1WPV

Crystal Structure of Activated Binary complex of HutP, an RNA binding anti-termination protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis of HutP-mediated anti-termination and roles of the Mg2+ ion and L-histidine ligand.

Kumarevel, T.Mizuno, H.Kumar, P.K.

(2005) Nature 434: 183-191

  • DOI: 10.1038/nature03355
  • Primary Citation of Related Structures:  
  • Also Cited By: 3BOY, 2GZT, 1WRQ, 1WRO, 1WRN

  • PubMed Abstract: 
  • HutP regulates the expression of the hut structural genes of Bacillus subtilis by an anti-termination mechanism and requires two components, Mg2+ ions and L-histidine. HutP recognizes three UAG triplet units, separated by four non-conserved nucleotid ...

    HutP regulates the expression of the hut structural genes of Bacillus subtilis by an anti-termination mechanism and requires two components, Mg2+ ions and L-histidine. HutP recognizes three UAG triplet units, separated by four non-conserved nucleotides on the terminator region. Here we report the 1.60-A resolution crystal structure of the quaternary complex (HutP-L-histidine-Mg2+-21-base single-stranded RNA). In the complex, the RNA adopts a novel triangular fold on the hexameric surface of HutP, without any base-pairing, and binds to the protein mostly by specific protein-base interactions. The structure explains how the HutP and RNA interactions are regulated critically by the l-histidine and Mg2+ ion through the structural rearrangement. To gain insights into these structural rearrangements, we solved two additional crystal structures (uncomplexed HutP and HutP-L-histidine-Mg2+) that revealed the intermediate structures of HutP (before forming an active structure) and the importance of the Mg2+ ion interactions in the complexes.


    Related Citations: 
    • Crystal Structure of Activated HutP; An RNA Binding Protein that Regulates Transcription of the hut Operon in Bacillus subtilis
      Kumarevel, T.S.,Fujimoto, Z.,Karthe, P.,Oda, M.,Mizuno, H.,Kumar, P.K.R.
      (2004) Structure 12: 1269
    • Identification of important chemical groups of the hut mRNA for HutP interactions that regulate the hut operon in Bacillus subtilis
      Kumarevel, T.S.,Gopinath, S.C.,Nishikawa, S.,Mizuno, H.,Kumar, P.K.R.
      (2004) Nucleic Acids Res. 32: 3904


    Organizational Affiliation

    Functional Nucleic Acids Group, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hut operon positive regulatory protein
A, B, C
147Bacillus subtilis (strain 168)Mutation(s): 1 
Gene Names: hutP
Find proteins for P10943 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P10943
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.233 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.790α = 90.00
b = 80.880β = 90.00
c = 75.170γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
HKL-2000data reduction
PHASERphasing
MOLREPphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-15
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Advisory, Refinement description