Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.49 kDa 
• Atom Count: 3358 
• Modelled Residue Count: 412 
• Deposited Residue Count: 468 
• Unique protein chains: 1

4F4Q

Crystal structure of M. smegmatis DprE1 in complex with FAD and covalently bound BTZ043

• DOI: 10.2210/pdb4F4Q/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-11 Released: 2012-09-05 
• Deposition Author(s): Neres, J., Pojer, F., Molteni, E., Chiarelli, L., Riccardi, G., Mattevi, A., Cole, S.T., Binda, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 0.240 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Literature

Structural Basis for Benzothiazinone-Mediated Killing of Mycobacterium tuberculosis.

Neres, J., Pojer, F., Molteni, E., Chiarelli, L.R., Dhar, N., Boy-Rottger, S., Buroni, S., Fullam, E., Degiacomi, G., Lucarelli, A.P., Read, R.J., Zanoni, G., Edmondson, D.E., De Rossi, E., Pasca, M.R., McKinney, J.D., Dyson, P.J., Riccardi, G., Mattevi, A., Cole, S.T., Binda, C.

(2012) Sci Transl Med 4: 150ra121-150ra121

• PubMed: 22956199 
• DOI: 10.1126/scitranslmed.3004395
• Primary Citation of Related Structures:  
  4AUT, 4F4Q


• PubMed Abstract: 
  

The benzothiazinone BTZ043 is a tuberculosis drug candidate with nanomolar whole-cell activity. BTZ043 targets the DprE1 catalytic component of the essential enzyme decaprenylphosphoryl-β-D-ribofuranose-2'-epimerase, thus blocking biosynthesis of arabinans, vital components of mycobacterial cell walls. Crystal structures of DprE1, in its native form and in a complex with BTZ043, reveal formation of a semimercaptal adduct between the drug and an active-site cysteine, as well as contacts to a neighboring catalytic lysine residue. Kinetic studies confirm that BTZ043 is a mechanism-based, covalent inhibitor. This explains the exquisite potency of BTZ043, which, when fluorescently labeled, localizes DprE1 at the poles of growing bacteria. Menaquinone can reoxidize the flavin adenine dinucleotide cofactor in DprE1 and may be the natural electron acceptor for this reaction in the mycobacterium. Our structural and kinetic analysis provides both insight into a critical epimerization reaction and a platform for structure-based design of improved inhibitors.

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Organizational Affiliation: 

Global Health Institute, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DprE1	A	468	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEG_6382, dprE1, MSMEI_6214, LJ00_31545 EC: 1.1.98.3
UniProt
Find proteins for A0R607 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R607  Go to UniProtKB:  A0R607

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
0SK	B [auth A]	8-(hydroxyamino)-2-[(2S)-2-methyl-1,4-dioxa-8-azaspiro[4.5]dec-8-yl]-6-(trifluoromethyl)-4H-1,3-benzothiazin-4-one C17 H18 F3 N3 O4 S WTTODOLGMIMGNK-VIFPVBQESA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 0.240 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.924	α = 90
b = 64.309	β = 90
c = 202.841	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-05-11 
• Released Date: 2012-09-05 
Deposition Author(s): Neres, J., Pojer, F., Molteni, E., Chiarelli, L., Riccardi, G., Mattevi, A., Cole, S.T., Binda, C.

Revision History  

• Version 1.0: 2012-09-05
  Type: Initial release
  
• Version 1.1: 2012-09-12
  Changes: Database references
• Version 1.2: 2012-09-19
  Changes: Database references
• Version 1.3: 2017-11-15
  Changes: Refinement description