7MII

Human CTPS2 bound to inhibitor T35


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for isoform-specific inhibition of human CTPS1.

Lynch, E.M.DiMattia, M.A.Albanese, S.van Zundert, G.C.P.Hansen, J.M.Quispe, J.D.Kennedy, M.A.Verras, A.Borrelli, K.Toms, A.V.Kaila, N.Kreutter, K.D.McElwee, J.J.Kollman, J.M.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2107968118
  • Primary Citation of Related Structures:  
    7MGZ, 7MH0, 7MH1, 7MIF, 7MIG, 7MIH, 7MII, 7MIP, 7MIU, 7MIV

  • PubMed Abstract: 

    Cytidine triphosphate synthase 1 (CTPS1) is necessary for an effective immune response, as revealed by severe immunodeficiency in CTPS1-deficient individuals [E. Martin et al ], [ Nature ] [510], [288-292] ([2014]). CTPS1 expression is up-regulated in activated lymphocytes to expand CTP pools [E. Martin et al ], [ Nature ] [510], [288-292] ([2014]), satisfying increased demand for nucleic acid and lipid synthesis [L. D. Fairbanks, M. Bofill, K. Ruckemann, H. A. Simmonds], [ J. Biol. Chem. ] [270], [29682-29689] ([1995]). Demand for CTP in other tissues is met by the CTPS2 isoform and nucleoside salvage pathways [E. Martin et al ], [ Nature ] [510], [288-292] ([2014]). Selective inhibition of the proliferative CTPS1 isoform is therefore desirable in the treatment of immune disorders and lymphocyte cancers, but little is known about differences in regulation of the isoforms or mechanisms of known inhibitors. We show that CTP regulates both isoforms by binding in two sites that clash with substrates. CTPS1 is less sensitive to CTP feedback inhibition, consistent with its role in increasing CTP levels in proliferation. We also characterize recently reported small-molecule inhibitors, both CTPS1 selective and nonselective. Cryo-electron microscopy (cryo-EM) structures reveal these inhibitors mimic CTP binding in one inhibitory site, where a single amino acid substitution explains selectivity for CTPS1. The inhibitors bind to CTPS assembled into large-scale filaments, which for CTPS1 normally represents a hyperactive form of the enzyme [E. M. Lynch et al ], [ Nat. Struct. Mol. Biol. ] [24], [507-514] ([2017]). This highlights the utility of cryo-EM in drug discovery, particularly for cases in which targets form large multimeric assemblies not amenable to structure determination by other techniques. Both inhibitors also inhibit the proliferation of human primary T cells. The mechanisms of selective inhibition of CTPS1 lay the foundation for the design of immunosuppressive therapies.


  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CTP synthase 2A,
B,
C,
D [auth E]
586Homo sapiensMutation(s): 0 
Gene Names: CTPS2
EC: 6.3.4.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRF8 (Homo sapiens)
Explore Q9NRF8 
Go to UniProtKB:  Q9NRF8
PHAROS:  Q9NRF8
GTEx:  ENSG00000047230 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NRF8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZFY (Subject of Investigation/LOI)
Query on ZFY

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
M [auth C],
R [auth E]
2-{2-[(cyclopropanesulfonyl)amino]-1,3-thiazol-4-yl}-2-methyl-N-{5-[6-(trifluoromethyl)pyrazin-2-yl]pyridin-2-yl}propanamide
C20 H19 F3 N6 O3 S2
CZIDGRDZSFIUHX-UHFFFAOYSA-N
UTP
Query on UTP

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
N [auth C],
S [auth E]
URIDINE 5'-TRIPHOSPHATE
C9 H15 N2 O15 P3
PGAVKCOVUIYSFO-XVFCMESISA-N
GLN
Query on GLN

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
O [auth C],
T [auth E]
GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-VKHMYHEASA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A],
I [auth B],
P [auth C],
Q [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
ZFY BindingDB:  7MII IC50: min: 18, max: 33 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM118396

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Data collection