6VUY | pdb_00006vuy

Crystal structure of Eis from Mycobacterium tuberculosis in complex with inhibitor SGT358

• PDB DOI: https://doi.org/10.2210/pdb6VUY/pdb

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


• Deposited: 2020-02-16 Released: 2020-06-03 
• Deposition Author(s): Punetha, A., Hou, C., Ngo, H.X., 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: 2.70 Å
• R-Value Free: 
  0.213 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Structure-Guided Optimization of Inhibitors of Acetyltransferase Eis fromMycobacterium tuberculosis.

Punetha, A., Ngo, H.X., Holbrook, S.Y.L., Green, K.D., Willby, M.J., Bonnett, S.A., Krieger, K., Dennis, E.K., Posey, J.E., Parish, T., Tsodikov, O.V., Garneau-Tsodikova, S.

(2020) ACS Chem Biol 15: 1581-1594

• PubMed: 32421305 
• DOI: https://doi.org/10.1021/acschembio.0c00184
• Primary Citation Related Structures: 
  6VUR, 6VUS, 6VUT, 6VUU, 6VUW, 6VUX, 6VUY, 6VUZ, 6VV0, 6VV1, 6VV2, 6VV3


• PubMed Abstract: 
  

  The enhanced intracellular survival (Eis) protein of Mycobacterium tuberculosis ( Mtb ) is a versatile acetyltransferase that multiacetylates aminoglycoside antibiotics abolishing their binding to the bacterial ribosome. When overexpressed as a result of promoter mutations, Eis causes drug resistance. In an attempt to overcome the Eis-mediated kanamycin resistance of Mtb , we designed and optimized structurally unique thieno[2,3- d ]pyrimidine Eis inhibitors toward effective kanamycin adjuvant combination therapy. We obtained 12 crystal structures of enzyme-inhibitor complexes, which guided our rational structure-based design of 72 thieno[2,3- d ]pyrimidine analogues divided into three families. We evaluated the potency of these inhibitors in vitro as well as their ability to restore the activity of kanamycin in a resistant strain of Mtb , in which Eis was upregulated. Furthermore, we evaluated the metabolic stability of 11 compounds in vitro . This study showcases how structural information can guide Eis inhibitor design.

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Organizational Affiliation: 
• Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States.
Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, United States.
TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington 98102, United States.
Center for Global Infectious Disease, Seattle Children's Research Institute, Seattle Children's Hospital, Seattle, Washington 98145, 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 47.18 kDa 
• Atom Count: 3,300 
• Modeled Residue Count: 396 
• Deposited Residue Count: 422 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetyltransferase Eis	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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RN4 (Subject of Investigation/LOI)	B [auth A]	(7S)-7-phenyl-2-{[3-(piperidin-1-yl)propyl]sulfanyl}-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4-amine C24 H30 N4 S2 IMHDFRLOCDDLHN-SFHVURJKSA-N
PEG	C [auth A], D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	E [auth A], F [auth A], G [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG	N [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	J [auth A], K [auth A], L [auth A], M [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.213 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175.047	α = 90
b = 175.047	β = 90
c = 123.557	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-06-03 
Deposition Author(s): Punetha, A., Hou, C., Ngo, H.X., 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: 2020-06-03
  Type: Initial release
  
• Version 1.1: 2020-07-01
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description