7D82

Crystal Structure of the Domain2 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+), soaked in Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding.

Chen, H.Egger, M.Xu, X.Flemmich, L.Krasheninina, O.Sun, A.Micura, R.Ren, A.

(2020) Nucleic Acids Res 48: 12394-12406

  • DOI: 10.1093/nar/gkaa1029
  • Primary Citation of Related Structures:  
    7D7Z, 7D7X, 7D7Y, 7D7V, 7D7W, 7D81, 7D82

  • PubMed Abstract: 
  • Riboswitches are important gene regulatory elements frequently encountered in bacterial mRNAs. The recently discovered nadA riboswitch contains two similar, tandemly arrayed aptamer domains, with the first domain possessing high affinity for nicotina ...

    Riboswitches are important gene regulatory elements frequently encountered in bacterial mRNAs. The recently discovered nadA riboswitch contains two similar, tandemly arrayed aptamer domains, with the first domain possessing high affinity for nicotinamide adenine dinucleotide (NAD+). The second domain which comprises the ribosomal binding site in a putative regulatory helix, however, has withdrawn from detection of ligand-induced structural modulation thus far, and therefore, the identity of the cognate ligand and the regulation mechanism have remained unclear. Here, we report crystal structures of both riboswitch domains, each bound to NAD+. Furthermore, we demonstrate that ligand binding to domain 2 requires significantly higher concentrations of NAD+ (or ADP retaining analogs) compared to domain 1. Using a fluorescence spectroscopic approach, we further shed light on the structural features which are responsible for the different ligand affinities, and describe the Mg2+-dependent, distinct folding and pre-organization of their binding pockets. Finally, we speculate about possible scenarios for nadA RNA gene regulation as a putative two-concentration sensor module for a time-controlled signal that is primed and stalled by the gene regulation machinery at low ligand concentrations (domain 1), and finally triggers repression of translation as soon as high ligand concentrations are reached in the cell (domain 2).


    Organizational Affiliation

    Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
832GAAA (50-MER)A50Acidobacteriaceae bacterium KBS 83
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.916α = 90
b = 75.916β = 90
c = 50.289γ = 120
Software Package:
Software NamePurpose
HKL-3000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-10-06 
  • Released Date: 2020-11-25 
  • Deposition Author(s): Chen, H., Ren, A.M.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History 

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2020-12-02
    Changes: Database references
  • Version 1.2: 2020-12-23
    Changes: Database references