2M57 | pdb_00002m57

NMR solution structure of domain 5 from Azotobacter vinelandii Intron 5 at pH 7.8

• PDB DOI: https://doi.org/10.2210/pdb2M57/pdb
• BMRB: 19039
• NAKB: 2M57

• Classification: RNA
• Organism(s): Azotobacter vinelandii
• Mutation(s): No 


• Deposited: 2013-02-15 Released: 2014-02-26 
• Deposition Author(s): Pechlaner, M., Donghi, D., Zelenay, V., Sigel, R.K.O.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Protonation-Dependent Base Flipping at Neutral pH in the Catalytic Triad of a Self-Splicing Bacterial Group II Intron.

Pechlaner, M., Donghi, D., Zelenay, V., Sigel, R.K.

(2015) Angew Chem Int Ed Engl 54: 9687-9690

• PubMed: 26119804 
• DOI: https://doi.org/10.1002/anie.201504014
• Primary Citation of Related Structures:  
  2M57


• PubMed Abstract: 
  

  NMR spectroscopy has revealed pH-dependent structural changes in the highly conserved catalytic domain 5 of a bacterial group II intron. Two adenines with pK(a) values close to neutral pH were identified in the catalytic triad and the bulge. Protonation of the adenine opposite to the catalytic triad is stabilized within a G(syn)-AH(+) (anti) base pair. The pH-dependent anti-to-syn flipping of this G in the catalytic triad modulates the known interaction with the linker region between domains 2 and 3 (J23) and simultaneously the binding of the catalytic Mg(2+) ion to its backbone. Hence, this here identified shifted pK(a) value controls the conformational change between the two steps of splicing.

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Organizational Affiliation: 
• Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich (Switzerland) http://www.chem.uzh.ch/rna.
Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich (Switzerland) http://www.chem.uzh.ch/rna. [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 11.27 kDa 
• Atom Count: 745 
• Modeled Residue Count: 35 
• Deposited Residue Count: 35 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA_(35-MER)	A	35	Azotobacter vinelandii

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-26 
Deposition Author(s): Pechlaner, M., Donghi, D., Zelenay, V., Sigel, R.K.O.

Revision History  

• Version 1.0: 2014-02-26
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Data collection, Database references, Other
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references
• Version 1.3: 2025-03-12
  Changes: Database references, Structure summary