8UAY

Structure of Arginyl-5'-O-adenosine phosphoramidate/RNase A

  • Classification: HYDROLASE
  • Organism(s): Bos taurus
  • Mutation(s): No 

  • Deposited: 2023-09-22 Released: 2024-10-16 
  • Deposition Author(s): Pallan, P.S., Egli, M.
  • Funding Organization(s): German Research Foundation (DFG), Volkswagen Foundation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 

Starting Model: experimental
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Literature

Prolinyl Phosphoramidates of Nucleotides with Increased Reactivity.

Humboldt, A.Rami, F.Topp, F.M.Arnold, D.Gohringer, D.Pallan, P.S.Egli, M.Richert, C.

(2024) Angew Chem Int Ed Engl 63: e202319958-e202319958

  • DOI: https://doi.org/10.1002/anie.202319958
  • Primary Citation of Related Structures:  
    8UAX, 8UAY, 8UAZ, 8UB0, 8UB1, 8UB2

  • PubMed Abstract: 

    Nucleoside monophosphates (NMPs) are the subunits of RNA. They are incorporated into growing complementary strands when sequences are copied in enzyme-free reactions using organic leaving groups at the phosphates. Amino acids are rarely considered as leaving groups, but proline can act as a leaving group when N-linked to NMPs, so that prolinyl NMPs hydrolyze in aqueous buffer at 37 °C, with half-life times as short as 2.4 h, and they act as monomers in enzyme-free primer extension. Still, their level of reactivity is insufficient for practical purposes, requiring months for some extensions. Herein we report the synthesis of eight substituted prolinyl AMPs together with seven related compounds and the results of a study of their reactivity. A δ-carboxy prolinyl NMP was found to be converted with a half-life time of just 11 min in magnesium-free buffer, and a δ-isopropyl prolinyl NMP was shown to react sevenfold faster than its prolinyl counterpart in enzyme-free genetic copying of RNA. Our results indicate that both anchimeric and steric effects can be employed to increase the reactivity of aminoacidyl nucleotides, i.e. compounds that combine two fundamental classes of biomolecules in one functional entity.


  • Organizational Affiliation

    Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease pancreatic
A, B
124Bos taurusMutation(s): 0 
EC: 4.6.1.18
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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WF9 (Subject of Investigation/LOI)
Query on WF9

Download Ideal Coordinates CCD File 
C [auth A](2S)-2-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]amino}-5-carbamimidamidopentanoic acid (non-preferred name)
C16 H26 N9 O8 P
AXUGFAXGFGAXFD-TWBCTODHSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
D [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.508α = 90
b = 31.128β = 91.75
c = 68.575γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany364653263
Volkswagen FoundationGermanyAZ 92768

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release