ISDA

Entry Detail

PDB ID:

6FPU

Keywords:

Title:

tRNA guanine Transglycosylase (TGT) in co-crystallized complex with 6-amino-2-((((3aS,5aR,8bS)-2,2,7,7-tetramethyltetrahydro-3aH-bis([1,3]dioxolo)[4,5-b:4',5'-d]pyran-3a-yl)methyl)amino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one

Biological Source:

Source Organism:

Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)

Host Organism:

Escherichia coli

PDB Version:

Deposition Date:

2018-02-12

Release Date:

2019-03-13

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.36 Å

R-Value Free:

0.15

R-Value Work:

0.12

R-Value Observed:

0.12

Space Group:

C 1 2 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:Queuine tRNA-ribosyltransferase
Mutations:T312K
Chain IDs:A
Chain Length:386
Number of Molecules:1
Biological Source:Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)

UniProt ID:P28720 Pfam ID:PF01702 EC:2.4.2.29

Ligand Molecules

E48

GOL

Primary Citation

Sugar Acetonides are a Superior Motif for Addressing the Large, Solvent-Exposed Ribose-33 Pocket of tRNA-Guanine Transglycosylase.

Movsisyan, L.D, Schafer, E, Nguyen, A, Ehrmann, F.R, Schwab, A, Rossolini, T, Zimmerli, D, Wagner, B, Daff, H, Heine, A, Klebe, G, Diederich, F.Show

Chemistry 24 9957 9967 (2018)

PMID: 29939431 DOI: 10.1002/chem.201801756

Abstact

The intestinal disease shigellosis caused by Shigella bacteria affects over 120 million people annually. There is an urgent demand for new drugs as resistance against common antibiotics emerges. Bacterial tRNA-guanine transglycosylase (TGT) is a druggable target and controls the pathogenicity of Shigella flexneri. We report the synthesis of sugar-functionalized lin-benzoguanines addressing the ribose-33 pocket of TGT from Zymomonas mobilis. Ligand binding was analyzed by isothermal titration calorimetry and X-ray crystallography. Pocket occupancy was optimized by variation of size and protective groups of the sugars. The participation of a polycyclic water-cluster in the recognition of the sugar moiety was revealed. Acetonide-protected ribo- and psicofuranosyl derivatives are highly potent, benefiting from structural rigidity, good solubility, and metabolic stability. We conclude that sugar acetonides have a significant but not yet broadly recognized value in drug development.

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Primary Citation of related structures