5L8Z

Structure of thermostable DNA-binding HU protein from micoplasma Spiroplasma melliferum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of the high thermal stability of the histone-like HU protein from the mollicute Spiroplasma melliferum KC3.

Boyko, K.M.Rakitina, T.V.Korzhenevskiy, D.A.Vlaskina, A.V.Agapova, Y.K.Kamashev, D.E.Kleymenov, S.Y.Popov, V.O.

(2016) Sci Rep 6: 36366-36366

  • DOI: 10.1038/srep36366

  • PubMed Abstract: 
  • The three-dimensional structure of the histone-like HU protein from the mycoplasma Spiroplasma melliferum KC3 (HUSpm) was determined at 1.4 Å resolution, and the thermal stability of the protein was evaluated by differential scanning calorimetry. A d ...

    The three-dimensional structure of the histone-like HU protein from the mycoplasma Spiroplasma melliferum KC3 (HUSpm) was determined at 1.4 Å resolution, and the thermal stability of the protein was evaluated by differential scanning calorimetry. A detailed analysis revealed that the three-dimensional structure of the HUSpm dimer is similar to that of its bacterial homologues but is characterized by stronger hydrophobic interactions at the dimer interface. This HUSpm dimer interface lacks salt bridges but is stabilized by a larger number of hydrogen bonds. According to the DSC data, HUSpm has a high denaturation temperature, comparable to that of HU proteins from thermophilic bacteria. To elucidate the structural basis of HUSpm thermal stability, we identified amino acid residues potentially responsible for this property and modified them by site-directed mutagenesis. A comparative analysis of the melting curves of mutant and wild-type HUSpm revealed the motifs that play a key role in protein thermal stability: non-conserved phenylalanine residues in the hydrophobic core, an additional hydrophobic loop at the N-terminal region of the protein, the absence of the internal cavity present at the dimer interface of some HU proteins, and the presence of additional hydrogen bonds between the monomers that are missing in homologous proteins.


    Organizational Affiliation

    Kurchatov Complex of NBICS-Technologies, National Research Center "Kurchatov Institute", Akad. Kurchatova pl., 1, Moscow, 123182, Russian Federation.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-binding protein
A
96Spiroplasma melliferum KC3Mutation(s): 0 
Find proteins for A0A037USE5 (Spiroplasma melliferum KC3)
Go to UniProtKB:  A0A037USE5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 57.000α = 90.00
b = 39.010β = 108.36
c = 38.780γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
BALBESphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation15-14-00063

Revision History 

  • Version 1.0: 2016-06-22
    Type: Initial release
  • Version 1.1: 2017-04-12
    Type: Database references