4ZCP | pdb_00004zcp

Crystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase in complex with CMP

• PDB DOI: https://doi.org/10.2210/pdb4ZCP/pdb

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


• Deposited: 2015-04-16 Released: 2016-09-14 
• Deposition Author(s): Guca, E., Hoh, F., Guichou, J.-F., Cerdan, R.
• Funding Organization(s): EU-ITN Marie Curie Paramet

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.247 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Structural determinants of the catalytic mechanism of Plasmodium CCT, a key enzyme of malaria lipid biosynthesis.

Guca, E., Nagy, G.N., Hajdu, F., Marton, L., Izrael, R., Hoh, F., Yang, Y., Vial, H., Vertessy, B.G., Guichou, J.F., Cerdan, R.

(2018) Sci Rep 8: 11215-11215

• PubMed: 30046154 
• DOI: https://doi.org/10.1038/s41598-018-29500-9
• Primary Citation Related Structures: 
  4ZCP, 4ZCQ, 4ZCR, 4ZCS, 4ZCT


• PubMed Abstract: 
  

  The development of the malaria parasite, Plasmodium falciparum, in the human erythrocyte, relies on phospholipid metabolism to fulfil the massive need for membrane biogenesis. Phosphatidylcholine (PC) is the most abundant phospholipid in Plasmodium membranes. PC biosynthesis is mainly ensured by the de novo Kennedy pathway that is considered as an antimalarial drug target. The CTP:phosphocholine cytidylyltransferase (CCT) catalyses the rate-limiting step of the Kennedy pathway. Here we report a series of structural snapshots of the PfCCT catalytic domain in its free, substrate- and product-complexed states that demonstrate the conformational changes during the catalytic mechanism. Structural data show the ligand-dependent conformational variations of a flexible lysine. Combined kinetic and ligand-binding analyses confirm the catalytic roles of this lysine and of two threonine residues of the helix αE. Finally, we assessed the variations in active site residues between Plasmodium and mammalian CCT which could be exploited for future antimalarial drug design.

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Organizational Affiliation: 
• Dynamique des Interactions Membranaires Normales et Pathologiques, UMR 5235, CNRS, Université de Montpellier, Montpellier, France.
Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Carrer de Baldiri Reixac 10, 08028, Barcelona, Spain.
Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest, Hungary.
Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.
Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford, OX37BN, United Kingdom.
Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged, Hungary.
CNRS UMR5048, Centre de Biochimie Structurale, Université de Montpellier, Montpellier, France.
INSERM U1054, Montpellier, France.
Dynamique des Interactions Membranaires Normales et Pathologiques, UMR 5235, CNRS, Université de Montpellier, Montpellier, France. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.13 kDa 
• Atom Count: 1,087 
• Modeled Residue Count: 129 
• Deposited Residue Count: 180 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholinephosphate cytidylyltransferase	A	180	Plasmodium falciparum	Mutation(s): 0  Gene Names: ctP, MAL13P1.86 EC: 2.7.7.15
UniProt
Find proteins for Q8IEE9 (Plasmodium falciparum (isolate 3D7)) Explore Q8IEE9  Go to UniProtKB:  Q8IEE9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C5P	B [auth A]	CYTIDINE-5'-MONOPHOSPHATE C9 H14 N3 O8 P IERHLVCPSMICTF-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.247 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.52	α = 90
b = 69.3	β = 90
c = 116.44	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
SCALA	data scaling
Coot	model building
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Guca, E., Hoh, F., Guichou, J.-F., Cerdan, R.

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Funding Organization	Location	Grant Number
EU-ITN Marie Curie Paramet	France	290080

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2018-08-29
  Changes: Data collection, Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description