1EJB

LUMAZINE SYNTHASE FROM SACCHAROMYCES CEREVISIAE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The atomic structure of pentameric lumazine synthase from Saccharomyces cerevisiae at 1.85 A resolution reveals the binding mode of a phosphonate intermediate analogue.

Meining, W.Mortl, S.Fischer, M.Cushman, M.Bacher, A.Ladenstein, R.

(2000) J.Mol.Biol. 299: 181-197

  • DOI: 10.1006/jmbi.2000.3742

  • PubMed Abstract: 
  • Lumazine synthase of Saccharomyces cerevisiae is a homopentamer with a molecular weight of 90 kDa. Crystals of the recombinant enzyme with a size of up to 1.6 mm were obtained. The space group is P4(1)2(1)2 with lattice dimensions 82.9 A x 82.9 A x 3 ...

    Lumazine synthase of Saccharomyces cerevisiae is a homopentamer with a molecular weight of 90 kDa. Crystals of the recombinant enzyme with a size of up to 1.6 mm were obtained. The space group is P4(1)2(1)2 with lattice dimensions 82.9 A x 82.9 A x 300.2 A. X-ray diffraction data collected under cryogenic conditions were complete to 1.85 A resolution. The structure of the enzyme in complex with the intermediate analogue, 5-(6-D-ribitylamino-2,4-dihydroxypyrimidine-5-yl)-1-pentyl-p hosphonic acid was solved via molecular replacement using the structure of the Bacillus subtilis enzyme as search model and was refined to a final R-factor of 19.8% (Rfree: 22.5%). The conformation of the active site ligand of the enzyme mimicks that of the Schiff base intermediate of the enzyme-catalyzed reaction. The data enable the reconstruction of the reactant topology during the early steps of the catalytic reaction. Structural determinants, which are likely to be responsible for the inability of the S. cerevisiae enzyme to form icosahedral capsids, will be discussed.


    Related Citations: 
    • Design and Biological Evaluation of Homologous Phosphonic Acids and Sulfonic Acids as Inhibitors of Lumazine Synthase
      Cushman, M.,Mihalic, J.T.,Kis, K.,Bacher, A.
      (1999) J.Org.Chem. 64: 3838


    Organizational Affiliation

    Södertörns Högskola, Huddinge, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LUMAZINE SYNTHASE
A, B, C, D, E
168Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RIB4
EC: 2.5.1.78
Find proteins for P50861 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P50861
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
INJ
Query on INJ

Download SDF File 
Download CCD File 
A, B, C, D, E
5-(6-D-RIBITYLAMINO-2,4-DIHYDROXYPYRIMIDIN-5-YL)-1-PENTYL-PHOSPHONIC ACID
C14 H26 N3 O9 P
BMATWAHJJFXMFA-AXFHLTTASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.197 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 82.893α = 90.00
b = 82.893β = 90.00
c = 298.842γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
AMoREphasing
MAR345data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-03-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2013-01-16
    Type: Structure summary
  • Version 1.4: 2017-10-04
    Type: Advisory, Refinement description