9RSA

CRYSTAL STRUCTURE OF TWO COVALENT NUCLEOSIDE DERIVATIVES OF RIBONUCLEASE A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of two covalent nucleoside derivatives of ribonuclease A.

Nachman, J.Miller, M.Gilliland, G.L.Carty, R.Pincus, M.Wlodawer, A.

(1990) Biochemistry 29: 928-937

  • Primary Citation of Related Structures:  8RSA

  • PubMed Abstract: 
  • Crystal structures of two forms of ribonuclease A with deoxynucleosides covalently bound to respectively His 12 and His 119 have been solved. One form, T-H12-RNase, has a deoxythymidine bound to N epsilon 2 of His 12, while the other one, U-H119-RNas ...

    Crystal structures of two forms of ribonuclease A with deoxynucleosides covalently bound to respectively His 12 and His 119 have been solved. One form, T-H12-RNase, has a deoxythymidine bound to N epsilon 2 of His 12, while the other one, U-H119-RNase, has a deoxyuridine bound to N delta 1 of His 119. The two crystal forms are nearly isomorphous, with two molecules in the asymmetric unit. However, the modified ribonucleases differ both in their enzymatic activities and in the conformation of the catalytic site and of the deoxynucleoside-histidine moiety. T-H12-RNase is characterized by complete loss of enzymatic activity; in this form the deoxynucleoside completely blocks the catalytic site and forms intramolecular contacts with residues associated with both the B1 and B2 sites. U-H119-RNase retains 1% of the activity of the unmodified enzyme, and in this form His 119 adopts a different orientation, corresponding to the alternate conformation reported for this residue; the deoxynucleoside-histidine moiety points out of the active site and does not form any contacts with the rest of the protein, thus allowing partial access to the catalytic site. On the basis of these structures, we propose possible mechanisms for the reactions of bromoacetamido nucleosides with ribonuclease A.


    Related Citations: 
    • The Refined Crystal Structure of Ribonuclease A at 2.0 Angstroms Resolution
      Wlodawer, A.,Bott, R.,Sjolin, L.
      (1982) J.Biol.Chem. .257: 1325
    • Comparison of Two Independently Refined Models of Ribonuclease-A
      Wlodawer, A.,Borkakoti, N.,Moss, D.S.,Howlin, B.
      (1986) Acta Crystallogr.,Sect.B 42: 379
    • Structure of Phosphate-Free Ribonuclease A Refined at 1.26 Angstroms
      Wlodawer, A.,Svensson, L.A.,Sjolin, L.,Gilliland, G.L.
      (1988) Biochemistry 27: 2705
    • Multiple Conformations of Amino Acid Residues in Ribonuclease A
      Svensson, L.A.,Sjolin, L.,Gilliland, G.L.,Finzel, B.C.,Wlodawer, A.
      (1986) Proteins 1: 370


    Organizational Affiliation

    BRI Basic Research Program, NCI-Frederick Cancer Research Facility, Maryland 21701.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEASE A
A, B
124Bos taurusGene Names: RNASE1 (RNS1)
EC: 3.1.27.5
Find proteins for P61823 (Bos taurus)
Go to Gene View: RNASE1
Go to UniProtKB:  P61823
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADU
Query on ADU

Download SDF File 
Download CCD File 
A, B
3'-DEOXY-3'-ACETAMIDO-URIDINE
((((3'-DEOXY-3'-URIDINYL)-AMINO)CARBONYL)METHYL)
C11 H15 N3 O6
BUUSLPRPRSICHU-JLRHVRHOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.750α = 90.00
b = 64.100β = 90.00
c = 73.150γ = 90.00
Software Package:
Software NamePurpose
PROFFTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1991-04-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance