229D

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


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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.Mol.Biol. 3: 38-44


  • 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 modi ...

    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.


    Related Citations: 
    • Direct Observation of Two Base-Pairing Modes of a Cytosine-Thymine Analogue with Guanine in a DNA Z-Form Duplex: Significance for Base Analogue Mutagenesis
      Moore, M.H.,Van Meervelt, L.,Salisbury, S.A.,Lin, P.K.T.,Brown, D.M.
      (1995) J.Mol.Biol. 251: 665


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
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')A17N/A
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
A
DNA LINKINGC10 H16 N3 O7 PDC
MG1
Query on MG1
A
DNA LINKINGC11 H16 N5 O7 PDG
UMP
Query on UMP
A
NON-POLYMERC9 H13 N2 O8 P

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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-12-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance