7ELQ

Crystal structure of xanthine riboswitch with xanthine, manganese saok


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

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Literature

Insights into xanthine riboswitch structure and metal ion-mediated ligand recognition.

Xu, X.Egger, M.Chen, H.Bartosik, K.Micura, R.Ren, A.

(2021) Nucleic Acids Res 49: 7139-7153

  • DOI: 10.1093/nar/gkab486
  • Primary Citation of Related Structures:  
    7ELP, 7ELQ, 7ELR, 7ELS

  • PubMed Abstract: 
  • Riboswitches are conserved functional domains in mRNA that mostly exist in bacteria. They regulate gene expression in response to varying concentrations of metabolites or metal ions. Recently, the NMT1 RNA motif has been identified to selectively bind xanthine and uric acid, respectively, both are involved in the metabolic pathway of purine degradation ...

    Riboswitches are conserved functional domains in mRNA that mostly exist in bacteria. They regulate gene expression in response to varying concentrations of metabolites or metal ions. Recently, the NMT1 RNA motif has been identified to selectively bind xanthine and uric acid, respectively, both are involved in the metabolic pathway of purine degradation. Here, we report a crystal structure of this RNA bound to xanthine. Overall, the riboswitch exhibits a rod-like, continuously stacked fold composed of three stems and two internal junctions. The binding-pocket is determined by the highly conserved junctional sequence J1 between stem P1 and P2a, and engages a long-distance Watson-Crick base pair to junction J2. Xanthine inserts between a G-U pair from the major groove side and is sandwiched between base triples. Strikingly, a Mg2+ ion is inner-sphere coordinated to O6 of xanthine and a non-bridging oxygen of a backbone phosphate. Two further hydrated Mg2+ ions participate in extensive interactions between xanthine and the pocket. Our structure model is verified by ligand binding analysis to selected riboswitch mutants using isothermal titration calorimetry, and by fluorescence spectroscopic analysis of RNA folding using 2-aminopurine-modified variants. Together, our study highlights the principles of metal ion-mediated ligand recognition by the xanthine riboswitch.


    Organizational Affiliation

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



Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
NMT1_Mn (46-MER)A, B45Ideonella sp. B508-1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
C [auth A], N [auth B]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
XAN (Subject of Investigation/LOI)
Query on XAN

Download Ideal Coordinates CCD File 
D [auth A], O [auth B]XANTHINE
C5 H4 N4 O2
LRFVTYWOQMYALW-UHFFFAOYSA-N
 Ligand Interaction
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], P [auth B], Q [auth B], R [auth B]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
J [auth A] , K [auth A] , L [auth A] , M [auth A] , S [auth B] , T [auth B] , U [auth B] , V [auth B] , 
J [auth A], K [auth A], L [auth A], M [auth A], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.472α = 90
b = 92.944β = 90
c = 40.298γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2021-04-12 
  • Released Date: 2021-06-30 
  • Deposition Author(s): Xu, X.C., Ren, A.M.

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

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2021-07-21
    Changes: Database references