7MH0

Human CTPS1 bound to CTP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 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: 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 ...

    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; jkoll@uw.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CTP synthase 1A, B, C, D591Homo sapiensMutation(s): 0 
Gene Names: CTPS1CTPS
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CTP (Subject of Investigation/LOI)
Query on CTP

Download Ideal Coordinates CCD File 
E [auth A], G [auth A], J [auth B], L [auth B], M [auth C], O [auth C], R [auth D], T [auth D]CYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O14 P3
PCDQPRRSZKQHHS-XVFCMESISA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A], H [auth A], I [auth B], K [auth B], N [auth C], P [auth C], Q [auth D], S [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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