1NQU

Crystal Structure of Lumazine Synthase from Aquifex aeolicus in Complex with Inhibitor: 6,7-dioxo-5H-8-ribitylaminolumazine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A structure-based model of the reaction catalyzed by lumazine synthase from Aquifex aeolicus.

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

(2003) J.Mol.Biol. 328: 167-182

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 6,7-Dimethyl-8-ribityllumazine is the biosynthetic precursor of riboflavin, which, as a coenzyme, plays a vital role in the electron transfer process for energy production in all cellular organisms. The enzymes involved in lumazine biosynthesis have ...

    6,7-Dimethyl-8-ribityllumazine is the biosynthetic precursor of riboflavin, which, as a coenzyme, plays a vital role in the electron transfer process for energy production in all cellular organisms. The enzymes involved in lumazine biosynthesis have been studied in considerable detail. However, the conclusive mechanism of the reaction catalyzed by lumazine synthase has remained unclear. Here, we report four crystal structures of the enzyme from the hyperthermophilic bacterium Aquifex aeolicus in complex with different inhibitor compounds. The structures were refined at resolutions of 1.72 A, 1.85 A, 2.05 A and 2.2 A, respectively. The inhibitors have been designed in order to mimic the substrate, the putative reaction intermediates and the final product. Structural comparisons of the native enzyme and the inhibitor complexes as well as the kinetic data of single-site mutants of lumazine synthase from Bacillus subtilis showed that several highly conserved residues at the active site, namely Phe22, His88, Arg127, Lys135 and Glu138 are most likely involved in catalysis. A structural model of the catalytic process, which illustrates binding of substrates, enantiomer specificity, proton abstraction/donation, inorganic phosphate elimination, formation of the Schiff base and cyclization is proposed.


    Organizational Affiliation

    Karolinska Institute, NOVUM, Centre for Structural Biochemistry, S-14157 Huddinge, 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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D, E
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
RDL
Query on RDL

Download SDF File 
Download CCD File 
A, B, C, D, E
6,7-DIOXO-5H-8-RIBITYLAMINOLUMAZINE
C11 H14 N4 O8
MIBROOURCUHKMD-RPDRRWSUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.142 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 180.570α = 90.00
b = 180.570β = 90.00
c = 180.570γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-01-23
    Type: Initial release
  • Version 1.1: 2008-04-29
    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