1RCL

THE THREE DIMENSIONAL STRUCTURE OF GUANINE-SPECIFIC RIBONUCLEASE F1 IN SOLUTION DETERMINED BY NMR SPECTROSCOPY AND DISTANCE GEOMETRY


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

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Literature

The three-dimensional structure of guanine-specific ribonuclease F1 in solution determined by NMR spectroscopy and distance geometry.

Nakai, T.Yoshikawa, W.Nakamura, H.Yoshida, H.

(1992) Eur J Biochem 208: 41-51

  • DOI: 10.1111/j.1432-1033.1992.tb17157.x
  • Primary Citation of Related Structures:  
    1RCL, 1RCK

  • PubMed Abstract: 
  • Two-dimensional 1H-NMR studies have been performed on ribonuclease F1 (RNase F1), which contains 106 amino acid residues. Sequence-specific resonance assignments were accomplished for the backbone protons of 99 amino acid residues and for most of the ...

    Two-dimensional 1H-NMR studies have been performed on ribonuclease F1 (RNase F1), which contains 106 amino acid residues. Sequence-specific resonance assignments were accomplished for the backbone protons of 99 amino acid residues and for most of their side-chain protons. The three-dimensional structures were constructed on the basis of 820 interproton-distance restraints derived from NOE, 64 distance restraints for 32 hydrogen bonds and 33 phi torsion-angle restraints. A total of 40 structures were obtained by distance geometry and simulated-annealing calculations. The average root-mean-square deviation (residues 1-106) between the 40 converged structures and the mean structure obtained by averaging their coordinates was 0.116 +/- 0.018 nm for the backbone atoms and 0.182 +/- 0.015 nm for all atoms including the hydrogen atoms. RNase F1 was determined to be an alpha/beta-type protein. A well-defined structure constitutes the core region, which consists of a small N-terminal beta-sheet (beta 1, beta 2) and a central five-stranded beta-sheet (beta 3-beta 7) packed on a long helix. The structure of RNase F1 has been compared with that of RNase T1, which was determined by X-ray crystallography. Both belong to the same family of microbial ribonucleases. The polypeptide backbone fold of RNase F1 is basically identical to that of RNase T1. The conformation-dependent chemical shifts of the C alpha protons are well conserved between RNase F1 and RNase T1. The residues implicated in catalysis are all located on the central beta-sheet in a geometry similar to that of RNase T1.


    Related Citations: 
    • Accurate Determination of Protein Conformations by Nuclear Magnetic Resonance Spectroscopy and Distance Geometry and Analysis of Their Structural Features
      Nakai, T.
      () To be published --: --
    • Crystal Structures of Ribonuclease F1 of Fusarium Moniliforme in its Free Form and in Complex with 2'Gmp
      Vassylyev, D.G., Katayanagi, K., Ishikawa, K., Tsujimoto-Hirano, M., Danno, M., Pahler, A., Matsumoto, O., Matsushima, M., Yoshida, H., Morikawa, K.
      (1993) J Mol Biol 230: 979

    Organizational Affiliation

    Protein Engineering Research Institute, Osaka, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBONUCLEASE F1A106Fusarium fujikuroiMutation(s): 0 
EC: 3.1.27.3 (PDB Primary Data), 4.6.1.24 (UniProt)
Find proteins for P10282 (Gibberella fujikuroi)
Explore P10282 
Go to UniProtKB:  P10282
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
AL-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 
  • OLDERADO: 1RCL Olderado

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-11-30
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 2.0: 2019-12-25
    Changes: Database references, Derived calculations, Polymer sequence