6PVV

RNase A in complex with p5A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Nucleoside Tetra- and Pentaphosphates Prepared Using a Tetraphosphorylation Reagent Are Potent Inhibitors of Ribonuclease A.

Shepard, S.M.Windsor, I.W.Raines, R.T.Cummins, C.C.

(2019) J Am Chem Soc 141: 18400-18404

  • DOI: 10.1021/jacs.9b09760
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Adenosine and uridine 5'-tetra- and 5'-pentaphosphates were synthesized from an activated tetrametaphosphate ([PPN] 2 [P 4 O 11 ], [PPN] 2 [ 1 ], PPN = bis(triphenylphosphine)iminium) and subsequentl ...

    Adenosine and uridine 5'-tetra- and 5'-pentaphosphates were synthesized from an activated tetrametaphosphate ([PPN] 2 [P 4 O 11 ], [PPN] 2 [ 1 ], PPN = bis(triphenylphosphine)iminium) and subsequently tested for inhibition of the enzymatic activity of ribonuclease A (RNase A). Reagent [PPN] 2 [ 1 ] reacts with unprotected uridine and adenosine in the presence of a base under anhydrous conditions to give nucleoside tetrametaphosphates. Ring opening of these intermediates with tetrabutylammonium hydroxide ([TBA][OH]) yields adenosine and uridine tetraphosphates ( p 4 A , p 4 U ) in 92% and 85% yields, respectively, from the starting nucleoside. Treatment of ([PPN] 2 [ 1 ]) with AMP or UMP yields nucleoside-monophosphate tetrametaphosphates ( cp 4 pA, cp 4 pU ) having limited aqueous stability. Ring opening of these ultraphosphates with [TBA][OH] yields p 5 A and p 5 U in 58% and 70% yield from AMP and UMP, respectively. We characterized inorganic and nucleoside-conjugated linear and cyclic oligophosphates as competitive inhibitors of RNase A. Increasing the chain length in both linear and cyclic inorganic oligophosphates resulted in improved binding affinity. Increasing the length of oligophosphates on the 5' position of adenosine beyond three had a deleterious effect on binding. Conversely, uridine nucleotides bearing 5' oligophosphates saw progressive increases in binding with chain length. We solved X-ray cocrystal structures of the highest affinity binders from several classes. The terminal phosphate of p 5 A binds in the P 1 enzymic subsite and forces the oligophosphate to adopt a convoluted conformation, while the oligophosphate of p 5 U binds in several extended conformations, targeting multiple cationic regions of the active-site cleft.


    Organizational Affiliation

    Department of Chemistry , Massachusetts Institute of Technology , Cambridge Massachusetts 02139 , United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease pancreatic
A, B
124Bos taurusMutation(s): 0 
Gene Names: RNASE1RNS1
EC: 4.6.1.18
Find proteins for P61823 (Bos taurus)
Go to UniProtKB:  P61823
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5FA
Query on 5FA

Download CCD File 
A, B
ADENOSINE-5'-PENTAPHOSPHATE
C10 H18 N5 O19 P5
WYJWVZZCMBUPSP-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.79α = 90
b = 32.25β = 90.3
c = 71.95γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
SAINTdata reduction
SADABSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA073808

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence, Database references