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PDBsum entry 1q2r

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protein dna_rna ligands metals Protein-protein interface(s) links
Transferase/RNA PDB id
1q2r
Jmol
Contents
Protein chains
376 a.a. *
DNA/RNA
Ligands
9DG ×4
Metals
_ZN ×4
Waters ×126
* Residue conservation analysis
PDB id:
1q2r
Name: Transferase/RNA
Title: Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate
Structure: RNA (5'-r( Ap Gp Cp Ap Cp Gp Gp Cp Up (N) p Up Ap Ap Ap Cp Cp Gp Up Gp C)-3'). Chain: e, f. Engineered: yes. Queuine tRNA-ribosyltransferase. Chain: a, b, c, d. Synonym: tRNA-guanine transglycosylase, guanine insertion enzyme. Engineered: yes
Source: Synthetic: yes. Zymomonas mobilis. Organism_taxid: 542. Strain: zm4-cp4. Atcc: 31821. Gene: tgt. Expressed in: escherichia. Expression_system_taxid: 561
Biol. unit: Trimer (from PQS)
Resolution:
2.90Å     R-factor:   0.181     R-free:   0.230
Authors: W.Xie,X.Liu,R.H.Huang
Key ref:
W.Xie et al. (2003). Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate. Nat Struct Biol, 10, 781-788. PubMed id: 12949492 DOI: 10.1038/nsb976
Date:
25-Jul-03     Release date:   09-Sep-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P28720  (TGT_ZYMMO) -  Queuine tRNA-ribosyltransferase
Seq:
Struc:
386 a.a.
376 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
= queuosine(34) in tRNA
+
guanine
Bound ligand (Het Group name = 9DG)
matches with 83.00% similarity
Guanine(34) in tRNA
+ 7-aminomethyl-7-carbaguanine
= 7-aminomethyl-7- carbaguanine(34) in tRNA
+
guanine
Bound ligand (Het Group name = 9DG)
matches with 83.00% similarity
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: 10.1038/nsb976 Nat Struct Biol 10:781-788 (2003)
PubMed id: 12949492  
 
 
Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate.
W.Xie, X.Liu, R.H.Huang.
 
