1VEA

Crystal Structure of HutP, an RNA binding antitermination protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 1269-1280

  • DOI: 10.1016/j.str.2004.05.005
  • Also Cited By: 3BOY, 2GZT, 1WRQ, 1WRO, 1WRN, 1WPV, 1WPU, 1WPT, 1WPS, 1WMQ

  • PubMed Abstract: 
  • HutP is an L-histidine-activated RNA binding protein that regulates the expression of the histidine utilization (hut) operon in Bacillus subtilis by binding to cis-acting regulatory sequences on the hut mRNA. The crystal structure of HutP complexed w ...

    HutP is an L-histidine-activated RNA binding protein that regulates the expression of the histidine utilization (hut) operon in Bacillus subtilis by binding to cis-acting regulatory sequences on the hut mRNA. The crystal structure of HutP complexed with an L-histidine analog showed a novel fold; there are four antiparallel beta strands in the central region of each monomer, with two alpha helices each on the front and back. Two HutP monomers form a dimer, and three dimers are arranged in crystallographic 3-fold symmetry to form a hexamer. A histidine analog was located in between the two monomers of HutP, with the imidazole group of L-histidine hydrogen bonded to Glu81. An activation mechanism is proposed based on the identification of key residues of HutP. The HutP binding region in hut mRNA was defined: it consists of three UAG trinucleotide motifs separated by four spacer nucleotides. Residues of HutP potentially important for RNA binding were identified.


    Related Citations: 
    • cis-acting regulatory sequences for antitermination in the transcript of the Bacillus subtilis hut operon and histidine-dependent binding of HutP to the transcript containing the regulatory sequences
      Oda, M.,Kobayashi, N.,Ito, A.,Kurusu, Y.,Taira, K.
      (2000) Mol.Microbiol. 35: 1244
    • Crystallization and preliminary X-ray diffraction studies of HutP protein: an RNA-binding protein that regulates the transcription of hut operon in Bacillus subtilis
      Kumarevel, T.S.,Fujimoto, Z.,Padmanabhan, B.,Oda, M.,Nishikawa, S.,Mizuno, H.,Kumar, P.K.R.
      (2002) J.Struct.Biol. 138: 237


    Organizational Affiliation

    Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 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
148Bacillus subtilis (strain 168)Mutation(s): 1 
Gene Names: hutP
Find proteins for P10943 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P10943
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HBN
Query on HBN

Download SDF File 
Download CCD File 
B
N-(2-NAPHTHYL)HISTIDINAMIDE
L-HISTIDINE BETA NAPHTHYLAMIDE
C16 H16 N4 O
DKDILZBBFKZMRO-OAHLLOKOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HBNKd: 30 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.230 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 95.410α = 90.00
b = 95.410β = 90.00
c = 95.410γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
CNSrefinement
CCP4data scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Data collection