11BG

A POTENTIAL ALLOSTERIC SUBSITE GENERATED BY DOMAIN SWAPPING IN BOVINE SEMINAL RIBONUCLEASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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: 569-577

  • DOI: 10.1006/jmbi.1999.3158
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Bovine seminal ribonuclease (BS-RNase) is a peculiar member of the pancreatic-like ribonuclease superfamily endowed with unique biological functions. It has been shown that native BS-RNase is a mixture of two distinct dimeric forms. The most abundant ...

    Bovine seminal ribonuclease (BS-RNase) is a peculiar member of the pancreatic-like ribonuclease superfamily endowed with unique biological functions. It has been shown that native BS-RNase is a mixture of two distinct dimeric forms. The most abundant form is characterised by the swapping of the N-terminal helix. Kinetic studies have shown that this dimer is allosterically regulated, whereas the minor component, in which no swapping occurs, exhibits typical Michaelian kinetics. In order to correlate the catalytic properties with the structural features of BS-RNase, we have determined the crystal structure of the BS-RNase swapping dimer complexed with uridylyl(2'-5')guanosine. The structure of the complex was refined to an R value of 0.189 at 1.9 A resolution. Surprisingly, the enzyme binds four dinucleotide molecules, all in a non-productive way. In the two active sites, the guanine base is located in the subsite that is specific for pyrimidines. This unusual binding has been observed also in complexes of RNase A with guanine-containing nucleotides (retro-binding). One of the two additional dinucleotide molecules bound to the enzyme is located on the surface of the protein in a pocket generated by crystal packing; the second was found in a cavity at the interface between the two subunits of the swapping dimer. There are indications that the interface site plays a role in the allosteric regulation exhibited by BS-RNase. This finding suggests that domain swapping may not merely be a mechanism that proteins adopt for the transition from a monomeric to oligomeric state but can be used to achieve modulations in catalytic function.


    Related Citations: 
    • Crystallization of Multiple Forms of Bovine Seminal Ribonuclease in the Liganded and Unliganded State
      Sica, F., Adinolfi, S., Berisio, R., De Lorenzo, C., Mazzarella, L., Piccoli, R., Vitagliano, L., Zagari, A.
      (1999) J Cryst Growth 196: 305
    • 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
    • Cosolute Effect on Crystallization of Two Dinucleotide Complexes of Bovine Seminal Ribonuclease from Concentrated Salt Solutions
      Sica, F., Adinolfi, S., Vitagliano, L., Zagari, A., Capasso, S., Mazzarella, L.
      (1997) J Cryst Growth 168: 192
    • Swapping structural determinants of ribonucleases: an energetic analysis of the hinge peptide 16-22.
      Mazzarella, L., Vitagliano, L., Zagari, A.
      (1995) Proc Natl Acad Sci U S A 92: 3799
    • 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 D Biol Crystallogr 49: 389

    Organizational Affiliation

    Centro di Studio di Biocristallografia, CNR, and Dipartimento di Chimica, Universita' degli Studi di Napoli "Federico II", Via Mezzocannone 4, Napoli, I-80134, Italy.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (BOVINE SEMINAL RIBONUCLEASE)
A, B
124Bos taurusMutation(s): 0 
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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U2G
Query on U2G

Download CCD File 
A, B
URIDYLYL-2'-5'-PHOSPHO-GUANOSINE
C19 H24 N7 O13 P
DFYLLEBFVZTKHD-VMIOUTBZSA-N
 Ligand Interaction
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 Work: 0.189 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.4α = 90
b = 66.7β = 90
c = 107.7γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-11-05
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2019-11-06
    Changes: Data collection, Database references