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PDBsum entry 2bbf

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protein ligands metals links
Transferase PDB id
2bbf
Jmol
Contents
Protein chain
367 a.a. *
Ligands
344
Metals
_ZN
Waters ×369
* Residue conservation analysis
PDB id:
2bbf
Name: Transferase
Title: Crystal structure of tRNA-guanine transglycosylase (tgt) fro zymomonas mobilis in complex with 6-amino-3,7-dihydro-imida g]quinazolin-8-one
Structure: tRNA guanine transglycosylase. Chain: a. Synonym: tRNA-guanine transglycosylase, guanine insertion e tgt. Engineered: yes
Source: Zymomonas mobilis. Organism_taxid: 542. Gene: tgt. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.70Å     R-factor:   0.196     R-free:   0.220
Authors: B.Stengl,E.A.Meyer,A.Heine,R.Brenk,F.Diederich,G.Klebe
Key ref:
B.Stengl et al. (2007). Crystal structures of tRNA-guanine transglycosylase (TGT) in complex with novel and potent inhibitors unravel pronounced induced-fit adaptations and suggest dimer formation upon substrate binding. J Mol Biol, 370, 492-511. PubMed id: 17524419 DOI: 10.1016/j.jmb.2007.04.008
Date:
17-Oct-05     Release date:   24-Apr-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P28720  (TGT_ZYMMO) -  Queuine tRNA-ribosyltransferase
Seq:
Struc:
386 a.a.
367 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.4.2.29  - tRNA-guanine(34) transglycosylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. Guanine34 in tRNA + queuine = queuosine34 in tRNA + guanine
2. Guanine34 in tRNA + 7-aminomethyl-7-carbaguanine = 7-aminomethyl-7- carbaguanine34 in tRNA + guanine
Guanine(34) in tRNA
+
queuine
Bound ligand (Het Group name = 344)
matches with 75.00% similarity
= queuosine(34) in tRNA
+ guanine
Guanine(34) in tRNA
+
7-aminomethyl-7-carbaguanine
Bound ligand (Het Group name = 344)
matches with 75.00% similarity
= 7-aminomethyl-7- carbaguanine(34) in tRNA
+ guanine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     tRNA processing   3 terms 
  Biochemical function     transferase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2007.04.008 J Mol Biol 370:492-511 (2007)
PubMed id: 17524419  
 
 
Crystal structures of tRNA-guanine transglycosylase (TGT) in complex with novel and potent inhibitors unravel pronounced induced-fit adaptations and suggest dimer formation upon substrate binding.
B.Stengl, E.A.Meyer, A.Heine, R.Brenk, F.Diederich, G.Klebe.
 
