1LSQ

RIBONUCLEASE A WITH ASN 67 REPLACED BY A BETA-ASPARTYL RESIDUE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Deamidation in proteins: the crystal structure of bovine pancreatic ribonuclease with an isoaspartyl residue at position 67.

Capasso, S.Di Donato, A.Esposito, L.Sica, F.Sorrentino, G.Vitagliano, L.Zagari, A.Mazzarella, L.

(1996) J Mol Biol 257: 492-496

  • DOI: 10.1006/jmbi.1996.0179
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The non-enzymatic deamidation of asparagine residues in proteins is a widely occurring reaction, both in vivo and in vitro. Although the importance of this process is commonly recognised, only little structural information is available on it. In orde ...

    The non-enzymatic deamidation of asparagine residues in proteins is a widely occurring reaction, both in vivo and in vitro. Although the importance of this process is commonly recognised, only little structural information is available on it. In order to evaluate the structural effects of this reaction in proteins, we have determined the crystal structure of a ribonuclease A derivative in which asparagine 67 has been replaced by an isoaspartyl residue, as a consequence of an in vitro deamidation reaction. The overall structure of the model, refined to a crystallographic R-factor of 0.159 at a resolution of 1.9 A, is very similar to that of the native protein, but considerable deviations are observed in the region delimited by the disulphide bridge 65-72. In particular, the insertion of an extra methylene group in the main chain at residue 67 breaks up the hydrogen bond network that makes this region rather rigid in ribonuclease A. On the basis of the structure observed, some of the slightly but significantly different properties of this deamidated derivative, with respect to the native enzyme, can be explained.


    Related Citations: 
    • Selective Deamidation of Ribonuclease A
      Di Donato, A., Ciardiello, M.A., De Nigris, M., Piccoli, R., Mazzarella, L., D'Alessio, G.
      (1993) J Biol Chem 268: 4745

    Organizational Affiliation

    CNR Dipartimento di Chimica, Universitá di Napoli Federico II, Italy.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEASE A
A, B
124Bos taurusMutation(s): 1 
Gene Names: RNASE1RNS1
EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
Find proteins for P61823 (Bos taurus)
Go to UniProtKB:  P61823
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62α = 90
b = 37.8β = 96.42
c = 46.66γ = 90
Software Package:
Software NamePurpose
MOLENdata collection
MOLENdata reduction
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
MOLENdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-01-11
    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: 2011-07-27
    Changes: Database references, Derived calculations, Non-polymer description