PDBsum entry 6tuz

Signaling protein

PDB id: 6tuz

Contents

Protein chain

351 a.a.

Ligands

SO4 ×5

DMS ×4

EDO ×20

NAG

TEP

Waters ×177

PDB id:

6tuz

Name:

Signaling protein

Title:

Theophylline-notum complex

Structure:

Palmitoleoyl-protein carboxylesterase notum. Chain: a. Synonym: hnotum. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: notum, ok/sw-cl.30. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: hek293s gnti-

Resolution:

1.24Å R-factor: 0.202 R-free: 0.217

Authors:

Y.Zhao,E.Y.Jones

Key ref:

Y.Zhao et al. (2020). Caffeine inhibits Notum activity by binding at the catalytic pocket. Commun Biol, 3, 555. PubMed id: 33033363 DOI: 10.1038/s42003-020-01286-5

Date:

08-Jan-20 Release date: 28-Oct-20

Protein chain

Q6P988  (NOTUM_HUMAN) -  Palmitoleoyl-protein carboxylesterase NOTUM from Homo sapiens

Seq: 496 a.a.

Struc: 351 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.1.1.98 - [Wnt protein] O-palmitoleoyl-L-serine hydrolase.
• Reaction: [Wnt protein]-O-(9Z)-hexadecenoyl-L-serine + H2O = [Wnt protein]-L-serine + (9Z)-hexadecenoate + H⁺

DOI no: 10.1038/s42003-020-01286-5

Commun Biol 3:555 (2020)

PubMed id: 33033363

Caffeine inhibits Notum activity by binding at the catalytic pocket.

Y.Zhao, J.Ren, J.Hillier, W.Lu, E.Y.Jones.

ABSTRACT

Notum inhibits Wnt signalling via enzymatic delipidation of Wnt ligands. Restoration of Wnt signalling by small molecule inhibition of Notum may be of therapeutic benefit in a number of pathologies including Alzheimer's disease. Here we report Notum activity can be inhibited by caffeine (IC₅₀ 19 µM), but not by demethylated caffeine metabolites: paraxanthine, theobromine and theophylline. Cellular luciferase assays show Notum-suppressed Wnt3a function can be restored by caffeine with an EC₅₀ of 46 µM. The dissociation constant (K_d) between Notum and caffeine is 85 µM as measured by surface plasmon resonance. High-resolution crystal structures of Notum complexes with caffeine and its minor metabolite theophylline show both compounds bind at the centre of the enzymatic pocket, overlapping the position of the natural substrate palmitoleic lipid, but using different binding modes. The structural information reported here may be of relevance for the design of more potent brain-accessible Notum inhibitors.