6TJ9

Escherichia coli transketolase in complex with cofactor analog 2'-methoxythiamine and substrate xylulose 5-phosphate

Summary for 6TJ9

• Entry DOI: 10.2210/pdb6tj9/pdb
• Descriptor: Transketolase 1, 5-O-phosphono-D-xylulose, 2-[3-[(4-azanyl-2-methoxy-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate, ... (7 entities in total)
• Functional Keywords: thiamin diphosphate, enzyme catalysis, pentose phosphate pathway, transferase
• Biological source: Escherichia coli (strain K12)
• Total number of polymer chains: 2
• Total formula weight: 149325.77

Authors

Rabe von Pappenheim, F.,Tittmann, K. (deposition date: 2019-11-25, release date: 2020-07-08, Last modification date: 2024-01-24)

Primary citation

Rabe von Pappenheim, F.,Aldeghi, M.,Shome, B.,Begley, T.,de Groot, B.L.,Tittmann, K.
Structural basis for antibiotic action of the B 1 antivitamin 2'-methoxy-thiamine.
Nat.Chem.Biol., 16:1237-1245, 2020

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.

PubMed: 32839604
DOI: 10.1038/s41589-020-0628-4

Experimental method

X-RAY DIFFRACTION (0.95 Å)