8F2L

Crystal structure of Mycobacterium tuberculosis Homoserine transacetylase in complex with L-Homoserine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structural and Functional Characterization of Mycobacterium tuberculosis Homoserine Transacetylase.

Sharma, S.Jayasinghe, Y.P.Mishra, N.K.Orimoloye, M.O.Wong, T.Y.Dalluge, J.J.Ronning, D.R.Aldrich, C.C.

(2023) ACS Infect Dis 9: 540-553

  • DOI: https://doi.org/10.1021/acsinfecdis.2c00541
  • Primary Citation of Related Structures:  
    7RYT, 8F2L

  • PubMed Abstract: 

    Mycobacterium tuberculosis ( Mtb ) lacking functional homoserine transacetylase (HTA) is compromised in methionine biosynthesis, protein synthesis, and in the activity of multiple essential S -adenosyl-l-methionine-dependent enzymes. Additionally, deficient mutants are further disarmed by the toxic accumulation of lysine due to a redirection of the metabolic flux toward the lysine biosynthetic pathway. Studies with deletion mutants and crystallographic studies of the apoenzyme have, respectively, validated Mtb HTA as an essential enzyme and revealed a ligandable binding site. Seeking a mechanistic characterization of this enzyme, we report crucial structural details and comprehensive functional characterization of Mtb HTA. Crystallographic and mass spectral observation of the acetylated HTA intermediate and initial velocity studies were consistent with a ping-pong kinetic mechanism. Wild-type HTA and its site-directed mutants were kinetically characterized with a panel of natural and alternative substrates to understand substrate specificity and identify critical residues for catalysis. Titration experiments using fluorescence quenching showed that both substrates─acetyl-CoA and l-homoserine─engage in a strong and weak binding interaction with HTA. Additionally, substrate inhibition by acetyl-CoA and product inhibition by CoA and O -acetyl-l-homoserine were proposed to form the basis of a feedback regulation mechanism. By furnishing key mechanistic and structural information, these studies provide a foundation for structure-based design efforts around this attractive Mtb target.


  • Organizational Affiliation

    Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Homoserine O-acetyltransferase368Mycobacterium tuberculosisMutation(s): 0 
Gene Names: metXAmetARv3341MTV016.41
EC: 2.3.1.31
UniProt
Find proteins for P9WJY9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WJY9 
Go to UniProtKB:  P9WJY9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WJY9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HSE (Subject of Investigation/LOI)
Query on HSE

Download Ideal Coordinates CCD File 
M [auth B]
N [auth A]
O [auth C]
P [auth D]
Q [auth F]
M [auth B],
N [auth A],
O [auth C],
P [auth D],
Q [auth F],
R [auth G],
S [auth H],
T [auth I],
U [auth J],
V [auth K],
W [auth L]
L-HOMOSERINE
C4 H9 N O3
UKAUYVFTDYCKQA-VKHMYHEASA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.735α = 90
b = 161.735β = 90
c = 249.235γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
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 StatesR21-AI151924

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-01
    Type: Initial release
  • Version 1.1: 2023-03-22
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection