5TVJ | pdb_00005tvj

Crystal structure of acetyltransferase Eis from Mycobacterium tuberculosis in complex with CoA and inhibitor 2k*: 1-(4-fluorophenyl)-2-[2-(4-methylphenyl)-2-oxoethyl]pyrrolo[1,2-a]pyrazin-2-ium

• PDB DOI: https://doi.org/10.2210/pdb5TVJ/pdb

• Classification: TRANSFERASE/TRANSFERASE Inhibitor
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-11-09 Released: 2017-03-01 
• Deposition Author(s): Gajadeera, C.S., Garzan, A., Hou, C., Garneau-Tsodikova, S., Tsodikov, O.V.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.224 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Combating Enhanced Intracellular Survival (Eis)-Mediated Kanamycin Resistance of Mycobacterium tuberculosis by Novel Pyrrolo[1,5-a]pyrazine-Based Eis Inhibitors.

Garzan, A., Willby, M.J., Ngo, H.X., Gajadeera, C.S., Green, K.D., Holbrook, S.Y., Hou, C., Posey, J.E., Tsodikov, O.V., Garneau-Tsodikova, S.

(2017) ACS Infect Dis 3: 302-309

• PubMed: 28192916 
• DOI: https://doi.org/10.1021/acsinfecdis.6b00193
• Primary Citation Related Structures: 
  5TVJ


• PubMed Abstract: 
  

  Tuberculosis (TB) remains one of the leading causes of mortality worldwide. Hence, the identification of highly effective antitubercular drugs with novel modes of action is crucial. In this paper, we report the discovery and development of pyrrolo[1,5-a]pyrazine-based analogues as highly potent inhibitors of the Mycobacterium tuberculosis (Mtb) acetyltransferase enhanced intracellular survival (Eis), whose up-regulation causes clinically observed resistance to the aminoglycoside (AG) antibiotic kanamycin A (KAN). We performed a structure-activity relationship (SAR) study to optimize these compounds as potent Eis inhibitors both against purified enzyme and in mycobacterial cells. A crystal structure of Eis in complex with one of the most potent inhibitors reveals that the compound is bound to Eis in the AG binding pocket, serving as the structural basis for the SAR. These Eis inhibitors have no observed cytotoxicity to mammalian cells and are promising leads for the development of innovative AG adjuvant therapies against drug-resistant TB.

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Organizational Affiliation: 
• Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States.
Laboratory Branch, Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention , Atlanta, Georgia 30329, United States.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 47.24 kDa 
• Atom Count: 3,217 
• Modeled Residue Count: 396 
• Deposited Residue Count: 422 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enhanced intracellular survival protein	A	422	Mycobacterium tuberculosis H37Rv	Mutation(s): 1  Gene Names: eis, Rv2416c, MTCY253.04 EC: 2.3.1
UniProt
Find proteins for P9WFK7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFK7  Go to UniProtKB:  P9WFK7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	B [auth A]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
7LF	C [auth A]	1-(4-fluorophenyl)-2-[2-(4-methylphenyl)-2-oxoethyl]pyrrolo[1,2-a]pyrazin-2-ium C22 H18 F N2 O ZBYPLLMQZPJMEM-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.224 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175.106	α = 90
b = 175.106	β = 90
c = 122.94	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-03-01 
Deposition Author(s): Gajadeera, C.S., Garzan, A., Hou, C., Garneau-Tsodikova, S., Tsodikov, O.V.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI090048

Revision History  

• Version 1.0: 2017-03-01
  Type: Initial release
  
• Version 1.1: 2017-04-26
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description