8A7K | pdb_00008a7k

PcIDS1 in complex with Mg2+/Mn2+, IPP, and ZOL

PDB DOI: https://doi.org/10.2210/pdb8A7K/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Phaedon cochleariae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-06-21 Released: 2023-05-31
Deposition Author(s): Ecker, F., Boland, W., Groll, M.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.168 (Depositor), 0.187 (DCC)
R-Value Work:
0.142 (Depositor)
R-Value Observed:
0.143 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Metal-dependent enzyme symmetry guides the biosynthetic flux of terpene precursors.

Ecker, F., Vattekkatte, A., Boland, W., Groll, M.

(2023) Nat Chem 15: 1188-1195

PubMed: 37308711 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41557-023-01235-9
Primary Citation Related Structures:
8A6U, 8A6V, 8A6Z, 8A70, 8A73, 8A74, 8A78, 8A7A, 8A7B, 8A7C, 8A7J, 8A7K, 8A7L, 8A7R, 8A7U

PubMed Abstract:
Terpenoids account for more than 60% of all natural products, and their carbon skeletons originate from common isoprenoid units of different lengths such as geranyl pyrophosphate and farnesyl pyrophosphate. Here we characterize a metal-dependent, bifunctional isoprenyl diphosphate synthase from the leaf beetle Phaedon cochleariae by structural and functional analyses. Inter- and intramolecular cooperative effects in the homodimer strongly depend on the provided metal ions and regulate the biosynthetic flux of terpene precursors to either biological defence or physiological development. Strikingly, a unique chain length determination domain adapts to form geranyl or farnesyl pyrophosphate by altering enzyme symmetry and ligand affinity between both subunits. In addition, we identify an allosteric geranyl-pyrophosphate-specific binding site that shares similarity with end-product inhibition in human farnesyl pyrophosphate synthase. Our combined findings elucidate a deeply intertwined reaction mechanism in the P. cochleariae isoprenyl diphosphate synthase that integrates substrate, product and metal-ion concentrations to harness its dynamic potential.

Organizational Affiliation

Center for Protein Assemblies, Technical University of Munich, Garching, Germany.

Macromolecule Content

Total Structure Weight: 81.75 kDa
Atom Count: 6,325
Modeled Residue Count: 690
Deposited Residue Count: 692
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoprenyl diphosphate synthase	A, B	346	Phaedon cochleariae	Mutation(s): 0 EC: 2.5.1.1
UniProt
Find proteins for M1JS91 (Phaedon cochleariae) Explore M1JS91 Go to UniProtKB: M1JS91
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	M1JS91
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZOL (Subject of Investigation/LOI) Query on ZOL Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain U [auth B] MOL2 format, chain L [auth A] MOL2 format, chain U [auth B] mmCIF format, chain L [auth A] mmCIF format, chain U [auth B]	L [auth A], U [auth B]	ZOLEDRONIC ACID C₅ H₁₀ N₂ O₇ P₂ XRASPMIURGNCCH-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain U [auth B]
IPE (Subject of Investigation/LOI) Query on IPE Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain T [auth B] MOL2 format, chain K [auth A] MOL2 format, chain T [auth B] mmCIF format, chain K [auth A] mmCIF format, chain T [auth B]	K [auth A], T [auth B]	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE C₅ H₁₂ O₇ P₂ NUHSROFQTUXZQQ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain T [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain S [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain S [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain S [auth B]	I [auth A], J [auth A], S [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain S [auth B]
MN (Subject of Investigation/LOI) 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 M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	C [auth A] D [auth A] E [auth A] M [auth B] N [auth B] C [auth A], D [auth A], E [auth A], M [auth B], N [auth B], O [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 M [auth B] Focus chain N [auth B] Focus chain O [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	F [auth A] G [auth A] H [auth A] P [auth B] Q [auth B] F [auth A], G [auth A], H [auth A], P [auth B], Q [auth B], R [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]