6TJ8 | pdb_00006tj8

Escherichia coli transketolase in complex with cofactor analog 2'-methoxythiamine diphosphate

• PDB DOI: https://doi.org/10.2210/pdb6TJ8/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-11-25 Released: 2020-07-08 
• Deposition Author(s): Rabe von Pappenheim, F., Tittmann, K.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.92 Å
• R-Value Free: 
  0.106 (Depositor), 0.106 (DCC) 
• R-Value Work: 
  0.095 (Depositor), 0.095 (DCC) 
• R-Value Observed: 
  0.095 (Depositor) 

Starting Model: experimental

Literature

Structural basis for antibiotic action of the B 1 antivitamin 2'-methoxy-thiamine.

Rabe von Pappenheim, F., Aldeghi, M., Shome, B., Begley, T., de Groot, B.L., Tittmann, K.

(2020) Nat Chem Biol 16: 1237-1245

• PubMed: 32839604 
• DOI: https://doi.org/10.1038/s41589-020-0628-4
• Primary Citation Related Structures: 
  6TJ8, 6TJ9


• PubMed Abstract: 
  

  The natural antivitamin 2'-methoxy-thiamine (MTh) is implicated in the suppression of microbial growth. However, its mode of action and enzyme-selective inhibition mechanism have remained elusive. Intriguingly, MTh inhibits some thiamine diphosphate (ThDP) enzymes, while being coenzymatically active in others. Here we report the strong inhibition of Escherichia coli transketolase activity by MTh and unravel its mode of action and the structural basis thereof. The unique 2'-methoxy group of MTh diphosphate (MThDP) clashes with a canonical glutamate required for cofactor activation in ThDP-dependent enzymes. This glutamate is forced into a stable, anticatalytic low-barrier hydrogen bond with a neighboring glutamate, disrupting cofactor activation. Molecular dynamics simulations of transketolases and other ThDP enzymes identify active-site flexibility and the topology of the cofactor-binding locale as key determinants for enzyme-selective inhibition. Human enzymes either retain enzymatic activity with MThDP or preferentially bind authentic ThDP over MThDP, while core bacterial metabolic enzymes are inhibited, demonstrating therapeutic potential.

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Organizational Affiliation: 
• Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, University of Göttingen, Göttingen, Germany.
Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
Research Group of Computational Biomolecular Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
Department of Chemistry, Texas A&M University, College Station, TX, USA.
Research Group of Computational Biomolecular Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. [e-mail].
Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, University of Göttingen, Göttingen, Germany. [e-mail].
Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 149.25 kDa 
• Atom Count: 13,390 
• Modeled Residue Count: 1,331 
• Deposited Residue Count: 1,338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transketolase 1	A, B	669	Escherichia coli K-12	Mutation(s): 0  Gene Names: tktA, tkt, b2935, JW5478 EC: 2.2.1.1
UniProt
Find proteins for P27302 (Escherichia coli (strain K12)) Explore P27302  Go to UniProtKB:  P27302

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDQ (Subject of Investigation/LOI)	C [auth A], U [auth B]	2-[3-[(4-azanyl-2-methoxy-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate C12 H19 N4 O8 P2 S PWBCVHDHRGCQHM-UHFFFAOYSA-O
EDO	AA [auth B], BA [auth B], CA [auth B], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	D [auth A], V [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.92 Å
• R-Value Free:  0.106 (Depositor), 0.106 (DCC) 
• R-Value Work:  0.095 (Depositor), 0.095 (DCC) 
• R-Value Observed: 0.095 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.55	α = 90
b = 101.91	β = 90
c = 132.96	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data processing
XSCALE	data scaling
PHENIX	phasing
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): Rabe von Pappenheim, F., Tittmann, K.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	FOR 1296/TP3

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2020-09-02
  Changes: Database references, Derived calculations
• Version 1.2: 2020-09-30
  Changes: Database references
• Version 1.3: 2020-10-28
  Changes: Database references
• Version 1.4: 2024-01-24
  Changes: Data collection, Database references, Refinement description