4H4L

Crystal Structure of ternary complex of HutP(HutP-L-His-Zn)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Alternative binding modes of l-histidine guided by metal ions for the activation of the antiterminator protein HutP of Bacillus subtilis.

Dhakshnamoorthy, B.Mizuno, H.Kumar, P.K.R.

(2013) J.Struct.Biol. 183: 512-518

  • DOI: 10.1016/j.jsb.2013.05.019

  • PubMed Abstract: 
  • Anti-terminator proteins control gene expression by recognizing control signals within cognate transcripts and then preventing transcription termination. HutP is such a regulatory protein that regulates the expression of the histidine utilization (hu ...

    Anti-terminator proteins control gene expression by recognizing control signals within cognate transcripts and then preventing transcription termination. HutP is such a regulatory protein that regulates the expression of the histidine utilization (hut) operon in Bacillus subtilis by binding to cis-acting regulatory sequences in hut mRNAs. During the anti-termination process, l-histidine and a divalent ion are required for hutP to bind to the specific sequence within the hut mRNA. Our previous crystal structure of the HutP-l-histidine-Mg(2+)-RNA ternary complex demonstrated that the l-histidine ligand and Mg(2+) bind together such that the backbone nitrogen and carboxyl oxygen of l-histidine coordinate with Mg(2+). In addition to the Mg(2+), other divalent ions are also known to efficiently support the l-histidine-dependent anti-termination of the hut operon, and the best divalent ion is Zn(2+). In this study, we determined the crystal structure of the HutP-l-histidine-Zn(2+) complex and found that the orientation of l-histidine coordinated to Zn(2+) is reversed relative to that of l-histidine coordinated to Mg(2+), i.e., the imidazole side chain nitrogen of l-histidine coordinates to Zn(2+). This alternative binding mode of the l-histidine ligand to a divalent ion provides further insight into the mechanisms responsible for the activation of RNA binding during the hut anti-termination process.


    Organizational Affiliation

    RNA Processing Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Central-6, 1-1-1 Higashi, Tsukuba 305-8566, Japan. Electronic address: pkr-kumar@aist.go.jp.,RNA Processing Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Central-6, 1-1-1 Higashi, Tsukuba 305-8566, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hut operon positive regulatory protein
A, B, C, D, E, F, G, H, I, J, K, L
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
HIS
Query on HIS

Download SDF File 
Download CCD File 
A, B, C, D, F, G, I, J, L
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: 0.298 
  • R-Value Work: 0.219 
  • Space Group: P 3
Unit Cell:
Length (Å)Angle (°)
a = 129.530α = 90.00
b = 129.530β = 90.00
c = 76.670γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
ADSCdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-04
    Type: Initial release
  • Version 1.1: 2014-09-10
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Advisory, Refinement description