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CRYSTAL STRUCTURE ANALYSIS OF LUMAZINE SYNTHASE FROM AQUIFEX AEOLICUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

X-ray structure analysis and crystallographic refinement of lumazine synthase from the hyperthermophile Aquifex aeolicus at 1.6 A resolution: determinants of thermostability revealed from structural comparisons.

Zhang, X.Meining, W.Fischer, M.Bacher, A.Ladenstein, R.

(2001) J.Mol.Biol. 306: 1099-1114

  • DOI: 10.1006/jmbi.2000.4435

  • PubMed Abstract: 
  • An open reading frame optimized for expression of 6,7-dimethyl-8-ribityl-lumazine synthase of the hyperthermophilic bacterium Aquifex aeolicus in Escherichia coli was synthesized and expressed in a recombinant E. coli strain to a level of around 15 % ...

    An open reading frame optimized for expression of 6,7-dimethyl-8-ribityl-lumazine synthase of the hyperthermophilic bacterium Aquifex aeolicus in Escherichia coli was synthesized and expressed in a recombinant E. coli strain to a level of around 15 %. The recombinant protein was purified by heat-treatment and gel-filtration. The protein was crystallized in the cubic space group I23 with the cell dimensions a = b = c = 180.8 A, and diffraction data were collected to 1.6 A resolution. The structure was solved by molecular replacement using lumazine synthase from Bacillus subtilis as search model. The structure of the A. aeolicus enzyme was refined to a resolution of 1.6 A. The spherical protein consists of 60 identical subunits with strict icosahedral 532 symmetry. The subunit fold is closely related to that of the B. subtilis enzyme (rmsd 0.80 A). The extremely thermostable lumazine synthase from A. aeolicus has a melting temperature of 119.9 degrees C. Compared to other icosahedral and pentameric lumazine synthases, the A. aeolicus enzyme has the largest accessible surface presented by charged residues and the smallest surface presented by hydrophobic residues. It also has the largest number of ion-pairs per subunit. Two ion-pair networks involving two, respectively three, stacking arginine residues assume a distinct role in linking adjacent subunits. The findings indicate the influence of the optimization of hydrophobic and ionic contacts in gaining thermostability.


    Organizational Affiliation

    Södertörns Högskola, Huddinge, S-14104, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE
A, B, C, D, E
154Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: ribH
EC: 2.5.1.78
Find proteins for O66529 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O66529
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.216 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 180.820α = 90.00
b = 180.820β = 90.00
c = 180.820γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
AUTOMARdata reduction
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-12-18
    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: 2013-01-16
    Type: Structure summary
  • Version 1.4: 2017-10-04
    Type: Refinement description
  • Version 1.5: 2017-10-11
    Type: Data collection