4ZNP

The structure of A pfI Riboswitch Bound to ZMP

  • Classification: RNA
  • Organism(s): synthetic construct

  • Deposited: 2015-05-05 Released: 2015-08-26 
  • Deposition Author(s): Ren, A., Patel, D.J., Rajashankar, R.K.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute; National Institutes of Health/National Institute of General Medical Sciences; NIH-ORIP HEI grant 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Global RNA Fold and Molecular Recognition for a pfl Riboswitch Bound to ZMP, a Master Regulator of One-Carbon Metabolism.

Ren, A.Rajashankar, K.R.Patel, D.J.

(2015) Structure 23: 1375-1381

  • DOI: 10.1016/j.str.2015.05.016

  • PubMed Abstract: 
  • ZTP, the pyrophosphorylated analog of ZMP (5-amino-4-imidazole carboxamide ribose-5'-monophosphate), was identified as an alarmone that senses 10-formyl-tetrahydroflate deficiency in bacteria. Recently, a pfl riboswitch was identified that selectivel ...

    ZTP, the pyrophosphorylated analog of ZMP (5-amino-4-imidazole carboxamide ribose-5'-monophosphate), was identified as an alarmone that senses 10-formyl-tetrahydroflate deficiency in bacteria. Recently, a pfl riboswitch was identified that selectively binds ZMP and regulates genes associated with purine biosynthesis and one-carbon metabolism. We report on the structure of the ZMP-bound Thermosinus carboxydivorans pfl riboswitch sensing domain, thereby defining the pseudoknot-based tertiary RNA fold, the binding-pocket architecture, and principles underlying ligand recognition specificity. Molecular recognition involves shape complementarity, with the ZMP 5-amino and carboxamide groups paired with the Watson-Crick edge of an invariant uracil, and the imidazole ring sandwiched between guanines, while the sugar hydroxyls form intermolecular hydrogen bond contacts. The burial of the ZMP base and ribose moieties, together with unanticipated coordination of the carboxamide by Mg(2+), contrasts with exposure of the 5'-phosphate to solvent. Our studies highlight the principles underlying RNA-based recognition of ZMP, a master regulator of one-carbon metabolism.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
pfI RiboswitchA,B73synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMZ
Query on AMZ

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

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.223 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 152.195α = 90.00
b = 152.195β = 90.00
c = 86.891γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHENIXrefinement
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesNIH U19 CA179564
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP41 GM103403
NIH-ORIP HEI grantUnited StatesS10 RR029205

Revision History 

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Derived calculations