2VI5

LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO N-6-(ribitylamino)pyrimidine-2,4(1H,3H)-dione-5-yl-propionamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.260 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A New Series of N-[2,4-Dioxo-6-D-Ribitylamino-1,2, 3,4-Tetrahydropyrimidin-5-Yl]Oxalamic Acid Derivatives as Inhibitors of Lumazine Syntase and Riboflavin Synthase: Design, Synthesis, Biochemical Evaluation, Crystallography and Mechanistic Implications.

Zhang, Y.Illarionov, B.Morgunova, E.Bacher, A.Fischer, M.Ladenstein, R.Cushman, M.

(2008) J.Org.Chem. 73: 2715

  • DOI: 10.1021/jo702631a

  • PubMed Abstract: 
  • The penultimate step in the biosynthesis of riboflavin is catalyzed by lumazine synthase. Three metabolically stable analogues of the hypothetical intermediate proposed to arise after phosphate elimination in the lumazine synthase-catalyzed reaction ...

    The penultimate step in the biosynthesis of riboflavin is catalyzed by lumazine synthase. Three metabolically stable analogues of the hypothetical intermediate proposed to arise after phosphate elimination in the lumazine synthase-catalyzed reaction were synthesized and evaluated as lumazine synthase inhibitors. All three intermediate analogues were inhibitors of Mycobacterium tuberculosis lumazine synthase, Bacillus subtilis lumazine synthase, and Schizosaccharomyces pombe lumazine synthase, while one of them proved to be an extremely potent inhibitor of Escherichia coli riboflavin synthase with a Ki of 1.3 nM. The crystal structure of M. tuberculosis lumazine synthase in complex with one of the inhibitors provides a model of the conformation of the intermediate occurring immediately after phosphate elimination, supporting a mechanism in which phosphate elimination occurs before a conformational change of the Schiff base intermediate toward a cyclic structure.


    Organizational Affiliation

    The Purdue Cancer Center, Purdue University, West Lafayette, IN 47907, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE
A, B, C, D, E, F, G, H, I, J
160Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: ribH
EC: 2.5.1.78
Find proteins for P9WHE9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHE9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Y19
Query on Y19

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
1-deoxy-1-{[(5S)-2,6-dioxo-5-(propanoylamino)-1,2,5,6-tetrahydropyrimidin-4-yl]amino}-D-ribitol
C12 H20 N4 O7
NPNFNBTUUJYCDD-FAYXRDSDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Y19Ki: 110000 nM BINDINGMOAD
Y19Ki: 110000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.260 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 77.033α = 64.32
b = 76.692β = 64.41
c = 86.254γ = 63.60
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance