1TQ9

Non-covalent swapped dimer of Bovine Seminal Ribonuclease in complex with 2'-DEOXYCYTIDINE-2'-DEOXYADENOSINE-3',5'-MONOPHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 36753-36760

  • DOI: 10.1074/jbc.M405655200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A growing number of pancreatic-type ribonucleases (RNases) present cytotoxic activity against malignant cells. The cytoxicity of these enzymes is related to their resistance to the ribonuclease protein inhibitor (RI). In particular, bovine seminal ri ...

    A growing number of pancreatic-type ribonucleases (RNases) present cytotoxic activity against malignant cells. The cytoxicity of these enzymes is related to their resistance to the ribonuclease protein inhibitor (RI). In particular, bovine seminal ribonuclease (BS-RNase) is toxic to tumor cells both in vitro and in vivo. BS-RNase is a covalent dimer with two intersubunit disulfide bridges between Cys(31) of one chain and Cys(32) of the second and vice versa. The native enzyme is an equilibrium mixture of two isomers, MxM and M=M. In the former the two subunits swap their N-terminal helices. The cytotoxic action is a peculiar property of MxM. In the reducing environment of cytosol, M=M dissociates into monomers, which are strongly inhibited by RI, whereas MxM remains as a non-covalent dimer (NCD), which evades RI. We have solved the crystal structure of NCD, carboxyamidomethylated at residues Cys(31) and Cys(32) (NCD-CAM), in a complex with 2'-deoxycitidylyl(3'-5')-2'-deoxyadenosine. The molecule reveals a quaternary structural organization much closer to MxM than to other N-terminal-swapped non-covalent dimeric forms of RNases. Model building of the complexes between these non-covalent dimers and RI reveals that NCD-CAM is the only dimer equipped with a quaternary organization capable of interfering seriously with the binding of the inhibitor. Moreover, a detailed comparative structural analysis of the dimers has highlighted the residues, which are mostly important in driving the quaternary structure toward that found in NCD-CAM.


    Related Citations: 
    • Bovine seminal ribonuclease: structure at 1.9 A resolution
      Mazzarella, L., Capasso, S., Demasi, D., Dilorenzo, G., Mattia, C.A., Zagari, A.
      (1993) Acta Crystallogr D Biol Crystallogr 49: 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
    • 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
    • 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
    • Crystal structure of the dimeric unswapped form of bovine seminal ribonuclease
      Berisio, R., Sica, F., De Lorenzo, C., Di Fiore, A., Piccoli, R., Zagari, A., Mazzarella, L.
      (2003) FEBS Lett 554: 105
    • 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

    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease, seminal
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
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
A,B
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.471α = 90
b = 69.689β = 90
c = 110.804γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
HKL-2000data reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance