3FKZ

X-ray structure of the non covalent swapped form of the S16G/T17N/A19P/A20S/K31C/S32C mutant of bovine pancreatic ribonuclease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Toward an antitumor form of bovine pancreatic ribonuclease: The crystal structure of three noncovalent dimeric mutants

Merlino, A.Russo Krauss, I.Perillo, M.Mattia, C.A.Ercole, C.Picone, D.Vergara, A.Sica, F.

(2009) Biopolymers 91: 1029-1037

  • DOI: 10.1002/bip.21183
  • Primary Citation of Related Structures:  
    3FL1, 3FL3, 3FL0, 3FKZ

  • PubMed Abstract: 
  • The cytotoxic action of bovine seminal ribonuclease (BS-RNase) depends on its noncovalent swapped dimeric form (NCD-BS), which presents a compact structure that allows the molecule to escape ribonuclease inhibitor (RI). A key role in the acquisition ...

    The cytotoxic action of bovine seminal ribonuclease (BS-RNase) depends on its noncovalent swapped dimeric form (NCD-BS), which presents a compact structure that allows the molecule to escape ribonuclease inhibitor (RI). A key role in the acquisition of this structure has been attributed to the concomitant presence of a proline in position 19 and a leucine in position 28. The introduction of Leu28, Cys31, and Cys32 and, in addition, of Pro19 in the sequence of bovine pancreatic ribonuclease (RNase A) has produced two dimeric variants LCC and PLCC, which do exhibit a cytotoxic activity, though at a much lower level than BS-RNase. The crystal structure analysis of the noncovalent swapped form (NCD) of LCC and PLCC, complexed with the substrate analogue 2 '-deoxycytidylyl(3 ',5 ')-2 '-deoxyguanosine, has revealed that, differently from NCD-BS, the dimers adopt an opened quaternary structure, with the two Leu residues fully exposed to the solvent, that does not hinder the binding of RI. Similar results have been obtained for a third mutant of the pancreatic enzyme, engineered with the hinge peptide sequence of the seminal enzyme (residues 16-22) and the two cysteines in position 31 and 32, but lacking the hydrophobic Leu residue in position 28. The comparison of these three structures with those previously reported for other ribonuclease swapped dimers strongly suggests that, in addition to Pro19 and Leu28, the presence of a glycine at the N-terminal end of the hinge peptide is also important to push the swapped form of RNase A dimer into the compact quaternary organization observed for NCD-BS.


    Related Citations: 
    • 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 buried diversity of bovine seminal ribonuclease: shape and cytotoxicity of the swapped non-covalent form of the enzyme
      Merlino, A., Ercole, C., Picone, D., Pizzo, E., Mazzarella, L., Sica, F.
      (2008) J Mol Biol 376: 427
    • Hints on the evolutionary design of a dimeric RNase with special bioactions
      Di Donato, A., Cafaro, V., Romeo, I., D'Alessio, G.
      (1995) Protein Sci 4: 1470

    Organizational Affiliation

    Department of Chemistry, University of Naples, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease pancreaticAB124Bos taurusMutation(s): 6 
Gene Names: RNASE1RNS1
EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
Find proteins for P61823 (Bos taurus)
Explore P61823 
Go to UniProtKB:  P61823
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
A,BL-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.14α = 90
b = 57.46β = 90.22
c = 58.5γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance