3BCO

Crystal Structure of The Swapped FOrm of P19A/L28Q/N67D BS-RNase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The buried diversity of bovine seminal ribonuclease: shape and cytotoxicity of the swapped non-covalent form of the enzyme

Merlino, A.Ercole, C.Picone, D.Pizzo, E.Mazzarella, L.Sica, F.

(2008) J.Mol.Biol. 376: 427-437

  • DOI: 10.1016/j.jmb.2007.11.008
  • Primary Citation of Related Structures:  
  • Also Cited By: 3FL3, 3FL1, 3FL0, 3FKZ, 3F8G

  • PubMed Abstract: 
  • Bovine seminal ribonuclease exists in the native state as an equilibrium mixture of a swapped and an unswapped dimer. The molecular envelope and the exposed surface of the two isomers are practically indistinguishable and their diversity is almost co ...

    Bovine seminal ribonuclease exists in the native state as an equilibrium mixture of a swapped and an unswapped dimer. The molecular envelope and the exposed surface of the two isomers are practically indistinguishable and their diversity is almost completely buried in the interior of the protein. Surprisingly, the cytotoxic and antitumor activity of the enzyme is a peculiar property of the swapped dimer. This buried diversity comes into light in the reducing environment of the cytosol, where the unswapped dimer dissociates into monomers, whereas the swapped one generates a metastable dimeric form (NCD-BS) with a quaternary assembly that allows the molecule to escape the protein inhibitor of ribonucleases. The stability of this quaternary shape was mainly attributed to the combined presence of Pro19 and Leu28. We have prepared and fully characterized by X-ray diffraction the double mutant P19A/L28Q (PALQ) of the seminal enzyme. While the swapped and unswapped forms of the mutant have structures very similar to that of the corresponding wild-type forms, the non-covalent form (NCD-PALQ) adopts an opened quaternary structure, different from that of NCD-BS. Moreover, model building clearly indicates that NCD-PALQ can be easily sequestered by the protein inhibitor. In agreement with these results, cytotoxic assays have revealed that PALQ has limited activity, whereas the single mutants P19A and L28Q display cytotoxic activity against malignant cells almost as large as the wild-type enzyme. The significant increase in the antitumor activity, brought about by the substitution of just two residues in going from the double mutant to the wild-type enzyme, suggests a new strategy to improve this important biological property by strengthening the interface that stabilizes the quaternary structure of NCD-BS.


    Related Citations: 
    • Population shift vs induced fit: the case of bovine seminal ribonuclease swapping dimer
      Merlino, A.,Vitagliano, L.,Sica, F.,Zagari, A.,Mazzarella, L.
      (2004) Biopolymers 73: 689
    • Bovine seminal ribonuclease: structure at 1.9 A resolution
      Mazzarella, L.,Capasso, S.,Demasi, D.,Di Lorenzo, G.,Mattia, C.A.,Zagari, A.
      (1993) Acta Crystallogr.,Sect.D 49: 389
    • Structure and stability of the non-covalent swapped dimer of bovine seminal ribonuclease: an enzyme tailored to evade ribonuclease protein inhibitor
      Sica, F.,Di Fiore, A.,Merlino, A.,Mazzarella, L.
      (2004) J.Biol.Chem. 279: 36753
    • A potential allosteric subsite generated by domain swapping in bovine seminal ribonuclease
      Vitagliano, L.,Adinolfi, S.,Sica, F.,Merlino, A.,Zagari, A.,Mazzarella, L.
      (1999) J.Mol.Biol. 293: 569
    • The unswapped chain of bovine seminal ribonuclease: Crystal structure of the free and liganded monomeric derivative
      Sica, F.,Di Fiore, A.,Zagari, A.,Mazzarella, L.
      (2003) Proteins 52: 263
    • 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


    Organizational Affiliation

    Dipartimento di Chimica, Università degli Studi di Napoli Federico II, Via Cintia, 80126 Naples, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Seminal ribonuclease
A, B
124Bos taurusMutation(s): 3 
Gene Names: SRN
EC: 3.1.27.5
Find proteins for P00669 (Bos taurus)
Go to UniProtKB:  P00669
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.551α = 90.00
b = 62.305β = 90.00
c = 81.143γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance