6PUX

Homoserine transacetylase MetX from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural analysis of mycobacterial homoserine transacetylases central to methionine biosynthesis reveals druggable active site.

Chaton, C.T.Rodriguez, E.S.Reed, R.W.Li, J.Kenner, C.W.Korotkov, K.V.

(2019) Sci Rep 9: 20267-20267

  • DOI: 10.1038/s41598-019-56722-2
  • Primary Citation of Related Structures:  
    5W8O, 5W8P, 6PUX

  • PubMed Abstract: 
  • Mycobacterium tuberculosis is the cause of the world's most deadly infectious disease. Efforts are underway to target the methionine biosynthesis pathway, as it is not part of the host metabolism. The homoserine transacetylase MetX converts L-homoserine to O-acetyl-L-homoserine at the committed step of this pathway ...

    Mycobacterium tuberculosis is the cause of the world's most deadly infectious disease. Efforts are underway to target the methionine biosynthesis pathway, as it is not part of the host metabolism. The homoserine transacetylase MetX converts L-homoserine to O-acetyl-L-homoserine at the committed step of this pathway. In order to facilitate structure-based drug design, we determined the high-resolution crystal structures of three MetX proteins, including M. tuberculosis (MtMetX), Mycolicibacterium abscessus (MaMetX), and Mycolicibacterium hassiacum (MhMetX). A comparison of homoserine transacetylases from other bacterial and fungal species reveals a high degree of structural conservation amongst the enzymes. Utilizing homologous structures with bound cofactors, we analyzed the potential ligandability of MetX. The deep active-site tunnel surrounding the catalytic serine yielded many consensus clusters during mapping, suggesting that MtMetX is highly druggable.


    Organizational Affiliation

    Department of Molecular & Cellular Biochemistry and the Center for Structural Biology, University of Kentucky, Lexington, KY, 40536, USA. kkorotkov@uky.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Homoserine O-acetyltransferaseA, B366Mycobacterium tuberculosis H37RvMutation(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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A] , D [auth A] , E [auth A] , L [auth B] , M [auth B] , N [auth B] , O [auth B] , P [auth B] , 
C [auth A],  D [auth A],  E [auth A],  L [auth B],  M [auth B],  N [auth B],  O [auth B],  P [auth B],  Q [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
K [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], U [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A], G [auth A], H [auth A], R [auth B], S [auth B], T [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.46α = 90
b = 86.68β = 90
c = 208.77γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP20GM103486
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30GM110787

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Database references, Structure summary
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2020-01-15
    Changes: Database references