1WRN

Metal Ion dependency of the antiterminator protein, HutP, for binding to the terminator region of hut mRNA- A structural basis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.254 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Characterization of the metal ion binding site in the anti-terminator protein, HutP, of Bacillus subtilis

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

(2005) Nucleic Acids Res. 33: 5494-5502

  • DOI: 10.1093/nar/gki868
  • Primary Citation of Related Structures:  
  • Also Cited By: 3BOY, 2GZT

  • PubMed Abstract: 
  • HutP is an RNA-binding protein that regulates the expression of the histidine utilization (hut) operon in Bacillus subtilis, by binding to cis-acting regulatory sequences on hut mRNA. It requires L-histidine and an Mg2+ ion for binding to the specifi ...

    HutP is an RNA-binding protein that regulates the expression of the histidine utilization (hut) operon in Bacillus subtilis, by binding to cis-acting regulatory sequences on hut mRNA. It requires L-histidine and an Mg2+ ion for binding to the specific sequence within the hut mRNA. In the present study, we show that several divalent cations can mediate the HutP-RNA interactions. The best divalent cations were Mn2+, Zn2+ and Cd2+, followed by Mg2+, Co2+ and Ni2+, while Cu2+, Yb2+ and Hg2+ were ineffective. In the HutP-RNA interactions, divalent cations cannot be replaced by monovalent cations, suggesting that a divalent metal ion is required for mediating the protein-RNA interactions. To clarify their importance, we have crystallized HutP in the presence of three different metal ions (Mg2+, Mn2+ and Ba2+), which revealed the importance of the metal ion binding site. Furthermore, these analyses clearly demonstrated how the metal ions cause the structural rearrangements that are required for the hut mRNA recognition.


    Related Citations: 
    • Structural basis of HutP-mediated anti-termination and roles of the Mg2+ ion and L-histidine ligand
      Kumarevel, T.,Mizuno, H.,Kumar, P.K.R.
      (2005) Nature 434: 183
    • Crystal Structure of Activated HutP; An RNA Binding Protein that Regulates Transcription of the hut Operon in Bacillus subtilis
      Kumarevel, T.,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.,Gopinath, S.C.B.,Nishikawa, S.,Mizuno, H.,Kumar, P.K.R.
      (2004) NUCLEIC ACIDS RES. 32: 3904


    Organizational Affiliation

    Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST) Central 6, 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
HIS
Query on HIS

Download SDF File 
Download CCD File 
A, B, C
HISTIDINE
C6 H10 N3 O2
HNDVDQJCIGZPNO-YFKPBYRVSA-O
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A, B, C
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.254 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.760α = 90.00
b = 81.400β = 90.00
c = 76.040γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CCP4data scaling
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-30
    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