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: 2.30 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.262 

wwPDB Validation   3D Report Full Report


This is version 1.2 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
  • Primary Citation of Related Structures:  
    2VI5

  • 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 were synthesized and evaluated as lumazine synthase inhibitors ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J
160Mycobacterium tuberculosisMutation(s): 0 
EC: 2.5.1.9 (PDB Primary Data), 2.5.1.78 (UniProt)
UniProt
Find proteins for P9WHE9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHE9 
Go to UniProtKB:  P9WHE9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Y19
Query on Y19

Download Ideal Coordinates CCD File 
AA [auth E] , EA [auth F] , HA [auth G] , K [auth A] , KA [auth H] , NA [auth I] , O [auth B] , QA [auth J] , 
AA [auth E],  EA [auth F],  HA [auth G],  K [auth A],  KA [auth H],  NA [auth I],  O [auth B],  QA [auth J],  S [auth C],  W [auth D]
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
PO4
Query on PO4

Download Ideal Coordinates CCD File 
DA [auth E] , GA [auth F] , JA [auth G] , MA [auth H] , N [auth A] , PA [auth I] , R [auth B] , SA [auth J] , 
DA [auth E],  GA [auth F],  JA [auth G],  MA [auth H],  N [auth A],  PA [auth I],  R [auth B],  SA [auth J],  V [auth C],  Z [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
BA [auth E] , CA [auth E] , FA [auth F] , IA [auth G] , L [auth A] , LA [auth H] , M [auth A] , OA [auth I] , 
BA [auth E],  CA [auth E],  FA [auth F],  IA [auth G],  L [auth A],  LA [auth H],  M [auth A],  OA [auth I],  P [auth B],  Q [auth B],  RA [auth J],  T [auth C],  U [auth C],  X [auth D],  Y [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Y19Ki:  110000   nM  Binding MOAD
Y19Ki :  110000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.262 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.033α = 64.32
b = 76.692β = 64.41
c = 86.254γ = 63.6
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2019-04-10
    Changes: Data collection, Other, Source and taxonomy