2C9B

Lumazine Synthase from Mycobacterium tuberculosus Bound to 3-(1,3,7- TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Thermodynamic Insights Into the Binding Mode of Five Novel Inhibitors of Lumazine Synthase from Mycobacterium Tuberculosis.

Morgunova, E.Illarionov, B.Sambaiah, T.Haase, I.Bacher, A.Cushman, M.Fischer, M.Ladenstein, R.

(2006) FEBS J. 273: 4790-4804

  • DOI: 10.1111/j.1742-4658.2006.05481.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Recently published genomic investigations of the human pathogen Mycobacterium tuberculosis have revealed that genes coding the proteins involved in riboflavin biosynthesis are essential for the growth of the organism. Because the enzymes involved in ...

    Recently published genomic investigations of the human pathogen Mycobacterium tuberculosis have revealed that genes coding the proteins involved in riboflavin biosynthesis are essential for the growth of the organism. Because the enzymes involved in cofactor biosynthesis pathways are not present in humans, they appear to be promising candidates for the development of therapeutic drugs. The substituted purinetrione compounds have demonstrated high affinity and specificity to lumazine synthase, which catalyzes the penultimate step of riboflavin biosynthesis in bacteria and plants. The structure of M. tuberculosis lumazine synthase in complex with five different inhibitor compounds is presented, together with studies of the binding reactions by isothermal titration calorimetry. The inhibitors showed the association constants in the micromolar range. The analysis of the structures demonstrated the specific features of the binding of different inhibitors. The comparison of the structures and binding modes of five different inhibitors allows us to propose the ribitylpurinetrione compounds with C4-C5 alkylphosphate chains as most promising leads for further development of therapeutic drugs against M. tuberculosis.


    Organizational Affiliation

    Karolinska Institutet, NOVUM, Centre for Structural Biochemistry, Huddinge, Sweden. katja.morgunova@biosci.ki.se




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 4 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
MPD
Query on MPD

Download SDF File 
Download CCD File 
C, J
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
PUG
Query on PUG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J
3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL)
C10 H14 N4 O7
XIBHHWBJHOTHGZ-KODRXGBYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PUGKd: 2880 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.250 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 78.045α = 64.39
b = 78.364β = 64.69
c = 88.843γ = 65.03
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
MOLREPphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2018-06-20
    Type: Data collection, Database references, Structure summary