1R5C

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

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
  • Structures With Same Primary Citation

  • 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 D Biol Crystallogr 49: 389
    • 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.
      (1996) J Cryst Growth 168: 192
    • 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
    • Crystallization of Multiple Forms of Bovine Seminal Ribonuclease: the liganded and Unliganded State
      (1999) J Cryst Growth 196: 305

    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 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CPA
Query on CPA

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: 2.10 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.54α = 90
b = 60.02β = 90
c = 83.69γ = 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: 2004-04-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance