7PDU | pdb_00007pdu

Pre-catalytic complex of 10-23 DNAzyme with RNA target

• PDB DOI: https://doi.org/10.2210/pdb7PDU/pdb
• BMRB: 34654
• NAKB: 7PDU

• Classification: DNA-RNA HYBRID
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2021-08-07 Released: 2021-12-15 
• Deposition Author(s): Etzkorn, M., Borggrafe, J., Viegas, A.
• Funding Organization(s): German Research Foundation (DFG), H2020 Marie Curie Actions of the European Commission

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 7 
• Selection Criteria: structures with the lowest energy 

Literature

Time-resolved structural analysis of an RNA-cleaving DNA catalyst.

Borggrafe, J., Victor, J., Rosenbach, H., Viegas, A., Gertzen, C.G.W., Wuebben, C., Kovacs, H., Gopalswamy, M., Riesner, D., Steger, G., Schiemann, O., Gohlke, H., Span, I., Etzkorn, M.

(2022) Nature 601: 144-149

• PubMed: 34949858 
• DOI: https://doi.org/10.1038/s41586-021-04225-4
• Primary Citation Related Structures: 
  7PDU


• PubMed Abstract: 
  

  The 10-23 DNAzyme is one of the most prominent catalytically active DNA sequences ^1,2 . Its ability to cleave a wide range of RNA targets with high selectivity entails a substantial therapeutic and biotechnological potential ² . However, the high expectations have not yet been met, a fact that coincides with the lack of high-resolution and time-resolved information about its mode of action ³ . Here we provide high-resolution NMR characterization of all apparent states of the prototypic 10-23 DNAzyme and present a comprehensive survey of the kinetics and dynamics of its catalytic function. The determined structure and identified metal-ion-binding sites of the precatalytic DNAzyme-RNA complex reveal that the basis of the DNA-mediated catalysis is an interplay among three factors: an unexpected, yet exciting molecular architecture; distinct conformational plasticity; and dynamic modulation by metal ions. We further identify previously hidden rate-limiting transient intermediate states in the DNA-mediated catalytic process via real-time NMR measurements. Using a rationally selected single-atom replacement, we could considerably enhance the performance of the DNAzyme, demonstrating that the acquired knowledge of the molecular structure, its plasticity and the occurrence of long-lived intermediate states constitutes a valuable starting point for the rational design of next-generation DNAzymes.

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Organizational Affiliation: 
• Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany.
UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal.
Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany.
Bruker Switzerland AG, Fällanden, Switzerland.
John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich, Jülich, Germany.
Department of Chemistry and Pharmacy, Bioinorganic Chemistry, Friedrich Alexander University Erlangen-Nürnberg, Erlangen, Germany.
Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Düsseldorf, Germany. [e-mail].
Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany. [e-mail].
Jülich Center for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany. [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis, NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 16.25 kDa 
• Atom Count: 1,077 
• Modeled Residue Count: 52 
• Deposited Residue Count: 52 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
10-23 DNAzyme (33-MER)	A	33	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA target (19-MER)	B	19	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 7 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-12-15 
Deposition Author(s): Etzkorn, M., Borggrafe, J., Viegas, A.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	European Union	ET 103/2-1
German Research Foundation (DFG)	European Union	ET 103/2-2
German Research Foundation (DFG)	European Union	ET 103/4-1
German Research Foundation (DFG)	European Union	ET 103/5-1
H2020 Marie Curie Actions of the European Commission	European Union	N 660258

Revision History  

• Version 1.0: 2021-12-15
  Type: Initial release
  
• Version 1.1: 2022-01-26
  Changes: Database references
• Version 1.2: 2024-06-19
  Changes: Data collection, Database references