auth A], E [auth A], I [auth B], J [auth B], K [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.241 (Depositor), 0.230 (DCC)
R-Value Work: 0.208 (Depositor), 0.220 (DCC)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 200.48	α = 90
b = 200.48	β = 90
c = 123.41	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
X-PLOR	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-03-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-03-06
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations
Version 1.4: 2023-08-30
Changes: Data collection, Refinement description
Version 2.0: 2025-10-01
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary