1KOS

SOLUTION NMR STRUCTURE OF AN ANALOG OF THE YEAST TRNA PHE T STEM LOOP CONTAINING RIBOTHYMIDINE AT ITS NATURALLY OCCURRING POSITION


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 
  • Selection Criteria: LOWEST ENERGY STRUCTURES 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A distinctive RNA fold: the solution structure of an analogue of the yeast tRNAPhe T Psi C domain.

Koshlap, K.M.Guenther, R.Sochacka, E.Malkiewicz, A.Agris, P.F.

(1999) Biochemistry 38: 8647-8656

  • DOI: 10.1021/bi990118w

  • PubMed Abstract: 
  • The structure of an analogue of the yeast tRNAPhe T Psi C stem-loop has been determined by NMR spectroscopy and restrained molecular dynamics. The molecule contained the highly conserved modification ribothymidine at its naturally occurring position. ...

    The structure of an analogue of the yeast tRNAPhe T Psi C stem-loop has been determined by NMR spectroscopy and restrained molecular dynamics. The molecule contained the highly conserved modification ribothymidine at its naturally occurring position. The ribothymidine-modified T Psi C stem-loop is the product of the m5U54-tRNA methyltransferase, but is not a substrate for the m1A58-tRNA methyltransferase. Site-specific substitutions and 15N labels were used to confirm the assignment of NOESY cross-peaks critical in defining the global fold of the molecule. The structure is unusual in that the loop folds far over into the major groove of the curved stem. This conformation is stabilized by both stacking interactions and hydrogen bond formation. Furthermore, this conformation appears to be unique among RNA hairpins of similar size. There is, however, a considerable resemblance to the analogous domain in the crystal structure of the full-length yeast tRNAPhe. We believe, therefore, that the structure we have determined may represent an intermediate in the folding pathway during the maturation of tRNA.


    Related Citations: 
    • Restrained Refinement of the Monoclinic Form of Yeast Phenylalanine Transfer RNA. Temperature Factors and Dynamics, Coordinated Waters, and Base-Pair Propeller Twist Angles
      Westhof, E.,Sundaralingam, M.
      (1986) Biochemistry 25: 4868
    • The Dynamic NMR Structure of the T Psi C-Loop: Implications for the Specificity of tRNA Methylation
      Yao, L.J.,James, T.L.,Kealey, J.T.,Santi, D.V.,Schmitz, U.
      (1997) J.Biomol.NMR 3: 229
    • Small Structural Ensembles for a 17-Nucleotide Mimic of the tRNA Tpsic-Loop Via Fitting Dipolar Relaxation Rates with the Quadratic Programming Algorithm
      Schmitz, U.,Donati, A.,James, T.L.,Ulyanov, N.B.,Yao, L.
      (1998) Biopolymers 46: 329


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*CP*UP*GP*UP*GP*(5MU)P*UP*CP*GP*AP*UP*(CH)P*CP*AP*CP*AP*G)- 3'A17N/A
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CH
Query on CH
A
RNA LINKINGC9 H15 N3 O8 PC
5MU
Query on 5MU
A
RNA LINKINGC10 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 
  • Selection Criteria: LOWEST ENERGY STRUCTURES 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-10-22
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance