6FPU

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

PDB DOI: https://doi.org/10.2210/pdb6FPU/pdb

Classification: TRANSFERASE
Organism(s): Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2018-02-12 Released: 2019-03-13
Deposition Author(s): Nguyen, A., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.36 Å
R-Value Free: 0.154
R-Value Work: 0.128
R-Value Observed: 0.129

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

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.

(2018) Chemistry 24: 9957-9967

PubMed: 29939431 Search on PubMed
DOI: https://doi.org/10.1002/chem.201801756
Primary Citation of Related Structures:
6FMN, 6FPU

PubMed Abstract:
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.

Organizational Affiliation

Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland.

Macromolecule Content

Total Structure Weight: 43.67 kDa
Atom Count: 3,366
Modelled Residue Count: 369
Deposited Residue Count: 386
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Queuine tRNA-ribosyltransferase	A	386	Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821	Mutation(s): 1 Gene Names: tgt, ZMO0363 EC: 2.4.2.29
UniProt
Find proteins for P28720 (Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)) Explore P28720 Go to UniProtKB: P28720
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28720
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
E48 Query on E48 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	6-azanyl-2-[[(1~{R},2~{S},6~{S},9~{R})-4,4,11,11-tetramethyl-3,5,7,10,12-pentaoxatricyclo[7.3.0.0^{2,6}]dodecan-6-yl]methylamino]-3,7-dihydroimidazo[4,5-g]quinazolin-8-one C₂₁ H₂₆ N₆ O₆ DBANTQMQBSPBCW-MBIULKOWSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]