  ABSTRACT  
 
The bacterial tRNA-guanine transglycosylase (TGT) is a tRNA modifying enzyme catalyzing the exchange of guanine 34 by the modified base preQ1. The enzyme is involved in the infection pathway of Shigella, causing bacterial dysentery. As no crystal structure of the Shigella enzyme is available the homologous Zymomonas mobilis TGT was used for structure-based drug design resulting in new, potent, lin-benzoguanine-based inhibitors. Thorough kinetic studies show size-dependent inhibition of these compounds resulting in either a competitive or non-competitive blocking of the base exchange reaction in the low micromolar range. Four crystal structures of TGT-inhibitor complexes were determined with a resolution of 1.58-2.1 A. These structures give insight into the structural flexibility of TGT necessary to perform catalysis. In three of the structures molecular rearrangements are observed that match with conformational changes also noticed upon tRNA substrate binding. Several water molecules are involved in these rearrangement processes. Two of them demonstrate the structural and catalytic importance of water molecules during TGT base exchange reaction. In the fourth crystal structure the inhibitor unexpectedly interferes with protein contact formation and crystal packing. In all presently known TGT crystal structures the enzyme forms tightly associated homodimers internally related by crystallographic symmetry. Upon binding of the fourth inhibitor the dimer interface, however, becomes partially disordered. This result prompted further analyses to investigate the relevance of dimer formation for the functional protein. Consultation of the available TGT structures and sequences from different species revealed structural and functional conservation across the contacting residues. This suggests that bacterial and eukaryotic TGT could possibly act as homodimers in catalysis. It is hypothesized that one unit of the dimer performs the catalytic reaction whereas the second is required to recognize and properly orient the bound tRNA for the catalytic reaction.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Assumed mechanism for the base exchange reaction catalyzed by TGT. The base exchange follows a ping-pong mechanism. First tRNA binds to TGT and Asp280 performs a nucleophilic attack onto C1 of the tRNA ribose cleaving guanine 34 from tRNA (a) and (b). Then preQ[1] replaces guanine to finally be incorporated in tRNA in a reverse reaction step (c) and (d). W1 and W2 represent catalytically important water molecules.
Figure 6.
Figure 6. Crystal structure of 4 in the binding pocket of TGT determined at 1.7 Å resolution. 4 is contoured at 2.4σ in the F[o] F[c] density map. The ligand is well-defined in the binding pocket. No split conformations can be observed. Asn70 adopts the same geometry as in TGT·1 (cf. (b)). A distinct water network is found between D102 and D280. (b) Binding mode of 1 in the binding pocket of TGT.^28 The binding pocket is characterized by split conformations of protein residues in the active site due to partial occupancy of the inhibitor in the crystals. Residues coloured in grey represent the apo conformation, residues in yellow correspond to the inhibitor-bound conformation. (c) Crystal structure of 5 in the binding pocket of TGT determined at 1.58 Å resolution. 5 is contoured at 2.4 σ in the F[o] F[c] density map. The lin-benzoguanine scaffold is in similar position as 4. The phenyl substituent adopts two conformations (grey, d; yellow, u) paralleled by two conformations for N70. The conformation of N70u is structurally similar to that of N70 in TGT·4 (a). (d) Electron density of the N70 loop in the binding pocket of TGT·5 contoured at 1.0σ in the 2 F[o] F[c] density map. Associated with the split conformations of 5 the residues G69–H73 adopt two arrangements. (e) Crystal structure of 6 in the binding pocket of TGT determined at 1.58 Å resolution. 6 is contoured at 2.4σ in the F[o] F[c] density map. The lin-benzoguanine scaffold is equally positioned to 4 and 5. The phenyl substituent was only refined in up-conformation (yellow). Nevertheless electron density suggests also the presence of the down-conformation (grey). Also in this structure N70 adopts two orientations. (f) Electron density of the N70 loop in the binding pocket of TGT·6 contoured at 1.0σ in the 2 F[o] F[c] density map. Residues G69–H73 adopt two almost equally distributed conformations (u-conformation shown in yellow and d-conformation in grey).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 370, 492-511) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21131277 Y.C.Chen, A.F.Brooks, D.M.Goodenough-Lashua, J.D.Kittendorf, H.D.Showalter, and G.A.Garcia (2011).
Evolution of eukaryal tRNA-guanine transglycosylase: insight gained from the heterocyclic substrate recognition by the wild-type and mutant human and Escherichia coli tRNA-guanine transglycosylases.
  Nucleic Acids Res, 39, 2834-2844.  
20345171 C.Bissantz, B.Kuhn, and M.Stahl (2010).
A medicinal chemist's guide to molecular interactions.
  J Med Chem, 53, 5061-5084.  
20354154 Y.C.Chen, V.P.Kelly, S.V.Stachura, and G.A.Garcia (2010).
Characterization of the human tRNA-guanine transglycosylase: confirmation of the heterodimeric subunit structure.
  RNA, 16, 958-968.  
19746363 P.C.Kohler, T.Ritschel, W.B.Schweizer, G.Klebe, and F.Diederich (2009).
High-affinity inhibitors of tRNA-guanine transglycosylase replacing the function of a structural water cluster.
  Chemistry, 15, 10809-10817.  
19894214 T.Ritschel, P.C.Kohler, G.Neudert, A.Heine, F.Diederich, and G.Klebe (2009).
How to Replace the Residual Solvation Shell of Polar Active Site Residues to Achieve Nanomolar Inhibition of tRNA-Guanine Transglycosylase.
  ChemMedChem, 4, 2012-2023.
PDB codes: 3eos 3eou 3gc4 3gc5 3ge7
19199329 T.Ritschel, S.Hoertner, A.Heine, F.Diederich, and G.Klebe (2009).
Crystal structure analysis and in silico pKa calculations suggest strong pKa shifts of ligands as driving force for high-affinity binding to TGT.
  Chembiochem, 10, 716-727.
PDB codes: 2z7k 3c2n 3c2y 3c2z
18278803 A.C.Carneiro, L.Fragel-Madeira, M.A.Silva-Neto, and R.Linden (2008).
A role for CK2 upon interkinetic nuclear migration in the cell cycle of retinal progenitor cells.
  Dev Neurobiol, 68, 620-631.  
17949745 N.Tidten, B.Stengl, A.Heine, G.A.Garcia, G.Klebe, and K.Reuter (2007).
Glutamate versus glutamine exchange swaps substrate selectivity in tRNA-guanine transglycosylase: insight into the regulation of substrate selectivity by kinetic and crystallographic studies.
  J Mol Biol, 374, 764-776.
PDB codes: 2oko 2pot 2pwu 2pwv 2qii 2z1v 2z1w 2z1x
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.