Graphics Gallery

Gale Rhodes
Chemistry Department
University of Southern Maine

Revised 2006/08/02

Learn how to use Swiss-PdbViewer. See the Swiss-PdbViewer Tutorial.

Topic: Translation and the Genetic Code

Examples:

 Molecules commonly discussed in biochemistry texts

tRNAPhe

To study the structure of a transfer RNA that carries phenylalanine (PHE), obtain the file 4TNA from the Protein Data Bank.

For SwissPdbViewer users, click here for a prepared view of the 4TNA model, color coded as follows:

  • Amino-acid arm, backbone red in the single-strand region, green in the double-strand region.
  • T-Psi-C arm, backbone cyan.
  • DHU arm, backbone yellow.
  • Anticodon arm, backbone magenta, with anticodon bases green.

Explore the structure, and find the following structural elements:

  • The 3'-CCA region and the hydroxyl group to which PHE would be attached.
  • The anticodon region. Use the genetic code table in your text to find the codons for PHE. Which of the PHE codons would this tRNA recognize?
  • What are the orientations of the anticodon bases with respect to each other? Do you think this orientation allows for matching with the codon?
  • Regions of Watson-Crick double helix.
  • Interactions that support the tertiary structure of the molecule.

Glutaminyl-tRNA Synthetase (A Type-1 Synthetase)

Protein Data Bank file 1QRT provides a model of glutaminyl-tRNA synthetase bound to tRNAglu. In addition, ATP is bound at the putative binding site for the glutaminyl adenylate. Read the Medline abstract linked to this file.

Swiss-PdbViewer users click here for a prepared view of the 1QRT model. The model is color coded as follows:

  • tRNA is shown in cyan, with the anticodon region in magenta backbone with green bases (doesn't look as bad as it sounds -- but now you know why I ask my wife to approve my clothing before I go out in public). The 3'-terminal A nucleotide is shown with a dotted surface, in CPK colors.
  • ATP is shown with a dotted surface, in CPK colors.
  • Synthetase is shown in ribbon, with helices red and beta strands yellow. Residues within 4 angstroms of the t-RNA or ATP are shown fully, CPK colored.

Explore the structure:

  • Compute H-bonds and explore the anticodon region of the t-RNA. Note that recognition of t-RNA by synthetase involves the anticodon region (residues 34-36, 5'-CUG-3'), but that there are also other regions of enzyme-tRNA contact (wherever you see enzyme residues fully displayed (not just ribbon), the enzyme and t-RNA are in contact).
  • Look at the ATP binding region. Measure the distance from the 2'-hydroxyl oxygen of t-RNA residue A76 (the 3'-terminal nucleotide, which carries the amino acid) to the phosphorus atom of the middle phosphate of ATP. This phosphorus is at approximately the position of the aminoacyl carbonyl carbon in the aminoacyl adenylate that would normally occupy the ATP position during catalysis.
  • Explore the binding of the anticodon bases to the protein. Compare their relative orientations to those in the anticodon bases in tRNAPhe, above.

Aspartyl-tRNA Synthetase (A Type-II Synthetase)

Protein Data Bank file 1ASZ proides a model of aspartyl-tRNA synthetase bound to tRNAasp. In addition, ATP is aboutn at the putative binding site for aspartyl adenylate. Read the Medline abstract linked to this file.

Swiss-PdbViewer users click here for a prepared view of 1ASZ that allows comparision of the rRNAasp conformation with that of free tRNAasp (PDB 2TRA). Only one of the two complete models from 1ASZ is shown, but both models are present in the file.The displayed model is color coded as follows:

  • In the 1ASZ layer, tRNA is shown in cyan, with the anticodon region in magenta backbone with green bases. The 3'-terminal CCA nucleotides are shown with a dotted surface, in CPK colors.
  • ATP is shown with a dotted surface, in CPK colors.
  • Synthetase is shown in ribbon, with helices red and beta strands yellow. Residues within 4 angstroms of the tRNA are shown fully, CPK colored.
  • In the 2TRA layer, the color coding of tRNA is that same. The 3'-CA dinucleotide is missing from this model.

Explore the structure:

  • First, using blinking (press tab while holding down ctrl) to compare the conformations for free and bound tRNAasp(layers 2TRA and 1ASZ). Give a general description of the differences between the conformations.
  • In layer 1ASZ, compute H-bonds and explore the anticodon region of the t-RNA. Note that recognition of t-RNA by synthetase involves the anticodon region, but that there are also other regions of enzyme-tRNA contact (wherever you see enzyme residues fully displayed (not just ribbon), the enzyme and t-RNA are in contact).
  • Look at the ATP binding region. Measure the distance from the 2'-hydroxyl oxygen of t-RNA residue A76 (the 3'-terminal nucleotide, which carries the amino acid) to the phosphorus atom of the middle phosphate of ATP. This phosphorus is at approximately the position of the aminoacyl carbonyl carbon in the aminoacyl adenylate that would normally occupy the ATP position during catalysis.
  • Explore the binding of the anticodon bases (magenta backbone, green bases) to the protein.
  • Blink to compare the stacked orientations of these bases in free tRNAasp to their orientations in bound tRNAasp.
  • Display the full dimer of 1ASZ (Select: All, <return>). Show the entire model in ribbons. The tRNA you have been exploring is green and the other is red.
  • Use Select: Groups Close to Another Chain to explore interactions between the two enzyme subunits.

Does EF-G Mimic EF-Tu/tRNA?

Swiss-PdbViewer users click here for a project file comparing elongation factor G (EF-G, PDB 2EFG) with a complex of elongation factor Tu (EF-Tu, PDB 1B23).

In the EF-G model, domains 1 and 2 are shown as ribbons, while domains 3, 4, and 5 are shown in full. In EF-Tu/tRNA, EF-Tu is shown in ribbon, while tRNA is shown in full. The tRNA is superimposed (by eye) on domains 3, 4, and 5 of EF-G.

  • Blink between the models (hold down ctrl and press tab repeatedly. Do the last 3 domains of EF-G have a shape similar to that of the tRNA?
  • How might you use Swiss-PdbViewer's tools to strengthen the case that EF-G might mimic EF-Tu/tRNA?
  • If this mimicry does occur, propose a sequence of events involving EF-G that results in translocation. Remember that an EF-G-bound GTP is hydrolyzed during this process.
  • Suggest a means of testing your proposal.

At each step of translation, a complex of EF-G and GTP is necessary for translocation of the ribosome to the next codon. Translocation moves the peptidyl-tRNA from the A site to the P-site. Next, a complex of EF-Tu and an aminoacyl-tRNA enters the A site, bringing the next aminoacyl group to be added to the growing peptide chain. Comparison of the two structures in this project file suggests that EF-G might mimic the EF-Tu/tRNA complex and displace it from the A site to the P site.

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