1C41

CRYSTAL STRUCTURES OF A PENTAMERIC FUNGAL AND AN ICOSAHEDRAL PLANT LUMAZINE SYNTHASE REVEALS THE STRUCTURAL BASIS FOR DIFFERENCES IN ASSEMBLY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure analysis of a pentameric fungal and an icosahedral plant lumazine synthase reveals the structural basis for differences in assembly

Persson, K.Schneider, G.Jordan, D.B.Viitanen, P.V.Sandalova, T.

(1999) Protein Sci. 8: 2355-2365

  • DOI: 10.1110/ps.8.11.2355
  • Primary Citation of Related Structures:  1C2Y

  • PubMed Abstract: 
  • Lumazine synthase catalyzes the penultimate step in the synthesis of riboflavin in plants, fungi, and microorganisms. The enzyme displays two quaternary structures, the pentameric forms in yeast and fungi and the 60-meric icosahedral capsids in plant ...

    Lumazine synthase catalyzes the penultimate step in the synthesis of riboflavin in plants, fungi, and microorganisms. The enzyme displays two quaternary structures, the pentameric forms in yeast and fungi and the 60-meric icosahedral capsids in plants and bacteria. To elucidate the structural features that might be responsible for differences in assembly, we have determined the crystal structures of lumazine synthase, complexed with the inhibitor 5-nitroso-6-ribitylamino-2,4-pyrimidinedione, from spinach and the fungus Magnaporthe grisea to 3.3 and 3.1 A resolution, respectively. The overall structure of the subunit and the mode of inhibitor binding are very similar in these enzyme species. The core of the subunit consists of a four-stranded parallel beta-sheet sandwiched between two helices on one side and three helices on the other. The packing of the five subunits in the pentameric M. grisea lumazine synthase is very similar to the packing in the pentameric substructures in the icosahedral capsid of the plant enzyme. Two structural features can be correlated to the differences in assembly. In the plant enzyme, the N-terminal beta-strand interacts with the beta-sheet of the adjacent subunit, thus extending the sheet from four to five strands. In fungal lumazine synthase, an insertion of two residues after strand beta1 results in a completely different orientation of this part of the polypeptide chain and this conformational difference prevents proper packing of the subunits at the trimer interface in the icosahedron. In the spinach enzyme, the beta-hairpin connecting helices alpha4 and alpha5 participates in the packing at the trimer interface of the icosahedron. Another insertion of two residues at this position of the polypeptide chain in the fungal enzyme disrupts the hydrogen bonding in the hairpin, and the resulting change in conformation of this loop also interferes with proper intrasubunit contacts at the trimer interface.


    Organizational Affiliation

    Molecular Structural Biology, Medical Biochemistry and Biophysics, Doktorsringen 9, Karolinska Institutet, Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LUMAZINE SYNTHASE
A, B, C, D, E, F, G, H, I, J
200Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958)EC: 2.5.1.78
Find proteins for Q9UVT8 (Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958))
Go to UniProtKB:  Q9UVT8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LMZ
Query on LMZ

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
5-NITROSO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE
C9 H14 N4 O7
YMWIHKCBRFEJMH-RPDRRWSUSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.248 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 98.800α = 90.00
b = 124.700β = 90.00
c = 141.400γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-08-06
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2013-01-16
    Type: Structure summary