1R5C

X-ray structure of the complex of Bovine seminal ribonuclease swapping dimer with d(CpA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 689-695

  • DOI: 10.1002/bip.20016
  • Primary Citation of Related Structures:  1R5D
  • Also Cited By: 1TQ9, 3BCM, 3BCO, 3BCP

  • PubMed Abstract: 
  • Bovine seminal ribonuclease (BS-RNase) is a unique member of the pancreatic-like ribonuclease superfamily. This enzyme exists as two conformational isomers with distinctive biological properties. The structure of the major isomer is characterized by ...

    Bovine seminal ribonuclease (BS-RNase) is a unique member of the pancreatic-like ribonuclease superfamily. This enzyme exists as two conformational isomers with distinctive biological properties. The structure of the major isomer is characterized by the swapping of the N-terminal segment (MxM BS-RNase). In this article, the crystal structures of the ligand-free MxM BS-RNase and its complex with 2'-deoxycitidylyl(3',5')-2'-deoxyadenosine derived from isomorphous crystals have been refined. Interestingly, the comparison between this novel ligand-free form and the previously published sulfate-bound structure reveals significant differences. In particular, the ligand-free MxM BS-RNase is closer to the structure of MxM BS-RNase productive complexes than to the sulfate-bound form. These results reveal that MxM BS-RNase presents a remarkable flexibility, despite the structural constraints of the interchain disulfide bridges and the swapping of the N-terminal helices. These findings have important implications to the ligand binding mechanism of MxM BS-RNase. Indeed, a population shift rather than a substrate-induced conformational transition may occur in the MxM BS-RNase ligand binding process.


    Related Citations: 
    • 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
    • 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.
      (1996) J.Cryst.Growth 168: 192
    • 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
      VITAGLIANO, L.,Adinolfi, S.,Sica, F.,Merlino, A.,Zagari, A.,Mazzarella, L.
      (1999) J.Mol.Biol. 293: 569


    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
Ribonuclease, seminal
A, B
124Bos taurusGene Names: SRN
EC: 3.1.27.5
Find proteins for P00669 (Bos taurus)
Go to UniProtKB:  P00669
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CPA
Query on CPA

Download SDF File 
Download CCD File 
A, B
2'-DEOXYCYTIDINE-2'-DEOXYADENOSINE-3',5'-MONOPHOSPHATE
C19 H25 N8 O9 P
LYWWDKIADIGKTH-IDMWBNCISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.540α = 90.00
b = 60.020β = 90.00
c = 83.690γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
DENZOdata reduction
X-PLORrefinement
X-PLORmodel building
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance