1N3Z

Crystal structure of the [S-carboxyamidomethyl-Cys31, S-carboxyamidomethyl-Cys32] monomeric derivative of the bovine seminal ribonuclease in the liganded state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

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 ...

    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 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
    • 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
    • Coulombic effects of remote subsites on the active site of ribonuclease A
      Fisher, B.M., Schultz, L.W., Raines, R.T.
      (1998) Biochemistry 37: 17386

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease, seminalA124Bos 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)
Explore P00669 
Go to UniProtKB:  P00669
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U3P
Query on U3P

Download CCD File 
A
3'-URIDINEMONOPHOSPHATE
C9 H13 N2 O9 P
FOGRQMPFHUHIGU-XVFCMESISA-N
 Ligand Interaction
ADN
Query on ADN

Download CCD File 
A
ADENOSINE
C10 H13 N5 O4
OIRDTQYFTABQOQ-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
AL-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
U3PKi:  63200   nM  BindingDB
U3PKi :  63200   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.69α = 90
b = 28.82β = 119.2
c = 67.52γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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