6FBA | pdb_00006fba

Crystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum with bound inhibitor 2,3-naphthalenediol

• PDB DOI: https://doi.org/10.2210/pdb6FBA/pdb

• Classification: TRANSFERASE
• Organism(s): Plasmodium falciparum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-12-18 Released: 2018-02-21 
• Deposition Author(s): Lunev, S., Bosch, S.S., Batista, F.A., Wang, C., Wrenger, C., Groves, M.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.225 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.184 (Depositor) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Identification of a non-competitive inhibitor of Plasmodium falciparum aspartate transcarbamoylase.

Lunev, S., Bosch, S.S., Batista, F.A., Wang, C., Li, J., Linzke, M., Kruithof, P., Chamoun, G., Domling, A.S.S., Wrenger, C., Groves, M.R.

(2018) Biochem Biophys Res Commun 497: 835-842

• PubMed: 29476738 
• DOI: https://doi.org/10.1016/j.bbrc.2018.02.112
• Primary Citation Related Structures: 
  6FBA


• PubMed Abstract: 
  

  Aspartate transcarbamoylase catalyzes the second step of de-novo pyrimidine biosynthesis. As malarial parasites lack pyrimidine salvage machinery and rely on de-novo production for growth and proliferation, this pathway is a target for drug discovery. Previously, an apo crystal structure of aspartate transcarbamoylase from Plasmodium falciparum (PfATC) in its T-state has been reported. Here we present crystal structures of PfATC in the liganded R-state as well as in complex with the novel inhibitor, 2,3-napthalenediol, identified by high-throughput screening. Our data shows that 2,3-napthalediol binds in close proximity to the active site, implying an allosteric mechanism of inhibition. Furthermore, we report biophysical characterization of 2,3-napthalenediol. These data provide a promising starting point for structure based drug design targeting PfATC and malarial de-novo pyrimidine biosynthesis.

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Organizational Affiliation: 
• Faculty of Science and Engineering, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713AV, The Netherlands.
Unit for Drug Discovery, Department of Parasitology, Institute of Biomedica Sciences, University of São Paulo, Avenida Professor Lineu Prestes 1374, Sao Paulo, SP, 05508-000, Brazil.
Unit for Drug Discovery, Department of Parasitology, Institute of Biomedica Sciences, University of São Paulo, Avenida Professor Lineu Prestes 1374, Sao Paulo, SP, 05508-000, Brazil. Electronic address: [e-mail].
Faculty of Science and Engineering, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713AV, The Netherlands. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 122.7 kDa 
• Atom Count: 8,085 
• Modeled Residue Count: 966 
• Deposited Residue Count: 1,047 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate transcarbamoylase	A, B	349	Plasmodium falciparum	Mutation(s): 0  Gene Names: ATCase EC: 2.1.3.2
UniProt
Find proteins for O15804 (Plasmodium falciparum) Explore O15804  Go to UniProtKB:  O15804

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate transcarbamoylase	C	349	Plasmodium falciparum	Mutation(s): 0  Gene Names: ATCase EC: 2.1.3.2
UniProt
Find proteins for O15804 (Plasmodium falciparum) Explore O15804  Go to UniProtKB:  O15804

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D48 (Subject of Investigation/LOI)	E [auth A], L [auth B], O [auth C]	naphthalene-2,3-diol C10 H8 O2 JRNGUTKWMSBIBF-UHFFFAOYSA-N
PEG	N [auth B], Q [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
MLI	G [auth A], H [auth A], R [auth C]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
SO4	D [auth A], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth A], S [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	F [auth A], M [auth B], P [auth C]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NA	J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	C	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.225 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.184 (Depositor) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.757	α = 90
b = 86.757	β = 90
c = 138.151	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
DIMPLE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-21 
Deposition Author(s): Lunev, S., Bosch, S.S., Batista, F.A., Wang, C., Wrenger, C., Groves, M.R.

Revision History  

• Version 1.0: 2018-02-21
  Type: Initial release
  
• Version 1.1: 2018-03-07
  Changes: Database references
• Version 1.2: 2018-03-14
  Changes: Database references
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary