6RSA

NUCLEAR MAGNETIC RESONANCE AND NEUTRON DIFFRACTION STUDIES OF THE COMPLEX OF RIBONUCLEASE*A WITH URIDINE VANADATE, A TRANSITION-STATE ANALOGUE


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.00 Å

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Nuclear magnetic resonance and neutron diffraction studies of the complex of ribonuclease A with uridine vanadate, a transition-state analogue.

Borah, B.Chen, C.W.Egan, W.Miller, M.Wlodawer, A.Cohen, J.S.

(1985) Biochemistry 24: 2058-2067

  • DOI: https://doi.org/10.1021/bi00329a038
  • Primary Citation of Related Structures:  
    6RSA

  • PubMed Abstract: 

    The complex of ribonuclease A (RNase A) with uridine vanadate (U-V), a transition-state analogue, has been studied with 51V and proton NMR spectroscopy in solution and by neutron diffraction in the crystalline state. Upon the addition of aliquots of U-V at pH 6.6, the C epsilon-H resonances of the two active-site histidine residues 119 and 12 decrease in intensity while four new resonances appear. Above pH 8 and below pH 5, these four resonances decrease in intensity as the complex dissociates. These four resonances are assigned to His-119 and His-12 in protonated and unprotonated forms in the RNase-U-V complex. These resonances do not titrate or change in relative area in the pH range 5-8, indicating a slow protonation process, and the extent of protonation remains constant with ca. 58% of His-12 and ca. 26% of His-119 being protonated. The results of diffraction studies show that both His-12 and His-119 occupy well-defined positions in the RNase-U-V complex and that both are protonated. However, while the classic interpretation of the mechanism of action of RNase based on the proposal of Findlay et al. [Findlay, D., Herries, D. G., Mathias, A. P., Rabin, B. R., & Ross, C. A. (1962) Biochem. J. 85, 152-153] requires both His-12 and His-119 to be in axial positions relative to the pentacoordinate transition state, in the diffraction structure His-12 is found to be in an equatorial position, while Lys-41 is close to an axial position. Hydrogen exchange data show that the mobility and accessibility of amides in the RNase-U-V complex do not significantly differ from what was observed in the native enzyme. The results of both proton NMR in solution and neutron diffraction in the crystal are compared and interpreted in terms of the mechanism of action of RNase.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RIBONUCLEASE A124Bos taurusMutation(s): 0 
EC: 3.1.27.5
UniProt
Find proteins for P61823 (Bos taurus)
Explore P61823 
Go to UniProtKB:  P61823
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61823
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UVC
Query on UVC

Download Ideal Coordinates CCD File 
B [auth A]URIDINE-2',3'-VANADATE
C9 H12 N2 O9 V
JSPAHXDHRUTBDP-ODQFIEKDSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
UVC PDBBind:  6RSA Ki: 4.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.00 Å
  • Space Group: P 1 21 1
  • Method: SOLUTION NMR
  • Conformers Submitted: 
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.3α = 90
b = 38.35β = 106.4
c = 53.7γ = 90

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 1986-05-07 
  • Deposition Author(s): Wlodawer, A.

Revision History  (Full details and data files)

  • Version 1.0: 1986-05-07
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Data collection, Non-polymer description
  • Version 1.4: 2011-10-05
    Changes: Derived calculations