7A9G

Truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Mycobacterium tuberculosis with intermediate 2-acetyl-thiamine diphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.154 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

First crystal structures of 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Mycobacterium tuberculosis indicate a distinct mechanism of intermediate stabilization.

Gierse, R.M.Oerlemans, R.Reddem, E.R.Gawriljuk, V.O.Alhayek, A.Baitinger, D.Jakobi, H.Laber, B.Lange, G.Hirsch, A.K.H.Groves, M.R.

(2022) Sci Rep 12: 7221-7221

  • DOI: https://doi.org/10.1038/s41598-022-11205-9
  • Primary Citation of Related Structures:  
    7A9G, 7A9H

  • PubMed Abstract: 

    The development of drug resistance by Mycobacterium tuberculosis and other pathogenic bacteria emphasizes the need for new antibiotics. Unlike animals, most bacteria synthesize isoprenoid precursors through the MEP pathway. 1-Deoxy-D-xylulose 5-phosphate synthase (DXPS) catalyzes the first reaction of the MEP pathway and is an attractive target for the development of new antibiotics. We report here the successful use of a loop truncation to crystallize and solve the first DXPS structures of a pathogen, namely M. tuberculosis (MtDXPS). The main difference found to other DXPS structures is in the active site where a highly coordinated water was found, showing a new mechanism for the enamine-intermediate stabilization. Unlike other DXPS structures, a "fork-like" motif could be identified in the enamine structure, using a different residue for the interaction with the cofactor, potentially leading to a decrease in the stability of the intermediate. In addition, electron density suggesting a phosphate group could be found close to the active site, provides new evidence for the D-GAP binding site. These results provide the opportunity to improve or develop new inhibitors specific for MtDXPS through structure-based drug design.


  • Organizational Affiliation

    Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, 66123, Saarbrücken, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
1-deoxy-D-xylulose-5-phosphate synthase,1-deoxy-D-xylulose-5-phosphate synthaseA [auth AAA],
B [auth BBB]
666Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: dxsRv2682cMTCY05A6.03c
EC: 2.2.1.7
UniProt
Find proteins for P9WNS3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WNS3 
Go to UniProtKB:  P9WNS3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WNS3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HTL (Subject of Investigation/LOI)
Query on HTL

Download Ideal Coordinates CCD File 
C [auth AAA],
O [auth BBB]
2-ACETYL-THIAMINE DIPHOSPHATE
C14 H21 N4 O8 P2 S
GYRGKLZCJRVYRV-UHFFFAOYSA-O
PG4
Query on PG4

Download Ideal Coordinates CCD File 
M [auth AAA],
T [auth BBB]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
I [auth AAA]
K [auth AAA]
L [auth AAA]
R [auth BBB]
W [auth BBB]
I [auth AAA],
K [auth AAA],
L [auth AAA],
R [auth BBB],
W [auth BBB],
X [auth BBB]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
E [auth AAA]
F [auth AAA]
G [auth AAA]
H [auth AAA]
J [auth AAA]
E [auth AAA],
F [auth AAA],
G [auth AAA],
H [auth AAA],
J [auth AAA],
S [auth BBB],
U [auth BBB],
V [auth BBB],
Y [auth BBB]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
Q [auth BBB]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

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N [auth AAA]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth AAA],
P [auth BBB]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.154 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.865α = 90
b = 126.17β = 106.285
c = 79.031γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
pointlessdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific Research (NWO)Netherlands731.015.414

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-23
    Type: Initial release
  • Version 1.1: 2022-05-25
    Changes: Database references
  • Version 1.2: 2022-10-05
    Changes: Derived calculations
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description