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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23831 | |||||||||
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Title | Human CTPS1 bound to UTP, AMPPNP, and glutamine | |||||||||
![]() | Human CTPS1 bound to UTP, AMPPNP, and glutamine | |||||||||
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![]() | glutaminase / amidoligase / nucleotide metabolism / LIGASE | |||||||||
Function / homology | ![]() CTP synthase (glutamine hydrolysing) / CTP synthase activity / cytoophidium / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / Interconversion of nucleotide di- and triphosphates / CTP biosynthetic process / nucleobase-containing compound metabolic process / glutamine metabolic process / B cell proliferation ...CTP synthase (glutamine hydrolysing) / CTP synthase activity / cytoophidium / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / Interconversion of nucleotide di- and triphosphates / CTP biosynthetic process / nucleobase-containing compound metabolic process / glutamine metabolic process / B cell proliferation / T cell proliferation / response to xenobiotic stimulus / ATP binding / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
![]() | Lynch EM / Dimattia MA | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for isoform-specific inhibition of human CTPS1. Authors: Eric M Lynch / Michael A DiMattia / Steven Albanese / Gydo C P van Zundert / Jesse M Hansen / Joel D Quispe / Madison A Kennedy / Andreas Verras / Kenneth Borrelli / Angela V Toms / Neelu ...Authors: Eric M Lynch / Michael A DiMattia / Steven Albanese / Gydo C P van Zundert / Jesse M Hansen / Joel D Quispe / Madison A Kennedy / Andreas Verras / Kenneth Borrelli / Angela V Toms / Neelu Kaila / Kevin D Kreutter / Joshua J McElwee / Justin M Kollman / ![]() Abstract: Cytidine triphosphate synthase 1 (CTPS1) is necessary for an effective immune response, as revealed by severe immunodeficiency in CTPS1-deficient individuals [E. Martin ], [] [510], [288-292] ([2014]) ...Cytidine triphosphate synthase 1 (CTPS1) is necessary for an effective immune response, as revealed by severe immunodeficiency in CTPS1-deficient individuals [E. Martin ], [] [510], [288-292] ([2014]). CTPS1 expression is up-regulated in activated lymphocytes to expand CTP pools [E. Martin ], [] [510], [288-292] ([2014]), satisfying increased demand for nucleic acid and lipid synthesis [L. D. Fairbanks, M. Bofill, K. Ruckemann, H. A. Simmonds], [ ] [270], [29682-29689] ([1995]). Demand for CTP in other tissues is met by the CTPS2 isoform and nucleoside salvage pathways [E. Martin ], [] [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 ], [] [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. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 6.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.3 KB 12.3 KB | Display Display | ![]() |
Images | ![]() | 189.6 KB | ||
Filedesc metadata | ![]() | 5.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mgzMC ![]() 7mh0C ![]() 7mh1C ![]() 7mifC ![]() 7migC ![]() 7mihC ![]() 7miiC ![]() 7mipC ![]() 7miuC ![]() 7mivC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Human CTPS1 bound to UTP, AMPPNP, and glutamine | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : CTPS1 tetramer
Entire | Name: CTPS1 tetramer |
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Components |
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-Supramolecule #1: CTPS1 tetramer
Supramolecule | Name: CTPS1 tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: CTP synthase 1
Macromolecule | Name: CTP synthase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: CTP synthase (glutamine hydrolysing) |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 66.777297 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MKYILVTGGV ISGIGKGIIA SSVGTILKSC GLHVTSIKID PYINIDAGTF SPYEHGEVFV LDDGGEVDLD LGNYERFLDI RLTKDNNLT TGKIYQYVIN KERKGDYLGK TVQVVPHITD AIQEWVMRQA LIPVDEDGLE PQVCVIELGG TVGDIESMPF I EAFRQFQF ...String: MKYILVTGGV ISGIGKGIIA SSVGTILKSC GLHVTSIKID PYINIDAGTF SPYEHGEVFV LDDGGEVDLD LGNYERFLDI RLTKDNNLT TGKIYQYVIN KERKGDYLGK TVQVVPHITD AIQEWVMRQA LIPVDEDGLE PQVCVIELGG TVGDIESMPF I EAFRQFQF KVKRENFCNI HVSLVPQPSS TGEQKTKPTQ NSVRELRGLG LSPDLVVCRC SNPLDTSVKE KISMFCHVEP EQ VICVHDV SSIYRVPLLL EEQGVVDYFL RRLDLPIERQ PRKMLMKWKE MADRYDRLLE TCSIALVGKY TKFSDSYASV IKA LEHSAL AINHKLEIKY IDSADLEPIT SQEEPVRYHE AWQKLCSAHG VLVPGGFGVR GTEGKIQAIA WARNQKKPFL GVCL GMQLA VVEFSRNVLG WQDANSTEFD PTTSHPVVVD MPEHNPGQMG GTMRLGKRRT LFQTKNSVMR KLYGDADYLE ERHRH RFEV NPVWKKCLEE QGLKFVGQDV EGERMEIVEL EDHPFFVGVQ YHPEFLSRPI KPSPPYFGLL LASVGRLSHY LQKGCR LSP RDTYSDRSGS SSPDSEITEL KFPSINHD UniProtKB: CTP synthase 1 |
-Macromolecule #2: URIDINE 5'-TRIPHOSPHATE
Macromolecule | Name: URIDINE 5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: UTP |
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Molecular weight | Theoretical: 484.141 Da |
Chemical component information | ![]() ChemComp-UTP: |
-Macromolecule #3: GLUTAMINE
Macromolecule | Name: GLUTAMINE / type: ligand / ID: 3 / Number of copies: 4 / Formula: GLN |
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Molecular weight | Theoretical: 146.144 Da |
Chemical component information | ![]() ChemComp-GLN: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 4 / Formula: ANP |
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Molecular weight | Theoretical: 506.196 Da |
Chemical component information | ![]() ChemComp-ANP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7.9 |
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Grid | Model: C-flat-2/2 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 90.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Applied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 147336 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) |