8CI0 | pdb_00008ci0

Maize Transketolase in complex with TPP and hydrolyzed (+)-Cornexistin

PDB DOI: https://doi.org/10.2210/pdb8CI0/pdb

Classification: TRANSFERASE
Organism(s): Zea mays
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-02-08 Released: 2023-03-22
Deposition Author(s): Freigang, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.184 (Depositor), 0.193 (DCC)
R-Value Work:
0.153 (Depositor), 0.165 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Investigations into Simplified Analogues of the Herbicidal Natural Product (+)-Cornexistin.

Steinborn, C., Tancredi, A., Habiger, C., Diederich, C., Kramer, J., Reingruber, A.M., Laber, B., Freigang, J., Lange, G., Schmutzler, D., Machettira, A., Besong, G., Magauer, T., Barber, D.M.

(2023) Chemistry 29: e202300199-e202300199

PubMed: 36807428 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/chem.202300199
Primary Citation Related Structures:
8CI0

PubMed Abstract:
We report the design, synthesis and biological evaluation of simplified analogues of the herbicidal natural product (+)-cornexistin. Guided by an X-Ray co-crystal structure of cornexistin bound to transketolase from Zea mays, we attempted to identify the key interactions that are necessary for cornexistin to maintain its herbicidal profile. This resulted in the preparation of three novel analogues investigating the importance of substituents that are located on the nine-membered ring of cornexistin. One analogue maintained a good level of biological activity and could provide researchers insights in how to further optimize the structure of cornexistin for commercialization in the future.

Organizational Affiliation

Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria.

Macromolecule Content

Total Structure Weight: 226.17 kDa
Atom Count: 17,364
Modeled Residue Count: 1,998
Deposited Residue Count: 2,064
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transketolase, chloroplastic	A [auth AAA], B [auth BBB], C [auth CCC]	688	Zea mays	Mutation(s): 0 EC: 2.2.1.1
UniProt
Find proteins for Q7SIC9 (Zea mays) Explore Q7SIC9 Go to UniProtKB: Q7SIC9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7SIC9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8EL Query on 8EL Download:Ideal Coordinates CCD File SDF format, chain J [auth CCC] MOL2 format, chain J [auth CCC] mmCIF format, chain J [auth CCC]	J [auth CCC]	2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2H-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate C₁₂ H₂₀ N₄ O₇ P₂ S FCUXBJDJFWOWMD-UHFFFAOYSA-N		Interactions Focus chain J [auth CCC] Interactions & Density Focus chain J [auth CCC]
TPP (Subject of Investigation/LOI) Query on TPP Download:Ideal Coordinates CCD File SDF format, chain G [auth BBB] SDF format, chain E [auth AAA] MOL2 format, chain G [auth BBB] MOL2 format, chain E [auth AAA] mmCIF format, chain G [auth BBB] mmCIF format, chain E [auth AAA]	E [auth AAA], G [auth BBB]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain E [auth AAA] Focus chain G [auth BBB] Interactions & Density Focus chain E [auth AAA] Focus chain G [auth BBB]
UP0 (Subject of Investigation/LOI) Query on UP0 Download:Ideal Coordinates CCD File SDF format, chain H [auth CCC] MOL2 format, chain H [auth CCC] mmCIF format, chain H [auth CCC]	H [auth CCC]	(1~{Z},3~{R},4~{S},7~{S},8~{Z})-8-ethylidene-4,7-bis(oxidanyl)-5-oxidanylidene-3-propyl-cyclononene-1,2-dicarboxylic acid C₁₆ H₂₂ O₇ YFQGJJCDYCWLSI-KRKAZGBPSA-N		Interactions Focus chain H [auth CCC] Interactions & Density Focus chain H [auth CCC]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth CCC] SDF format, chain F [auth BBB] SDF format, chain D [auth AAA] MOL2 format, chain I [auth CCC] MOL2 format, chain F [auth BBB] MOL2 format, chain D [auth AAA] mmCIF format, chain I [auth CCC] mmCIF format, chain F [auth BBB] mmCIF format, chain D [auth AAA]	D [auth AAA], F [auth BBB], I [auth CCC]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth AAA] Focus chain F [auth BBB] Focus chain I [auth CCC] Interactions & Density Focus chain D [auth AAA] Focus chain F [auth BBB] Focus chain I [auth CCC]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.184 (Depositor), 0.193 (DCC)
R-Value Work: 0.153 (Depositor), 0.165 (DCC)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.309	α = 90
b = 135.309	β = 90
c = 201.439	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-03-22

Deposition Author(s):

Freigang, J.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-03-22
Type: Initial release
Version 1.1: 2023-07-26
Changes: Database references, Refinement description
Version 1.2: 2024-06-19
Changes: Data collection