2VO1

CRYSTAL STRUCTURE OF THE SYNTHETASE DOMAIN OF HUMAN CTP SYNTHETASE

• PDB DOI:  https://doi.org/10.2210/pdb2VO1/pdb
• Entry: 2VO1 supersedes: 2C5M

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-02-08 Released: 2008-03-11 
• Deposition Author(s): Stenmark, P., Kursula, P., Arrowsmith, C., Berglund, H., Edwards, A., Ehn, M., Flodin, S., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg-Schiavone, L., Kotenyoa, T., Moche, M., Nilsson-Ehle, P., Ogg, D., Persson, C., Sagemark, J., Schuler, H., Sundstrom, M., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Nordlund, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.259 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 

Literature

Structure of the Synthetase Domain of Human Ctp Synthetase, a Target for Anticancer Therapy.

Kursula, P., Flodin, S., Ehn, M., Hammarstrom, M., Schuler, H., Nordlund, P., Stenmark, P.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 613

• PubMed: 16820675 
• DOI: https://doi.org/10.1107/S1744309106018136
• Primary Citation of Related Structures:  
  2VO1


• PubMed Abstract: 
  

Cytidine triphosphate synthetase (CTPS) is a key enzyme in nucleic acid and phospholipid biosynthesis and its activity is increased in certain human cancers, making it a promising drug target. The crystal structure of the synthetase domain of human CTPS, which represents the first structure of a CTPS from an eukaryote, has been determined. The structure is homotetrameric and each active site is formed by three different subunits. Sulfate ions bound to the active sites indicate the positions of phosphate-binding sites for the substrates ATP and UTP and the feedback inhibitor CTP. Together with earlier structures of bacterial CTPS, the human CTPS structure provides an extended understanding of the structure-function relationship of CTPS-family members. The structure also serves as a basis for structure-based design of anti-proliferative inhibitors.

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Organizational Affiliation: 

Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17177 Stockholm, Sweden.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 66.52 kDa 
• Atom Count: 3,661 
• Modelled Residue Count: 463 
• Deposited Residue Count: 590 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CTP SYNTHASE 1	A, B	295	Homo sapiens	Mutation(s): 0  Gene Names: CTPS1, CTPS EC: 6.3.4.2
UniProt & NIH Common Fund Data Resources
Find proteins for P17812 (Homo sapiens) Explore P17812  Go to UniProtKB:  P17812
PHAROS:  P17812

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.259 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.42	α = 90
b = 98.42	β = 90
c = 120.57	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-11 
Deposition Author(s): Stenmark, P., Kursula, P., Arrowsmith, C., Berglund, H., Edwards, A., Ehn, M., Flodin, S., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg-Schiavone, L., Kotenyoa, T., Moche, M., Nilsson-Ehle, P., Ogg, D., Persson, C., Sagemark, J., Schuler, H., Sundstrom, M., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Nordlund, P.
• This entry supersedes: 2C5M

Revision History  

• Version 1.0: 2008-03-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance