1Y92

Crystal structure of the P19A/N67D Variant Of Bovine seminal Ribonuclease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Role of the Hinge Loop in Domain Swapping: THE SPECIAL CASE OF BOVINE SEMINAL RIBONUCLEASE.

Picone, D.Di Fiore, A.Ercole, C.Franzese, M.Sica, F.Tomaselli, S.Mazzarella, L.

(2005) J Biol Chem 280: 13771-13778

  • DOI: 10.1074/jbc.M413157200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Bovine seminal ribonuclease (BS-RNase) is a covalent homodimeric enzyme homologous to pancreatic ribonuclease (RNase A), endowed with a number of special biological functions. It is isolated as an equilibrium mixture of swapped (MxM) and unswapped (M ...

    Bovine seminal ribonuclease (BS-RNase) is a covalent homodimeric enzyme homologous to pancreatic ribonuclease (RNase A), endowed with a number of special biological functions. It is isolated as an equilibrium mixture of swapped (MxM) and unswapped (M=M) dimers. The interchanged N termini are hinged on the main bodies through the peptide 16-22, which changes conformation in the two isomers. At variance with other proteins, domain swapping in BS-RNase involves two dimers having a similar and highly constrained quaternary association, mainly dictated by two interchain disulfide bonds. This provides the opportunity to study the intrinsic ability to swap as a function of the hinge sequence, without additional effects arising from dissociation or quaternary structure modifications. Two variants, having Pro19 or the whole sequence of the hinge replaced by the corresponding residues of RNase A, show equilibrium and kinetic parameters of the swapping similar to those of the parent protein. In comparison, the x-ray structures of MxM indicate, within a substantial constancy of the quaternary association, a greater mobility of the hinge residues. The relative insensitivity of the swapping tendency to the substitutions in the hinge region, and in particular to the replacement of Pro19 by Ala, contrasts with the results obtained for other swapped proteins and can be rationalized in terms of the unique features of the seminal enzyme. Moreover, the results indirectly lend credit to the hypothesis that the major role of Pro19 resides in directing the assembly of the non-covalent dimer, the species produced by selective reduction of the interchain disulfides and considered responsible for the special biological functions of BS-RNase.


    Related Citations: 
    • Bovine seminal ribonuclease: structure at 1.9 resolution
      Mazzarella, L., Capasso, S., Demasi, D., Di Lorenzo, G., Mattia, C.A., Zagari, A.
      (1993) Acta Crystallogr D Biol Crystallogr D49: 389
    • 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
    • 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
    • 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
    • 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
    • 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
    • A potential allosteric subsite generated by domain swapping in bovine seminal ribonuclease.
      (1999) J Mol Biol 293: 569

    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Seminal ribonuclease
A, B
124Bos taurusMutation(s): 2 
Gene Names: SRN
EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
Find proteins for P00669 (Bos taurus)
Go to UniProtKB:  P00669
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.5α = 90
b = 62.433β = 90
c = 81.594γ = 90
Software Package:
Software NamePurpose
ENRAF-NONIUSdata collection
DENZOdata reduction
AMoREphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance