1N1X

Crystal Structure Analysis of the monomeric [S-carboxyamidomethyl-Cys31, S-carboxyamidomethyl-Cys32] Bovine seminal ribonuclease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 263-271

  • DOI: 10.1002/prot.10407
  • Primary Citation of Related Structures:  
    1N1X, 1N3Z

  • PubMed Abstract: 
  • Bovine seminal ribonuclease, a homodimeric enzyme joined covalently by two interchain disulphide bonds, is an equilibrium mixture of two conformational isomers, MxM and M=M. The major form, MxM, whose crystal structure has been previously determined at 1 ...

    Bovine seminal ribonuclease, a homodimeric enzyme joined covalently by two interchain disulphide bonds, is an equilibrium mixture of two conformational isomers, MxM and M=M. The major form, MxM, whose crystal structure has been previously determined at 1.9 A resolution, presents the swapping of the N-terminal segments (residues 1-15) and composite active sites formed by residues of different chains. The three-dimensional domain swapping does not occur in the M=M form. The different fold of each N-terminal tail is directed by the hinge loop (residue 16-22) connecting the swapping domain to the body of the protein. Reduction and alkylation of interchain disulphide bridges produce a monomeric derivative and a noncovalent swapped dimer, which are both active. The free and nucleotide-bound forms of the monomer have been crystallized at an alkaline pH and refined at 1.45 and 1.65 A resolution, respectively. In both cases, the N-terminal fragment is folded on the main body of the protein to produce an intact active site and a chain architecture very similar to that of bovine pancreatic ribonuclease. In this new fold of the seminal chain, the hinge loop is disordered. Despite the difference between the tertiary structure of the monomer and that of the chains in the MxM form, the active sites of the two enzymes are virtually indistinguishable. Furthermore, the structure of the liganded enzyme represents the first example of a ribonuclease complex studied at an alkaline pH and provides new information on the binding of a nucleotide when the catalytic histidines are deprotonated.


    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
    • 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
    • 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
    • Assignment and secondary-structure determination of monomeric bovine seminal ribonuclease employing computer-assisted evaluation of homonuclear three-dimensional 1H-NMR spectra
      D'Ursi, A., Oschkinat, H., Cieslar, C., Picone, D., D'Alessio, G., Amodeo, P., Temussi, P.
      (1995) Eur J Biochem 229: 494

    Organizational Affiliation

    Dipartimento di Chimica, Università degli Studi di Napoli Federico II, Napoli, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease, seminalA124Bos taurusMutation(s): 2 
Gene Names: SRN
EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
UniProt
Find proteins for P00669 (Bos taurus)
Explore P00669 
Go to UniProtKB:  P00669
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00669
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
A L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.39α = 90
b = 28.73β = 119
c = 67.41γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-08-26
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance