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 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


  • 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 ...

    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.


    Related Citations: 
    • Orientation of Histidine Residues in Rnase A. Neutron Diffraction Study
      Wlodawer, A.,Sjolin, L.
      (1981) Proc.Natl.Acad.Sci.USA 78: 2853
    • Comparison of Two Independently Refined Models of Ribonuclease-A
      Wlodawer, A.,Borkakoti, N.,Moss, D.S.,Howlin, B.
      (1986) Acta Crystallogr.,Sect.B 42: 379
    • Hydrogen Exchange in Rnase A. Neutron Diffraction Study
      Wlodawer, A.,Sjolin, L.
      (1982) Proc.Natl.Acad.Sci.USA 79: 1418
    • Active Site of Rnase. Neutron Diffraction Study of a Complex with Uridine Vanadate, a Transition-State Analog
      Wlodawer, A.,Miller, M.,Sjolin, L.
      (1983) Proc.Natl.Acad.Sci.USA 80: 3628
    • Joint Refinement of Macromolecular Structures with X-Ray and Neutron Single-Crystal Diffraction Data
      Wlodawer, A.,Hendrickson, W.A.
      (1981) Acta Crystallogr.,Sect.A (Supplement) 37: 8
    • Studies of Ribonuclease-A by X-Ray and Neutron Diffraction
      Wlodawer, A.
      (1980) Acta Crystallogr.,Sect.B 36: 1826
    • The Refined Crystal Structure of Ribonuclease A at 2.0 Angstroms Resolution
      Wlodawer, A.,Bott, R.,Sjolin, L.
      (1982) J.Biol.Chem. .257: 1325
    • Structure of Ribonuclease A. Results of Joint Neutron and X-Ray Refinement at 2.0-Angstroms Resolution
      Wlodawer, A.,Sjolin, L.
      (1983) Biochemistry 22: 2720
    • Structure of Ribonuclease A. X-Ray and Neutron Refinement
      Wlodawer, A.,Bott, R.,Sjolin, L.
      (1981) Acta Crystallogr.,Sect.A (Supplement) 37: 13



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEASE A
A
124Bos taurusMutation(s): 0 
Gene Names: RNASE1 (RNS1)
EC: 4.6.1.18
Find proteins for P61823 (Bos taurus)
Go to Gene View: RNASE1
Go to UniProtKB:  P61823
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UVC
Query on UVC

Download SDF File 
Download CCD File 
A
URIDINE-2',3'-VANADATE
C9 H12 N2 O9 V
JSPAHXDHRUTBDP-ODQFIEKDSA-L
 Ligand Interaction
DOD
Query on DOD

Download SDF File 
Download CCD File 
A
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UVCKi: 40000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2 Å
  • Method: SOLUTION NMR
  • Conformers Submitted: 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1986-02-25 
  • Released Date: 1986-05-07 
  • Deposition Author(s): Wlodawer, A.

Revision History 

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