3KRA

Mint heterotetrameric geranyl pyrophosphate synthase in complex with magnesium

PDB DOI: https://doi.org/10.2210/pdb3KRA/pdb

Classification: TRANSFERASE
Organism(s): Mentha x piperita
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-11-18 Released: 2010-02-23
Deposition Author(s): Chang, T.-H., Ko, T.-P., Hsieh, F.-L., Wang, A.H.-J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.216
R-Value Work: 0.176
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structure of a heterotetrameric geranyl pyrophosphate synthase from mint (Mentha piperita) reveals intersubunit regulation

Chang, T.-H., Hsieh, F.-L., Ko, T.-P., Teng, K.-H., Liang, P.-H., Wang, A.H.-J.

(2010) Plant Cell 22: 454-467

PubMed: 20139160 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1105/tpc.109.071738
Primary Citation of Related Structures:
3KRA, 3KRC, 3KRF, 3KRO, 3KRP

PubMed Abstract:
Terpenes (isoprenoids), derived from isoprenyl pyrophosphates, are versatile natural compounds that act as metabolism mediators, plant volatiles, and ecological communicators. Divergent evolution of homomeric prenyltransferases (PTSs) has allowed PTSs to optimize their active-site pockets to achieve catalytic fidelity and diversity. Little is known about heteromeric PTSs, particularly the mechanisms regulating formation of specific products. Here, we report the crystal structure of the (LSU . SSU)(2)-type (LSU/SSU = large/small subunit) heterotetrameric geranyl pyrophosphate synthase (GPPS) from mint (Mentha piperita). The LSU and SSU of mint GPPS are responsible for catalysis and regulation, respectively, and this SSU lacks the essential catalytic amino acid residues found in LSU and other PTSs. Whereas no activity was detected for individually expressed LSU or SSU, the intact (LSU . SSU)(2) tetramer produced not only C(10)-GPP at the beginning of the reaction but also C(20)-GGPP (geranylgeranyl pyrophosphate) at longer reaction times. The activity for synthesizing C(10)-GPP and C(20)-GGPP, but not C(15)-farnesyl pyrophosphate, reflects a conserved active-site structure of the LSU and the closely related mustard (Sinapis alba) homodimeric GGPPS. Furthermore, using a genetic complementation system, we showed that no C(20)-GGPP is produced by the mint GPPS in vivo. Presumably through protein-protein interactions, the SSU remodels the active-site cavity of LSU for synthesizing C(10)-GPP, the precursor of volatile C(10)-monoterpenes.

Organizational Affiliation

Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan. r93b46009@ntu.edu.tw

Macromolecule Content

Total Structure Weight: 123.54 kDa
Atom Count: 9,540
Modelled Residue Count: 1,086
Deposited Residue Count: 1,138
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranyl diphosphate synthase large subunit	A, D	295	Mentha x piperita	Mutation(s): 0 Gene Names: GPPS Large Subunit EC: 2.5.1.1
UniProt
Find proteins for Q9SBR3 (Mentha piperita) Explore Q9SBR3 Go to UniProtKB: Q9SBR3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9SBR3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranyl diphosphate synthase small subunit	B, C	274	Mentha x piperita	Mutation(s): 0 Gene Names: GPPS Small subunit EC: 2.5.1.1
UniProt
Find proteins for Q9SBR4 (Mentha piperita) Explore Q9SBR4 Go to UniProtKB: Q9SBR4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9SBR4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth C] MOL2 format, chain G [auth C]	G [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Interactions & Density Focus chain G [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth D] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain F [auth A]	E [auth A], F [auth A], H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.216
R-Value Work: 0.176
R-Value Observed: 0.196
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.281	α = 90
b = 109.255	β = 90
c = 182.504	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-02-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-02-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2014-02-12
Changes: Database references
Version 1.3: 2017-11-01
Changes: Refinement description
Version 1.4: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description