4XW7

Crystal structure of the ZMP riboswitch at 2.50 angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Metal Ion-Mediated Nucleobase Recognition by the ZTP Riboswitch.

Trausch, J.J.Marcano-Velazquez, J.G.Matyjasik, M.M.Batey, R.T.

(2015) Chem.Biol. 22: 829-837

  • DOI: 10.1016/j.chembiol.2015.06.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The ZTP riboswitch is a widespread family of regulatory RNAs that upregulate de novo purine synthesis in response to increased intracellular levels of ZTP or ZMP. As an important intermediate in purine biosynthesis, ZMP also serves as a proxy for the ...

    The ZTP riboswitch is a widespread family of regulatory RNAs that upregulate de novo purine synthesis in response to increased intracellular levels of ZTP or ZMP. As an important intermediate in purine biosynthesis, ZMP also serves as a proxy for the concentration of N10-formyl-tetrahydrofolate, a key component of one-carbon metabolism. Here, we report the structure of the ZTP riboswitch bound to ZMP at a resolution of 1.80 Å. The RNA contains two subdomains brought together through a long-range pseudoknot further stabilized through helix-helix packing. ZMP is bound at the subdomain interface of the RNA through a set of interactions with the base, ribose sugar, and phosphate moieties of the ligand. Unique to nucleobase recognition by RNAs, the Z base is inner-sphere coordinated to a magnesium cation bound by two backbone phosphates. This interaction, along with steric hindrance by the backbone, imparts specificity over chemically similar compounds such as ATP/AMP.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO 80309-0596, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
pfl RNAA64Schaalia odontolytica
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMZ
Query on AMZ

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Download CCD File 
A
AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE
AICAR
C9 H15 N4 O8 P
NOTGFIUVDGNKRI-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
IRI
Query on IRI

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Download CCD File 
A
IRIDIUM HEXAMMINE ION
H18 Ir N6
CGMAOQLDNKCXGK-RIUFHJFFAL
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.249 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 40.160α = 90.00
b = 40.160β = 90.00
c = 234.910γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM073850

Revision History 

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Database references, Derived calculations, Refinement description