3RR4

tRNA-Guanine Transglycosylase in complex with N-Methyl-lin-Benzoguanine Inhibitor

Summary for 3RR4

• Entry DOI: 10.2210/pdb3rr4/pdb
• Related: 2Z7K 3EOS 3GEV 3GFN 3S1G 3SM0 3TLL 3V0Y
• Descriptor: Queuine tRNA-ribosyltransferase, ZINC ION, 2,6-bis(methylamino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one, ... (5 entities in total)
• Functional Keywords: tim barrel, glycosyltransferase, metal-binding, queuosine, biosynthesis, transferase, trna processing, trna, transferase-transferase inhibitor complex, transferase/transferase inhibitor
• Biological source: Zymomonas mobilis
• Total number of polymer chains: 1
• Total formula weight: 43419.55

Authors

Klebe, G.,Immekus, F.,Heine, A. (deposition date: 2011-04-29, release date: 2012-04-25, Last modification date: 2023-09-13)

Primary citation

Barandun, L.J.,Immekus, F.,Kohler, P.C.,Tonazzi, S.,Wagner, B.,Wendelspiess, S.,Ritschel, T.,Heine, A.,Kansy, M.,Klebe, G.,Diederich, F.
From lin-Benzoguanines to lin-Benzohypoxanthines as Ligands for Zymomonas mobilis tRNA-Guanine Transglycosylase: Replacement of Protein-Ligand Hydrogen Bonding by Importing Water Clusters.
Chemistry, 18:9246-9257, 2012

PubMed Abstract: The foodborne illness shigellosis is caused by Shigella bacteria that secrete the highly cytotoxic Shiga toxin, which is also formed by the closely related enterohemorrhagic Escherichia coli (EHEC). It has been shown that tRNA-guanine transglycosylase (TGT) is essential for the pathogenicity of Shigella flexneri. Herein, the molecular recognition properties of a guanine binding pocket in Zymomonas mobilis TGT are investigated with a series of lin-benzohypoxanthine- and lin-benzoguanine-based inhibitors that bear substituents to occupy either the ribose-33 or the ribose-34 pocket. The three inhibitor scaffolds differ by the substituent at C(6) being H, NH(2), or NH-alkyl. These differences lead to major changes in the inhibition constants, pK(a) values, and binding modes. Compared to the lin-benzoguanines, with an exocyclic NH(2) at C(6), the lin-benzohypoxanthines without an exocyclic NH(2) group have a weaker affinity as several ionic protein-ligand hydrogen bonds are lost. X-ray cocrystal structure analysis reveals that a new water cluster is imported into the space vacated by the lacking NH(2) group and by a conformational shift of the side chain of catalytic Asp102. In the presence of an N-alkyl group at C(6) in lin-benzoguanine ligands, this water cluster is largely maintained but replacement of one of the water molecules in the cluster leads to a substantial loss in binding affinity. This study provides new insight into the role of water clusters at enzyme active sites and their challenging substitution by ligand parts, a topic of general interest in contemporary structure-based drug design.

PubMed: 22736391
DOI: 10.1002/chem.201200809

Experimental method

X-RAY DIFFRACTION (1.68 Å)