229D

DNA ANALOG OF YEAST TRANSFER RNA PHE ANTICODON DOMAIN WITH MODIFIED BASES 5-METHYL CYTOSINE AND 1-METHYL GUANINE

• PDB DOI: https://doi.org/10.2210/pdb229D/pdb
• NAKB: 229D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1995-08-16 Released: 1995-12-07 
• Deposition Author(s): Basti, M.M., Stuart, J.W., Lam, A.T., Guenther, R., Agris, P.F.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 1 

Literature

Design, biological activity and NMR-solution structure of a DNA analogue of yeast tRNA(Phe) anticodon domain.

Basti, M.M., Stuart, J.W., Lam, A.T., Guenther, R., Agris, P.F.

(1996) Nat Struct Biol 3: 38-44

• PubMed: 8548453 
• DOI: https://doi.org/10.1038/nsb0196-38
• Primary Citation of Related Structures:  
  229D


• PubMed Abstract: 
  

  Design of biologically active DNA analogues of the yeast tRNA(Phe) anticodon domain, tDNAPheAC, required the introduction of a d(m5C)-dependent, Mg(2+)-induced structural transition and the d(m1G) disruption of an intra-loop dC.dG base pair. The modifications were introduced at residues corresponding to m5C-40 and wybutosine-37 in tRNA(Phe). Modified tDNAPheAC inhibited translation by 50% at a tDNAPheAC:ribosome ratio of 8:1. The molecule's structure has been determined by NMR spectroscopy and restrained molecular dynamics with an overall r.m.s.d. of 2.8 A and 1.7 A in the stem, and is similar to the tRNA(Phe) anticodon domain in conformation and dimensions. The tDNAPheAC structure may provide a guide for the design of translation inhibitors as potential therapeutic agents.

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Organizational Affiliation: 

Department of Biochemistry, North Carolina State University, Raleigh 27695-7622, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 5.22 kDa 
• Atom Count: 347 
• Modelled Residue Count: 17 
• Deposited Residue Count: 17 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*AP*GP*AP*CP*(UMP)P*GP*AP*AP*(MG1)P*AP*(UMP)P*(5CM)P*(UMP)P*GP*G)-3')	A	17	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 1 

Structure Validation

Currently 229D does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 1995-12-07 
Deposition Author(s): Basti, M.M., Stuart, J.W., Lam, A.T., Guenther, R., Agris, P.F.

Revision History  

• Version 1.0: 1995-12-07
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-09
  Changes: Data collection, Database references, Derived calculations, Other