1NQX

Crystal Structure of Lumazine Synthase from Aquifex aeolicus in Complex with Inhibitor: 3-(7-hydroxy-8-ribityllumazine-6-yl)propionic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

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

  • DOI: 10.1016/s0022-2836(03)00186-4
  • Structures With Same Primary Citation

  • 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 synthaseA, B, C, D, E154Aquifex aeolicusMutation(s): 0 
EC: 2.5.1.78
Find proteins for O66529 (Aquifex aeolicus (strain VF5))
Explore O66529 
Go to UniProtKB:  O66529
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RLP
Query on RLP

Download CCD File 
A, B, C, D, E
3-(7-HYDROXY-8-RIBITYLLUMAZINE-6-YL) PROPIONIC ACID
C14 H18 N4 O9
ZUXCIPRCLKZSHS-PJKMHFRUSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A, B, C, D, E
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.113α = 90
b = 180.113β = 90
c = 180.113γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-01-23
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2013-01-16
    Changes: Structure summary