8FV7

E coli. CTP synthase in complex with dF-dCTP + ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.203 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A metal-dependent conformational change provides a structural basis for the inhibition of CTP synthase by gemcitabine-5'-triphosphate.

McLeod, M.J.Tran, N.McCluskey, G.D.Gillis, T.D.Bearne, S.L.Holyoak, T.

(2023) Protein Sci 32: e4648-e4648

  • DOI: https://doi.org/10.1002/pro.4648
  • Primary Citation of Related Structures:  
    8FV6, 8FV7, 8FV8, 8FV9, 8FVA, 8FVB, 8FVC, 8FVD, 8FVE, 8SBR

  • PubMed Abstract: 

    CTP synthases (CTPS) catalyze the de novo production of CTP using UTP, ATP, and l-glutamine with the anticancer drug metabolite gemcitabine-5'-triphosphate (dF-dCTP) being one of its most potent nucleotide inhibitors. To delineate the structural origins of this inhibition, we solved the structures of Escherichia coli CTPS (ecCTPS) in complex with CTP (2.0 Å), 2'-ribo-F-dCTP (2.0 Å), 2'-arabino-F-CTP (2.4 Å), dF-dCTP (2.3 Å), dF-dCTP and ADP (2.1 Å), and dF-dCTP and ATP (2.1 Å). These structures revealed that the increased binding affinities observed for inhibitors bearing the 2'-F-arabino group (dF-dCTP and F-araCTP), relative to CTP and F-dCTP, arise from interactions between the inhibitor's fluorine atom exploiting a conserved hydrophobic pocket formed by F227 and an interdigitating loop from an adjacent subunit (Q114-V115-I116). Intriguingly, crystal structures of ecCTPS•dF-dCTP complexes in the presence of select monovalent and divalent cations demonstrated that the in crystallo tetrameric assembly of wild-type ecCTPS was induced into a conformation similar to inhibitory ecCTPS filaments solely through the binding of Na + -, Mg 2+ -, or Mn 2+ •dF-dCTP. However, in the presence of potassium, the dF-dCTP-bound structure is demetalated and in the low-affinity, non-filamentous conformation, like the conformation seen when bound to CTP and the other nucleotide analogues. Additionally, CTP can also induce the filament-competent conformation linked to high-affinity dF-dCTP binding in the presence of high concentrations of Mg 2+ . This metal-dependent, compacted CTP pocket conformation therefore furnishes the binding environment responsible for the tight binding of dF-dCTP and provides insights for further inhibitor design.


  • Organizational Affiliation

    Department of Biology, University of Waterloo, Waterloo, Ontario, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CTP synthaseA [auth AAA],
B [auth BBB]
545Escherichia coliMutation(s): 0 
Gene Names: pyrGECS88_3048
EC: 6.3.4.2
UniProt
Find proteins for P0A7E5 (Escherichia coli (strain K12))
Explore P0A7E5 
Go to UniProtKB:  P0A7E5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7E5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
C [auth AAA],
H [auth BBB]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
GTF (Subject of Investigation/LOI)
Query on GTF

Download Ideal Coordinates CCD File 
F [auth BBB],
I [auth BBB]
2'-deoxy-2',2'-difluorocytidine 5'-(tetrahydrogen triphosphate)
C9 H14 F2 N3 O13 P3
YMOXEIOKAJSRQX-QPPQHZFASA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth AAA],
E [auth AAA],
G [auth BBB],
J [auth BBB]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.982α = 90
b = 108.456β = 90
c = 128.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--
Canadian Institutes of Health Research (CIHR)Canada114895

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection