7SCF

M. tb EgtD in complex with HD2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.219 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Inhibitors of Mycobacterium tuberculosis EgtD target both substrate binding sites to limit hercynine production.

Sudasinghe, T.D.Banco, M.T.Ronning, D.R.

(2021) Sci Rep 11: 22240-22240

  • DOI: https://doi.org/10.1038/s41598-021-01526-6
  • Primary Citation of Related Structures:  
    7SCF, 7SEW, 7SEX, 7SEY, 7SF4, 7SF5

  • PubMed Abstract: 

    Ergothioneine (EGT) is a low molecular weight histidine betaine essential in all domains of life but only synthesized by selected few organisms. Synthesis of EGT by Mycobacterium tuberculosis (M. tb) is critical for maintaining bioenergetic homeostasis and protecting the bacterium from alkylating agents, oxidative stress, and anti-tubercular drugs. EgtD, an S-adenosylmethionine-dependent methyltransferase (AdoMet), catalyzes the trimethylation of L-Histidine to initiate EGT biosynthesis and this reaction has been shown to be essential for EGT production in mycobacteria and for long-term infection of murine macrophages by M. tb. In this work, library screening and structure-guided strategies identified multiple classes of M. tb EgtD inhibitors that bind in various regions of the enzyme active site. X-ray crystal structures of EgtD-inhibitor complexes confirm that L-Histidine analogs bind solely to the L-Histidine binding site while drug-like inhibitors, such as TGX-221, and S-Glycyl-H-1152 span both the L-Histidine and AdoMet binding sites. These enzyme-inhibitor complexes provide detailed structural information of compound scaffolds useful for developing more potent inhibitors that could shorten Tuberculosis treatment regimens by weakening important bacterial defenses.


  • Organizational Affiliation

    Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histidine N-alpha-methyltransferase
A, B
321Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
EC: 2.1.1.44
UniProt
Find proteins for P9WN47 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WN47 
Go to UniProtKB:  P9WN47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WN47
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8YI (Subject of Investigation/LOI)
Query on 8YI

Download Ideal Coordinates CCD File 
C [auth A],
M [auth B]
(2S)-3-(1H-imidazol-5-yl)-2-(1H-pyrrol-1-yl)propanoic acid
C10 H11 N3 O2
XTGWWGRMXKSWQM-VIFPVBQESA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
L [auth A],
R [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
K [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.102α = 90
b = 71.57β = 90
c = 145.095γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-01
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description