11BA

BINDING OF A SUBSTRATE ANALOGUE TO A DOMAIN SWAPPING PROTEIN IN THE COMPLEX OF BOVINE SEMINAL RIBONUCLEASE WITH URIDYLYL-2',5'-ADENOSINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Work: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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: 1691-1699

  • DOI: 10.1002/pro.5560070804
  • Primary Citation of Related Structures:  
    11BA

  • PubMed Abstract: 
  • Bovine seminal ribonuclease (BS-RNase) is a unique member of the pancreatic-like ribonuclease superfamily. The native enzyme is a mixture of two dimeric forms with distinct structural features. The most abundant form is characterized by the swapping of N-terminal fragments ...

    Bovine seminal ribonuclease (BS-RNase) is a unique member of the pancreatic-like ribonuclease superfamily. The native enzyme is a mixture of two dimeric forms with distinct structural features. The most abundant form is characterized by the swapping of N-terminal fragments. In this paper, the crystal structure of the complex between the swapping dimer and uridylyl(2',5')adenosine is reported at 2.06 A resolution. The refined model has a crystallographic R-factor of 0.184 and good stereochemistry. The quality of the electron density maps enables the structure of both the inhibitor and active site residues to be unambiguously determined. The overall architecture of the active site is similar to that of RNase A. The dinucleotide adopts an extended conformation with the pyrimidine and purine base interacting with Thr45 and Asn71, respectively. Several residues (Gln11, His12, Lys41, His119, and Phe120) bind the oxygens of the phosphate group. The structural similarity of the active sites of BS-RNase and RNase A includes some specific water molecules believed to be relevant to catalytic activity. Upon binding of the dinucleotide, small but significant modifications of the tertiary and quaternary structure of the protein are observed. The ensuing correlation of these modifications with the catalytic activity of the enzyme is discussed.


    Related Citations: 
    • 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.
      (1997) J Cryst Growth 168: 192
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (RIBONUCLEASE, SEMINAL)A, B124Bos taurusMutation(s): 0 
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
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UPA
Query on UPA

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
URIDYLYL-2'-5'-PHOSPHO-ADENOSINE
C19 H24 N7 O12 P
QARCCHXXGAIRFS-KPKSGTNCSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B],
F [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.45α = 90
b = 60.64β = 117.35
c = 50.75γ = 90
Software Package:
Software NamePurpose
bioteXdata collection
bioteXdata reduction
X-PLORmodel building
X-PLORrefinement
bioteXdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-03-26
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2019-11-06
    Changes: Data collection, Database references