4OKQ

Crystal structure of the single-stranded RNA binding protein HutP from Geobacillus thermodenitrificans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the single-stranded RNA binding protein HutP from Geobacillus thermodenitrificans

Thiruselvam, V.Sivaraman, P.Kumarevel, T.Ponnuswamy, M.N.

(2014) Biochem.Biophys.Res.Commun. 446: 945-951

  • DOI: 10.1016/j.bbrc.2014.03.036
  • Primary Citation of Related Structures:  4OK9

  • PubMed Abstract: 
  • RNA binding proteins control gene expression by the attenuation/antitermination mechanism. HutP is an RNA binding antitermination protein. It regulates the expression of hut operon when it binds with RNA by modulating the secondary structure of singl ...

    RNA binding proteins control gene expression by the attenuation/antitermination mechanism. HutP is an RNA binding antitermination protein. It regulates the expression of hut operon when it binds with RNA by modulating the secondary structure of single-stranded hut mRNA. HutP necessitates the presence of l-histidine and divalent metal ion to bind with RNA. Herein, we report the crystal structures of ternary complex (HutP-l-histidine-Mg(2+)) and EDTA (0.5 M) treated ternary complex (HutP-l-histidine-Mg(2+)), solved at 1.9 Å and 2.5 Å resolutions, respectively, from Geobacillus thermodenitrificans. The addition of 0.5 M EDTA does not affect the overall metal-ion mediated ternary complex structure and however, the metal ions at the non-specific binding sites are chelated, as evidenced from the results of structural features.


    Organizational Affiliation

    Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hut operon positive regulatory protein
A, B
149Geobacillus thermodenitrificans (strain NG80-2)Gene Names: hutP
Find proteins for A4IK89 (Geobacillus thermodenitrificans (strain NG80-2))
Go to UniProtKB:  A4IK89
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
HIS
Query on HIS

Download SDF File 
Download CCD File 
A, B
HISTIDINE
C6 H10 N3 O2
HNDVDQJCIGZPNO-YFKPBYRVSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.174 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 91.778α = 90.00
b = 91.778β = 90.00
c = 76.744γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data collection
REFMACrefinement
SCALAdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2014-12-17
    Type: Database references