  ABSTRACT  
 
Prokaryotic tRNA guanine transglycosylase (TGT) catalyzes replacement of guanine (G) by 7-aminomethyl-7-deazaguanine (PreQ1) at the wobble position of four specific tRNAs. Addition of 9-deazaguanine (9dzG) to a reaction mixture of Zymomonas mobilis TGT and an RNA substrate allowed us to trap, purify and crystallize a chemically competent covalent intermediate of the TGT-catalyzed reaction. The crystal structure of the TGT-RNA-9dzG ternary complex at a resolution of 2.9 A reveals, unexpectedly, that RNA is tethered to TGT through the side chain of Asp280. Thus, Asp280, instead of the previously proposed Asp102, acts as the nucleophile for the reaction. The RNA substrate adopts an unusual conformation, with four out of seven nucleotides in the loop region flipped out. Interactions between TGT and RNA revealed by the structure provide the molecular basis of the RNA substrate requirements by TGT. Furthermore, reaction of PreQ1 with the crystallized covalent intermediate provides insight into the necessary structural changes required for the TGT-catalyzed reaction to occur.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Overall structure of the trapped covalent intermediate. (a) Ribbon representation of the TGT -RNA -9dzG ternary complex. TGT is colored according to the assignment of the secondary structures in Figure 2. The RNA is dark green. 9dzG is shown in ball-and-stick model in red, and a zinc ion is represented by a ball in magenta. (b) Summary of TGT -RNA, TGT -9dzG and RNA -RNA interactions. TGT, RNA and 9dzG are colored as in a except the phosphate groups of RNA are in magenta. The conserved RNA nucleotides 33 -35, 9dzG and Asp280 are highlighted with color-filled boxes. Arrows in blue represent hydrogen bonds between RNA and TGT, RNA and water, or 9dzG and TGT. Arrows in red show stacking of amino acid side chains from TGT on bases of RNA or on 9dzG. Two arrows in green represent intramolecular interactions in RNA. 'W' in a circle represents well-positioned water molecules in the structure.
Figure 5.
Figure 5. The active site and molecular basis of substrate specificity. (a) Stereo view of TGT active site. The main chains of TGT are grayish blue, the side chains of TGT are orange and the RNA and 9dzG are green. The hetero-atoms are colored individually, with nitrogen in blue, oxygen in red and phosphate in magenta. The C9 of 9dzG is highlighted in black. A water molecule is shown as a small ball in red and labeled 'W'. Hydrogen bonds are indicated with dashed lines. The side chains of Asp106 and Cys158, which block 9dzG from the top, are omitted for clarity. (b,c) Recognition of U33 (b) and U35 (c) in RNA substrate by TGT. The color schemes are the same as in a. The structure of the phosphate group of A38 in c is omitted but labeled for clarity.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2003, 10, 781-788) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21397180 A.Guelorget, and B.Golinelli-Pimpaneau (2011).
Mechanism-based strategies for trapping and crystallizing complexes of RNA-modifying enzymes.
  Structure, 19, 282-291.  
21392131 S.Hebecker, W.Arendt, I.U.Heinemann, J.H.Tiefenau, M.Nimtz, M.Rohde, D.Söll, and J.Moser (2011).
Alanyl-phosphatidylglycerol synthase: mechanism of substrate recognition during tRNA-dependent lipid modification in Pseudomonas aeruginosa.
  Mol Microbiol, 80, 935-950.  
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.  
19925456 M.Vinayak, and C.Pathak (2010).
Queuosine modification of tRNA: its divergent role in cellular machinery.
  Biosci Rep, 30, 135-148.  
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.  
19414587 C.Boland, P.Hayes, I.Santa-Maria, S.Nishimura, and V.P.Kelly (2009).
Queuosine Formation in Eukaryotic tRNA Occurs via a Mitochondria-localized Heteromeric Transglycosylase.
  J Biol Chem, 284, 18218-18227.  
19874048 G.A.Garcia, S.M.Chervin, and J.D.Kittendorf (2009).
Identification of the rate-determining step of tRNA-guanine transglycosylase from Escherichia coli.
  Biochemistry, 48, 11243-11251.  
19847269 K.Nakanishi, L.Bonnefond, S.Kimura, T.Suzuki, R.Ishitani, and O.Nureki (2009).
Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase.
  Nature, 461, 1144-1148.
PDB codes: 3a2k 3hj7
19435325 S.Chimnaronk, F.Forouhar, J.Sakai, M.Yao, C.M.Tron, M.Atta, M.Fontecave, J.F.Hunt, and I.Tanaka (2009).
Snapshots of dynamics in synthesizing N(6)-isopentenyladenosine at the tRNA anticodon.
  Biochemistry, 48, 5057-5065.
PDB codes: 2zm5 2zxu
19749755 S.Goto-Ito, T.Ito, M.Kuratani, Y.Bessho, and S.Yokoyama (2009).
Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation.
  Nat Struct Mol Biol, 16, 1109-1115.
PDB codes: 2zzm 2zzn
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
  18259064 N.Cicmil, and L.Shi (2008).
Crystallization and preliminary X-ray characterization of queD from Bacillus subtilis, an enzyme involved in queuosine biosynthesis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 119-122.  
18491386 N.Cicmil, and R.H.Huang (2008).
Crystal structure of QueC from Bacillus subtilis: an enzyme involved in preQ1 biosynthesis.
  Proteins, 72, 1084-1088.
PDB code: 3bl5
17580114 H.Li (2007).
Complexes of tRNA and maturation enzymes: shaping up for translation.
  Curr Opin Struct Biol, 17, 293-301.  
17626052 J.K.Hurt, S.Olgen, and G.A.Garcia (2007).
Site-specific modification of Shigella flexneri virF mRNA by tRNA-guanine transglycosylase in vitro.
  Nucleic Acids Res, 35, 4905-4913.  
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
17673081 S.M.Chervin, J.D.Kittendorf, and G.A.Garcia (2007).
Probing the intermediacy of covalent RNA enzyme complexes in RNA modification enzymes.
  Methods Enzymol, 425, 121-137.  
17292915 W.Xie, C.Zhou, and R.H.Huang (2007).
Structure of tRNA dimethylallyltransferase: RNA modification through a channel.
  J Mol Biol, 367, 872-881.
PDB codes: 3crm 3crq 3crr
16415880 H.C.Losey, A.J.Ruthenburg, and G.L.Verdine (2006).
Crystal structure of Staphylococcus aureus tRNA adenosine deaminase TadA in complex with RNA.
  Nat Struct Mol Biol, 13, 153-159.
PDB code: 2b3j
16407303 J.Sabina, and D.Söll (2006).
The RNA-binding PUA domain of archaeal tRNA-guanine transglycosylase is not required for archaeosine formation.
  J Biol Chem, 281, 6993-7001.  
16206323 B.Stengl, K.Reuter, and G.Klebe (2005).
Mechanism and substrate specificity of tRNA-guanine transglycosylases (TGTs): tRNA-modifying enzymes from the three different kingdoms of life share a common catalytic mechanism.
  Chembiochem, 6, 1926-1939.  
15888313 G.A.Garcia, and J.D.Kittendorf (2005).
Transglycosylation: a mechanism for RNA modification (and editing?).
  Bioorg Chem, 33, 229-251.  
15951383 K.A.Todorov, X.J.Tan, S.T.Nonekowski, G.A.Garcia, and H.A.Carlson (2005).
The role of aspartic acid 143 in E. coli tRNA-guanine transglycosylase: insights from mutagenesis studies and computational modeling.
  Biophys J, 89, 1965-1977.  
15358762 H.Okamoto, K.Watanabe, Y.Ikeuchi, T.Suzuki, Y.Endo, and H.Hori (2004).
Substrate tRNA recognition mechanism of tRNA (m7G46) methyltransferase from Aquifex aeolicus.
  J Biol Chem, 279, 49151-49159.  
14990747 K.Phannachet, and R.H.Huang (2004).
Conformational change of pseudouridine 55 synthase upon its association with RNA substrate.
  Nucleic Acids Res, 32, 1422-1429.
PDB codes: 1ze1 1ze2
14730022 M.Del Campo, J.Ofengand, and A.Malhotra (2004).
Crystal structure of the catalytic domain of RluD, the only rRNA pseudouridine synthase required for normal growth of Escherichia coli.
  RNA, 10, 231-239.
PDB code: 1qyu
14999002 Y.Kaya, M.Del Campo, J.Ofengand, and A.Malhotra (2004).
Crystal structure of TruD, a novel pseudouridine synthase with a new protein fold.
  J Biol Chem, 279, 18107-18110.
PDB code: 1si7
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.