5LWJ

Solution NMR structure of the GTP binding Class II RNA aptamer-ligand-complex containing a protonated adenine nucleotide with a highly shifted pKa.


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: target function 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A Stably Protonated Adenine Nucleotide with a Highly Shifted pKa Value Stabilizes the Tertiary Structure of a GTP-Binding RNA Aptamer.

Wolter, A.C.Weickhmann, A.K.Nasiri, A.H.Hantke, K.Ohlenschlager, O.Wunderlich, C.H.Kreutz, C.Duchardt-Ferner, E.Wohnert, J.

(2017) Angew Chem Int Ed Engl 56: 401-404

  • DOI: https://doi.org/10.1002/anie.201609184
  • Primary Citation of Related Structures:  
    5LWJ

  • PubMed Abstract: 

    RNA tertiary structure motifs are stabilized by a wide variety of hydrogen-bonding interactions. Protonated A and C nucleotides are normally not considered to be suitable building blocks for such motifs since their pK a values are far from physiological pH. Here, we report the NMR solution structure of an in vitro selected GTP-binding RNA aptamer bound to GTP with an intricate tertiary structure. It contains a novel kind of base quartet stabilized by a protonated A residue. Owing to its unique structural environment in the base quartet, the pK a value for the protonation of this A residue in the complex is shifted by more than 5 pH units compared to the pK a for A nucleotides in single-stranded RNA. This is the largest pK a shift for an A residue in structured nucleic acids reported so far, and similar in size to the largest pK a shifts observed for amino acid side chains in proteins. Both RNA pre-folding and ligand binding contribute to the pK a shift.


  • Organizational Affiliation

    Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/Main, Germany.


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
GTP Class II RNA (34-MER)34synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
B [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyWO901/1-1 to J.W
German Research FoundationGermanyCollaborative Research Center (SFB) 902 Molecular principles of RNA based regulation

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2017-01-11
    Changes: Database references
  • Version 1.2: 2019-05-08
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 1.3: 2019-09-18
    Changes: Data collection
  • Version 1.4: 2024-05-15
    Changes: Data collection, Database references