1YV6

X-ray structure of M23L onconase at 298K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.178 

wwPDB Validation 3D Report Full Report



Literature

The Importance of Dynamic Effects on the Enzyme Activity: X-RAY STRUCTURE AND MOLECULAR DYNAMICS OF ONCONASE MUTANTS

Merlino, A.Mazzarella, L.Carannante, A.Di Fiore, A.Di Donato, A.Notomista, E.Sica, F.

(2005) J Biol Chem 280: 17953-17960

  • DOI: 10.1074/jbc.M501339200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Onconase (ONC), a member of the RNase A superfamily extracted from oocytes of Rana pipiens, is an effective cancer killer. It is currently used in treatment of various forms of cancer. ONC antitumor properties depend on its ribonucleolytic activity t ...

    Onconase (ONC), a member of the RNase A superfamily extracted from oocytes of Rana pipiens, is an effective cancer killer. It is currently used in treatment of various forms of cancer. ONC antitumor properties depend on its ribonucleolytic activity that is low in comparison with other members of the superfamily. The most damaging side effect from Onconase treatment is renal toxicity, which seems to be caused by the unusual stability of the enzyme. Therefore, mutants with reduced thermal stability and/or increased catalytic activity may have significant implications for human cancer chemotherapy. In this context, we have determined the crystal structures of two Onconase mutants (M23L-ONC and C87S,des103-104-ONC) and performed molecular dynamic simulations of ONC and C87S,des103-104-ONC with the aim of explaining on structural grounds the modifications of the activity and thermal stability of the mutants. The results also provide the molecular bases to explain the lower catalytic activity of Onconase compared with RNase A and the unusually high thermal stability of the amphibian enzyme.


    Related Citations: 
    • Reversible substrate-induced domain motions in ribonuclease A
      Vitagliano, L., Merlino, A., Zagari, A., Mazzarella, L.
      (2002) Proteins 46: 97
    • Productive and nonproductive binding to ribonuclease A: X-ray structure of two complexes with uridylyl(2',5')guanosine
      Vitagliano, L., Merlino, A., Zagari, A., Mazzarella, L.
      (2000) Protein Sci 9: 1217
    • Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2',5')adenosine
      Vitagliano, L., Adinolfi, S., Riccio, A., Sica, F., Zagari, A., Mazzarella, L.
      (1998) Protein Sci 7: 1691
    • Atomic resolution structures of ribonuclease A at six pH values
      Berisio, R., Sica, F., Lamzin, V.S., Wilson, K.S., Zagari, A., Mazzarella, L.
      (2002) Acta Crystallogr D Biol Crystallogr 58: 441

    Organizational Affiliation

    Dipartimento di Chimica, Università degli Studi di Napoli "Federico II," Via Cynthia, 80126 Napoli, Italy.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
P-30 protein
A
104Rana pipiensMutation(s): 1 
EC: 3.1.27
Find proteins for P22069 (Lithobates pipiens)
Go to UniProtKB:  P22069
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.533α = 90
b = 40.856β = 90
c = 69.393γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-12-25
    Changes: Database references, Derived calculations, Polymer sequence